1 |
tim |
2685 |
@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 |
tim |
2706 |
@string{jmb = "J. Mol. Biol."} |
18 |
tim |
2685 |
|
19 |
tim |
2706 |
|
20 |
tim |
2685 |
@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, |
517 |
|
|
pages = {2493-2496} |
518 |
|
|
} |
519 |
|
|
|
520 |
|
|
@Article{Calderbank96, |
521 |
|
|
author = {A.~R. Calderbank and P.~W. Shor}, |
522 |
|
|
title = {Good quantum error-correcting codes exist}, |
523 |
|
|
journal = {Phys. Rev. A}, |
524 |
|
|
year = 1996, |
525 |
|
|
volume = 54, |
526 |
|
|
pages = {1098-1105} |
527 |
|
|
} |
528 |
|
|
|
529 |
|
|
@Article{Steane96, |
530 |
|
|
author = {A.~M. Steane}, |
531 |
|
|
title = {Error correcting codes in quantum theory}, |
532 |
|
|
journal = prl, |
533 |
|
|
year = 1996, |
534 |
|
|
volume = 77, |
535 |
|
|
pages = {793-797} |
536 |
|
|
} |
537 |
|
|
|
538 |
|
|
@Article{Gezelter95, |
539 |
|
|
author = {J.~D. Gezelter and W.~H. Miller}, |
540 |
|
|
title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE |
541 |
|
|
RATE OF KETENE ISOMERIZATION}, |
542 |
|
|
journal = jcp, |
543 |
|
|
year = 1995, |
544 |
|
|
volume = 103, |
545 |
|
|
pages = {7868-7876} |
546 |
|
|
} |
547 |
|
|
|
548 |
|
|
@Article{Chakrabarti92, |
549 |
|
|
author = {A.~C. Chakrabarti and D.~W. Deamer}, |
550 |
|
|
title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE}, |
551 |
|
|
journal = {Biochimica et Biophysica Acta}, |
552 |
|
|
year = 1992, |
553 |
|
|
volume = 1111, |
554 |
|
|
pages = {171-177} |
555 |
|
|
} |
556 |
|
|
|
557 |
|
|
@Article{Paula96, |
558 |
|
|
author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and |
559 |
|
|
T.~H. Haines and D.~W. Deamer}, |
560 |
|
|
title = {Permeation of protons, potassium ions, and small |
561 |
|
|
polar molecules through phospholipid bilayers as a |
562 |
|
|
function of membrane thickness}, |
563 |
|
|
journal = {Biophys. J.}, |
564 |
|
|
year = 1996, |
565 |
|
|
volume = 70, |
566 |
|
|
pages = {339-348} |
567 |
|
|
} |
568 |
|
|
|
569 |
|
|
@Article{Little96, |
570 |
|
|
author = {H.~J. Little}, |
571 |
|
|
title = {How has molecular pharmacology contributed to our |
572 |
|
|
understanding of the mechanism(s) of general |
573 |
|
|
anesthesia?}, |
574 |
|
|
journal = {Pharmacology \& Therapeutics}, |
575 |
|
|
year = 1996, |
576 |
|
|
volume = 69, |
577 |
|
|
pages = {37-58} |
578 |
|
|
} |
579 |
|
|
|
580 |
|
|
@Article{McKinnon92, |
581 |
|
|
author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks}, |
582 |
|
|
title = {Nonequilibrium Molecular Dynamics Simulation of |
583 |
|
|
Oxygen Diffusion through Hexadecane Monolayers with |
584 |
|
|
Varying Concentrations of Cholesterol}, |
585 |
|
|
journal = jpc, |
586 |
|
|
year = 1992, |
587 |
|
|
volume = 96, |
588 |
|
|
pages = {10497-10506} |
589 |
|
|
} |
590 |
|
|
|
591 |
|
|
@Article{Venable93, |
592 |
|
|
author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and |
593 |
|
|
R.~W. Pastor}, |
594 |
|
|
title = {Molecular Dynamics Simulations of a Lipid Bilayer |
595 |
|
|
and of Hexadecane: An Investigation of Membrane Fluidity}, |
596 |
|
|
journal = {Science}, |
597 |
|
|
year = 1993, |
598 |
|
|
volume = 262, |
599 |
|
|
pages = {223-226} |
600 |
|
|
} |
601 |
|
|
|
602 |
|
|
@Article{Essmann99, |
603 |
|
|
author = {U. Essmann and M.~L. Berkowitz}, |
604 |
|
|
title = {Dynamical properties of phospholipid bilayers from |
605 |
|
|
computer simulation}, |
606 |
|
|
journal = {Biophys. J.}, |
607 |
|
|
year = 1999, |
608 |
|
|
volume = 76, |
609 |
|
|
pages = {2081-2089} |
610 |
|
|
} |
611 |
|
|
|
612 |
|
|
@Article{Tu98, |
613 |
|
|
author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf}, |
614 |
|
|
title = {Effects of anesthetics on the structure of a |
615 |
|
|
phospholipid bilayer: Molecular dynamics |
616 |
|
|
investigation of halothane in the hydrated liquid |
617 |
|
|
crystal phase of dipalmitoylphosphatidylcholine}, |
618 |
|
|
journal = {Biophys. J.}, |
619 |
|
|
year = 1998, |
620 |
|
|
volume = 75, |
621 |
|
|
pages = {2123-2134} |
622 |
|
|
} |
623 |
|
|
|
624 |
|
|
@Article{Pomes96, |
625 |
|
|
author = {R. Pomes and B. Roux}, |
626 |
|
|
title = {Structure and dynamics of a proton wire: A |
627 |
|
|
theoretical study of H+ translocation along the |
628 |
|
|
single-file water chain in the gramicidin a channel}, |
629 |
|
|
journal = {Biophys. J.}, |
630 |
|
|
year = 1996, |
631 |
|
|
volume = 71, |
632 |
|
|
pages = {19-39} |
633 |
|
|
} |
634 |
|
|
|
635 |
|
|
@Article{Duwez60, |
636 |
|
|
author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}}, |
637 |
|
|
title = {Continuous Series of Metastable Solid Solutions in |
638 |
|
|
Silver-Copper Alloys}, |
639 |
|
|
journal = {J. Appl. Phys.}, |
640 |
|
|
year = 1960, |
641 |
|
|
volume = 31, |
642 |
|
|
pages = {1136-1137} |
643 |
|
|
} |
644 |
|
|
|
645 |
|
|
@Article{Peker93, |
646 |
|
|
author = {A. Peker and W.~L. Johnson}, |
647 |
|
|
title = {A highly processable metallic-glass - |
648 |
|
|
$\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$}, |
649 |
|
|
journal = {Appl. Phys. Lett.}, |
650 |
|
|
year = 1993, |
651 |
|
|
volume = 63, |
652 |
|
|
pages = {2342-2344} |
653 |
|
|
} |
654 |
|
|
|
655 |
|
|
@Article{ChoiYim97, |
656 |
|
|
author = {H. Choi-Yim and W.~L. Johnson}, |
657 |
|
|
title = {Bulk metallic glass matrix composites}, |
658 |
|
|
journal = {Appl. Phys. Lett.}, |
659 |
|
|
year = 1997, |
660 |
|
|
volume = 71, |
661 |
|
|
pages = {3808-3810} |
662 |
|
|
} |
663 |
|
|
|
664 |
|
|
@Article{Sun96, |
665 |
|
|
author = {X. Sun and S. Schneider and U. Geyer and |
666 |
|
|
W.~L. Johnson and M.~A. Nicolet}, |
667 |
|
|
title = {Oxidation and crystallization of an amorphous |
668 |
|
|
$\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy}, |
669 |
|
|
journal = {J. Mater. Res.}, |
670 |
|
|
year = 1996, |
671 |
|
|
volume = 11, |
672 |
|
|
pages = {2738-2743} |
673 |
|
|
} |
674 |
|
|
|
675 |
|
|
@Article{Heller93, |
676 |
|
|
author = {H. Heller and M. Schaefer and K. Schulten}, |
677 |
|
|
title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 |
678 |
|
|
LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES}, |
679 |
|
|
journal = jpc, |
680 |
|
|
year = 1993, |
681 |
|
|
volume = 97, |
682 |
|
|
pages = {8343-8360} |
683 |
|
|
} |
684 |
|
|
|
685 |
|
|
@Article{Kushick76, |
686 |
|
|
author = {J. Kushick and B.~J. Berne}, |
687 |
|
|
title = {Computer Simulation of anisotropic molecular fluids}, |
688 |
|
|
journal = jcp, |
689 |
|
|
year = 1976, |
690 |
|
|
volume = 64, |
691 |
|
|
pages = {1362-1367} |
692 |
|
|
} |
693 |
|
|
|
694 |
|
|
@Article{Berardi96, |
695 |
|
|
author = {R. Berardi and S. Orlandi and C Zannoni}, |
696 |
|
|
title = {Antiphase structures in polar smectic liquid |
697 |
|
|
crystals and their molecular origin}, |
698 |
|
|
journal = cpl, |
699 |
|
|
year = 1996, |
700 |
|
|
volume = 261, |
701 |
|
|
pages = {357-362} |
702 |
|
|
} |
703 |
|
|
|
704 |
|
|
@Article{Berardi99, |
705 |
|
|
author = {R. Berardi and S. Orlandi and C. Zannoni}, |
706 |
|
|
title = {Monte Carlo simulations of rod-like Gay-Berne |
707 |
|
|
mesogens with transverse dipoles}, |
708 |
|
|
journal = {Int. J. Mod. Phys. C}, |
709 |
|
|
year = 1999, |
710 |
|
|
volume = 10, |
711 |
|
|
pages = {477-484} |
712 |
|
|
} |
713 |
|
|
|
714 |
|
|
@Article{Pasterny2000, |
715 |
|
|
author = {K. Pasterny and E. Gwozdz and A. Brodka}, |
716 |
|
|
title = {Properties of a model liquid crystal: Polar |
717 |
|
|
Gay-Berne particles}, |
718 |
|
|
journal = {J. Mol. Liq.}, |
719 |
|
|
year = 2000, |
720 |
|
|
volume = 85, |
721 |
|
|
pages = {173-184} |
722 |
|
|
} |
723 |
|
|
|
724 |
|
|
@Article{Jorgensen83, |
725 |
|
|
author = {W.~L. Jorgensen and J. Chandrasekhar and |
726 |
|
|
J.~D. Madura and R.~W. Impey and M.~L. Klein}, |
727 |
|
|
title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR |
728 |
|
|
SIMULATING LIQUID WATER}, |
729 |
|
|
journal = jcp, |
730 |
|
|
year = 1983, |
731 |
|
|
volume = 79, |
732 |
|
|
pages = {926-935} |
733 |
|
|
} |
734 |
|
|
|
735 |
|
|
@Article{Berardi98, |
736 |
|
|
author = {R. Berardi and C. Fava and C. Zannoni}, |
737 |
|
|
title = {A Gay-Berne potential for dissimilar biaxial particles}, |
738 |
|
|
journal = cpl, |
739 |
|
|
year = 1998, |
740 |
|
|
volume = 297, |
741 |
|
|
pages = {8-14} |
742 |
|
|
} |
743 |
|
|
|
744 |
|
|
@Article{Luckhurst90, |
745 |
|
|
author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen}, |
746 |
|
|
title = {Computer simulation studies of anisotropic systems |
747 |
|
|
{XIX}. Mesophases formed by the Gay-Berne model mesogen}, |
748 |
|
|
journal = {Liquid Crystals}, |
749 |
|
|
year = 1990, |
750 |
|
|
volume = 8, |
751 |
|
|
pages = {451-464} |
752 |
|
|
} |
753 |
|
|
|
754 |
|
|
@Article{Gay81, |
755 |
|
|
author = {J.~G. Gay and B.~J. Berne}, |
756 |
|
|
title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A |
757 |
|
|
LINEAR SITE-SITE POTENTIAL}, |
758 |
|
|
journal = jcp, |
759 |
|
|
year = 1981, |
760 |
|
|
volume = 74, |
761 |
|
|
pages = {3316-3319} |
762 |
|
|
} |
763 |
|
|
|
764 |
|
|
@Article{Berne72, |
765 |
|
|
author = {B.~J. Berne and P. Pechukas}, |
766 |
|
|
title = {Gaussian Model Potentials for Molecular Interactions}, |
767 |
|
|
journal = jcp, |
768 |
|
|
year = 1972, |
769 |
|
|
volume = 56, |
770 |
|
|
pages = {4213-4216} |
771 |
|
|
} |
772 |
|
|
|
773 |
|
|
@Article{Perram96, |
774 |
|
|
author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and |
775 |
|
|
J.~L. Lebowitz}, |
776 |
|
|
title = {Ellipsoid contact potential: Theory and relation to |
777 |
|
|
overlap potentials}, |
778 |
|
|
journal = pre, |
779 |
|
|
year = 1996, |
780 |
|
|
volume = 54, |
781 |
|
|
pages = {6565-6572} |
782 |
|
|
} |
783 |
|
|
|
784 |
|
|
@Article{Cornell95, |
785 |
|
|
author = {W.~D. Cornell and P. Cieplak and C.~I. Bayly and |
786 |
|
|
I.~R. Gould and K.~M. {Merz, Jr.} and D.~M. Ferguson |
787 |
|
|
and D.~C. Spellmeyer and T. Fox and J.~W. Caldwell |
788 |
|
|
and P.~A. Kollman}, |
789 |
|
|
title = {A second generation force field for the simulation |
790 |
|
|
of proteins and nucleic acids}, |
791 |
|
|
journal = jacs, |
792 |
|
|
year = 1995, |
793 |
|
|
volume = 117, |
794 |
|
|
pages = {5179-5197} |
795 |
|
|
} |
796 |
|
|
|
797 |
|
|
@Article{Brooks83, |
798 |
|
|
author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson |
799 |
|
|
and D.~J. States and S. Swaminathan and M. Karplus}, |
800 |
|
|
title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, |
801 |
|
|
journal = {J. Comp. Chem.}, |
802 |
|
|
year = 1983, |
803 |
|
|
volume = 4, |
804 |
|
|
pages = {187-217} |
805 |
|
|
} |
806 |
|
|
|
807 |
|
|
@InCollection{MacKerell98, |
808 |
|
|
author = {A.~D. {MacKerell, Jr.} and B. Brooks and |
809 |
|
|
C.~L. {Brooks III} and L. Nilsson and B. Roux and |
810 |
|
|
Y. Won and and M. Karplus}, |
811 |
|
|
title = {{\sc charmm}: The Energy Function and Its Parameterization |
812 |
|
|
with an Overview of the Program}, |
813 |
|
|
booktitle = {The Encyclopedia of Computational Chemistry}, |
814 |
|
|
pages = {271-277}, |
815 |
|
|
publisher = {John Wiley \& Sons}, |
816 |
|
|
year = 1998, |
817 |
|
|
editor = {P.~v.~R. {Schleyer, {\it et al.}}}, |
818 |
|
|
volume = 1, |
819 |
|
|
address = {New York} |
820 |
|
|
} |
821 |
|
|
|
822 |
|
|
@InCollection{Jorgensen98, |
823 |
|
|
author = {W.~L. Jorgensen}, |
824 |
|
|
title = {OPLS Force Fields}, |
825 |
|
|
booktitle = {The Encyclopedia of Computational Chemistry}, |
826 |
|
|
pages = {1986-1989}, |
827 |
|
|
publisher = {John Wiley \& Sons}, |
828 |
|
|
year = 1998, |
829 |
|
|
editor = {P.~v.~R. {Schleyer, {\it et al.}}}, |
830 |
|
|
volume = 3, |
831 |
|
|
address = {New York} |
832 |
|
|
} |
833 |
|
|
|
834 |
|
|
@Article{Rabani2000, |
835 |
|
|
author = {E. Rabani and J.~D. Gezelter and B.~J. Berne}, |
836 |
|
|
title = {Reply to `Comment on ``Direct Observation of |
837 |
|
|
Stretched-Exponential Relaxation in Low-Temperature |
838 |
|
|
Lennard-Jones Systems Using th eCage Correlation |
839 |
|
|
Function'' '}, |
840 |
|
|
journal = prl, |
841 |
|
|
year = 2000, |
842 |
|
|
volume = 85, |
843 |
|
|
pages = 467 |
844 |
|
|
} |
845 |
|
|
|
846 |
|
|
@Book{Cevc87, |
847 |
|
|
author = {G. Cevc and D. Marsh}, |
848 |
|
|
title = {Phospholipid Bilayers}, |
849 |
|
|
publisher = {John Wiley \& Sons}, |
850 |
|
|
year = 1987, |
851 |
|
|
address = {New York} |
852 |
|
|
} |
853 |
|
|
|
854 |
|
|
@Article{Janiak79, |
855 |
|
|
author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley}, |
856 |
|
|
title = {Temperature and Compositional Dependence of the |
857 |
|
|
Structure of Hydrated Dimyristoyl Lecithin}, |
858 |
|
|
journal = {J. Biol. Chem.}, |
859 |
|
|
year = 1979, |
860 |
|
|
volume = 254, |
861 |
|
|
pages = {6068-6078} |
862 |
|
|
} |
863 |
|
|
|
864 |
|
|
@Book{Tobias90, |
865 |
|
|
author = {Sheila Tobias}, |
866 |
|
|
title = {They're not Dumb. They're Different: Stalking the |
867 |
|
|
Second Tier}, |
868 |
|
|
publisher = {Research Corp.}, |
869 |
|
|
year = 1990, |
870 |
|
|
address = {Tucson} |
871 |
|
|
} |
872 |
|
|
|
873 |
|
|
@Article{Mazur92, |
874 |
|
|
author = {E. Mazur}, |
875 |
|
|
title = {Qualitative vs. Quantititative Thinking: Are we |
876 |
|
|
teaching the right thing? }, |
877 |
|
|
journal = {Optics and Photonics News}, |
878 |
|
|
year = 1992, |
879 |
|
|
volume = 3, |
880 |
|
|
pages = 38 |
881 |
|
|
} |
882 |
|
|
|
883 |
|
|
@Book{Mazur97, |
884 |
|
|
author = {Eric Mazur}, |
885 |
|
|
title = {Peer Instruction: A User's Manual}, |
886 |
|
|
publisher = {Prentice Hall}, |
887 |
|
|
year = 1997, |
888 |
|
|
address = {New Jersey} |
889 |
|
|
} |
890 |
|
|
|
891 |
|
|
@Article{Wigner55, |
892 |
|
|
author = {E.~P. Wigner}, |
893 |
|
|
title = {Characteristic Vectors of Bordered Matrices with |
894 |
|
|
Infinite Dimensions}, |
895 |
|
|
journal = {Annals of Mathematics}, |
896 |
|
|
year = 1955, |
897 |
|
|
volume = 62, |
898 |
|
|
pages = {548-564} |
899 |
|
|
} |
900 |
|
|
|
901 |
|
|
@Article{Gaukel98, |
902 |
|
|
author = {C. Gaukel and H.~R. Schober}, |
903 |
|
|
title = {Diffusion Mechanisms in under-cooled Binary Metal |
904 |
|
|
Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$}, |
905 |
|
|
journal = {Solid State Comm.}, |
906 |
|
|
year = 1998, |
907 |
|
|
volume = 107, |
908 |
|
|
pages = {1-5} |
909 |
|
|
} |
910 |
|
|
|
911 |
|
|
@Article{Qi99, |
912 |
|
|
author = {Y. Qi and T. \c{C}a\v{g}in and Y. |
913 |
|
|
Kimura and W.~A. {Goddard III}}, |
914 |
|
|
title = {Molecular-dynamics simulations of glass formation |
915 |
|
|
and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ |
916 |
|
|
and $\mbox{Cu-Ni}$}, |
917 |
|
|
journal = prb, |
918 |
|
|
year = 1999, |
919 |
|
|
volume = 59, |
920 |
|
|
number = 5, |
921 |
|
|
pages = {3527-3533} |
922 |
|
|
} |
923 |
|
|
|
924 |
|
|
@Article{Khorunzhy97, |
925 |
|
|
author = {A. Khorunzhy and G.~J. Rodgers}, |
926 |
|
|
title = {Eigenvalue distribution of large dilute random matrices}, |
927 |
|
|
journal = {J. Math. Phys.}, |
928 |
|
|
year = 1997, |
929 |
|
|
volume = 38, |
930 |
|
|
pages = {3300-3320} |
931 |
|
|
} |
932 |
|
|
|
933 |
|
|
@Article{Rodgers88, |
934 |
|
|
author = {G.~J. Rodgers and A. Bray}, |
935 |
|
|
title = {Density of States of a Sparse Random Matrix}, |
936 |
|
|
journal = {Phys. Rev. B}, |
937 |
|
|
year = 1988, |
938 |
|
|
volume = 37, |
939 |
|
|
pages = 355703562 |
940 |
|
|
} |
941 |
|
|
|
942 |
|
|
@Article{Rodgers90, |
943 |
|
|
author = {G.~J. Rodgers and C. {De Dominicis}}, |
944 |
|
|
title = {Density of states of sparse random matrices}, |
945 |
|
|
journal = {J. Phys. A: Math. Gen.}, |
946 |
|
|
year = 1990, |
947 |
|
|
volume = 23, |
948 |
|
|
pages = {1567-1573} |
949 |
|
|
} |
950 |
|
|
|
951 |
|
|
@InProceedings{Barker80, |
952 |
|
|
author = {J.~A. Barker}, |
953 |
|
|
title = {Reaction field method for polar fluids}, |
954 |
|
|
booktitle = {The problem of long-range forces in the computer |
955 |
|
|
simulation of condensed matter}, |
956 |
|
|
pages = {45-6}, |
957 |
|
|
year = 1980, |
958 |
|
|
editor = {D. Ceperley}, |
959 |
|
|
volume = 9, |
960 |
|
|
series = {NRCC Workshop Proceedings} |
961 |
|
|
} |
962 |
|
|
|
963 |
|
|
@Article{Smith82, |
964 |
|
|
author = {W. Smith}, |
965 |
|
|
title = {Point multipoles in the Ewald summation}, |
966 |
|
|
journal = {CCP5 Quarterly}, |
967 |
|
|
year = 1982, |
968 |
|
|
volume = 4, |
969 |
|
|
pages = {13-25} |
970 |
|
|
} |
971 |
|
|
|
972 |
|
|
@Article{Daw84, |
973 |
|
|
author = {M.~S. Daw and M.~I. Baskes}, |
974 |
|
|
title = {Embedded-atom method: Derivation and application to |
975 |
|
|
impurities, surfaces, and other defects in metals}, |
976 |
|
|
journal = prb, |
977 |
|
|
year = 1984, |
978 |
|
|
volume = 29, |
979 |
|
|
number = 12, |
980 |
|
|
pages = {6443-6453} |
981 |
|
|
} |
982 |
|
|
|
983 |
|
|
|
984 |
|
|
@Article{Chen90, |
985 |
|
|
author = {A.~P. Sutton and J. Chen}, |
986 |
|
|
title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials}, |
987 |
|
|
journal = {Phil. Mag. Lett.}, |
988 |
|
|
year = 1990, |
989 |
|
|
volume = 61, |
990 |
|
|
pages = {139-146} |
991 |
|
|
} |
992 |
|
|
|
993 |
|
|
@Article{Lu97, |
994 |
|
|
author = {J. Lu and J.~A. Szpunar}, |
995 |
|
|
title = {Applications of the embedded-atom method to glass |
996 |
|
|
formation and crystallization of liquid and glass |
997 |
|
|
transition-metal nickel}, |
998 |
|
|
journal = {Phil. Mag. A}, |
999 |
|
|
year = {1997}, |
1000 |
|
|
volume = {75}, |
1001 |
|
|
pages = {1057-1066}, |
1002 |
|
|
} |
1003 |
|
|
|
1004 |
|
|
@Article{Shlesinger99, |
1005 |
|
|
author = {M.~F. Shlesinger and J. Klafter and G. Zumofen}, |
1006 |
|
|
title = {Above, below, and beyond Brownian motion}, |
1007 |
|
|
journal = {Am. J. Phys.}, |
1008 |
|
|
year = 1999, |
1009 |
|
|
volume = 67, |
1010 |
|
|
pages = {1253-1259} |
1011 |
|
|
} |
1012 |
|
|
|
1013 |
|
|
@Article{Klafter96, |
1014 |
|
|
author = {J. Klafter and M. Shlesinger and G. Zumofen}, |
1015 |
|
|
title = {Beyond Brownian Motion}, |
1016 |
|
|
journal = {Physics Today}, |
1017 |
|
|
year = 1996, |
1018 |
|
|
volume = 49, |
1019 |
|
|
pages = {33-39} |
1020 |
|
|
} |
1021 |
|
|
|
1022 |
|
|
@Article{Blumen83, |
1023 |
|
|
author = {A. Blumen and J. Klafter and G. Zumofen}, |
1024 |
|
|
title = {Recombination in amorphous materials as a |
1025 |
|
|
continuous-time random-walk problem}, |
1026 |
|
|
journal = {Phys. Rev. B}, |
1027 |
|
|
year = 1983, |
1028 |
|
|
volume = 27, |
1029 |
|
|
pages = {3429-3435} |
1030 |
|
|
} |
1031 |
|
|
|
1032 |
|
|
@Article{Klafter94, |
1033 |
|
|
author = {J. Klafter and G. Zumofen}, |
1034 |
|
|
title = {Probability Distributions for Continuous-Time Random |
1035 |
|
|
Walks with Long Tails}, |
1036 |
|
|
journal = jpc, |
1037 |
|
|
year = 1994, |
1038 |
|
|
volume = 98, |
1039 |
|
|
pages = {7366-7370} |
1040 |
|
|
} |
1041 |
|
|
|
1042 |
|
|
|
1043 |
|
|
@Article{Dzugutov92, |
1044 |
|
|
author = {M. Dzugutov}, |
1045 |
|
|
title = {Glass formation in a simple monatomic liquid with |
1046 |
|
|
icosahedral inherent local order}, |
1047 |
|
|
journal = pra, |
1048 |
|
|
year = 1992, |
1049 |
|
|
volume = 46, |
1050 |
|
|
pages = {R2984-R2987} |
1051 |
|
|
} |
1052 |
|
|
|
1053 |
|
|
@Article{Moore94, |
1054 |
|
|
author = {P. Moore and T. Keyes}, |
1055 |
|
|
title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity |
1056 |
|
|
Correlation Functions and Self-Diffusion Constants}, |
1057 |
|
|
journal = jcp, |
1058 |
|
|
year = 1994, |
1059 |
|
|
volume = 100, |
1060 |
|
|
pages = 6709 |
1061 |
|
|
} |
1062 |
|
|
|
1063 |
|
|
@Article{Seeley89, |
1064 |
|
|
author = {G. Seeley and T. Keyes}, |
1065 |
|
|
title = {Normal-mode analysis of liquid-state dynamics}, |
1066 |
|
|
journal = jcp, |
1067 |
|
|
year = 1989, |
1068 |
|
|
volume = 91, |
1069 |
|
|
pages = {5581-5586} |
1070 |
|
|
} |
1071 |
|
|
|
1072 |
|
|
@Article{Madan90, |
1073 |
|
|
author = {B. Madan and T. Keyes and G. Seeley}, |
1074 |
|
|
title = {Diffusion in supercooled liquids via normal mode |
1075 |
|
|
analysis}, |
1076 |
|
|
journal = jcp, |
1077 |
|
|
year = 1990, |
1078 |
|
|
volume = 92, |
1079 |
|
|
pages = {7565-7569} |
1080 |
|
|
} |
1081 |
|
|
|
1082 |
|
|
@Article{Madan91, |
1083 |
|
|
author = {B. Madan and T. Keyes and G. Seeley}, |
1084 |
|
|
title = {Normal mode analysis of the velocity correlation |
1085 |
|
|
function in supercooled liquids}, |
1086 |
|
|
journal = jcp, |
1087 |
|
|
year = 1991, |
1088 |
|
|
volume = 94, |
1089 |
|
|
pages = {6762-6769} |
1090 |
|
|
} |
1091 |
|
|
|
1092 |
|
|
@Article{Buchner92, |
1093 |
|
|
author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt}, |
1094 |
|
|
title = {The short-time dynamics of molecular |
1095 |
|
|
liquids. Instantaneous-normal-mode theory}, |
1096 |
|
|
journal = jcp, |
1097 |
|
|
year = 1992, |
1098 |
|
|
volume = 97, |
1099 |
|
|
pages = {8522-8535} |
1100 |
|
|
} |
1101 |
|
|
|
1102 |
|
|
@Article{Wan94, |
1103 |
|
|
author = {Yi. Wan and R.~M. Stratt}, |
1104 |
|
|
title = {Liquid theory for the instantaneous normal modes of |
1105 |
|
|
a liquid}, |
1106 |
|
|
journal = jcp, |
1107 |
|
|
year = 1994, |
1108 |
|
|
volume = 100, |
1109 |
|
|
pages = {5123-5138} |
1110 |
|
|
} |
1111 |
|
|
|
1112 |
|
|
@article{Stratt95, |
1113 |
|
|
author = {R.~M. Stratt}, |
1114 |
|
|
title = {The instantaneous normal modes of liquids}, |
1115 |
|
|
journal = {Acc. Chem. Res.}, |
1116 |
|
|
year = 1995, |
1117 |
|
|
volume = 28, |
1118 |
|
|
pages = {201-207} |
1119 |
|
|
} |
1120 |
|
|
|
1121 |
|
|
@Article{Nitzan95, |
1122 |
|
|
author = {G.~V. Vijayadamodar and A. Nitzan}, |
1123 |
|
|
title = {On the application of instantaneous normal mode |
1124 |
|
|
analysis to long time dynamics of liquids}, |
1125 |
|
|
journal = jcp, |
1126 |
|
|
year = 1995, |
1127 |
|
|
volume = 103, |
1128 |
|
|
pages = {2169-2177} |
1129 |
|
|
} |
1130 |
|
|
|
1131 |
|
|
@Article{Ribeiro98, |
1132 |
|
|
author = "M.~C.~C. Ribeiro and P.~A. Madden", |
1133 |
|
|
title = "Unstable Modes in Ionic Melts", |
1134 |
|
|
journal = jcp, |
1135 |
|
|
year = 1998, |
1136 |
|
|
volume = 108, |
1137 |
|
|
pages = {3256-3263} |
1138 |
|
|
} |
1139 |
|
|
|
1140 |
|
|
@Article{Keyes98a, |
1141 |
|
|
author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher}, |
1142 |
|
|
title = {Comment on a critique of the instantaneous normal |
1143 |
|
|
mode (INM) approach to diffusion |
1144 |
|
|
(J. Chem. Phys. {\bf 107}, 4618 (1997))}, |
1145 |
|
|
journal = jcp, |
1146 |
|
|
year = 1998, |
1147 |
|
|
volume = 109, |
1148 |
|
|
pages = {4693-4694} |
1149 |
|
|
} |
1150 |
|
|
|
1151 |
|
|
@Article{Alemany98, |
1152 |
|
|
author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego}, |
1153 |
|
|
title = {Transport coefficients of liquid transition metals: |
1154 |
|
|
A computer simulation study using the embedded atom |
1155 |
|
|
model}, |
1156 |
|
|
journal = jcp, |
1157 |
|
|
year = 1998, |
1158 |
|
|
volume = 109, |
1159 |
|
|
pages = {5175-5176} |
1160 |
|
|
} |
1161 |
|
|
|
1162 |
|
|
@Article{Belonoshko00, |
1163 |
|
|
author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and |
1164 |
|
|
B. Johansson}, |
1165 |
|
|
title = {Quasi ab initio molecular dynamic study of Cu melting}, |
1166 |
|
|
journal = prb, |
1167 |
|
|
year = 2000, |
1168 |
|
|
volume = 61, |
1169 |
|
|
pages = {3838-3844} |
1170 |
|
|
} |
1171 |
|
|
|
1172 |
|
|
@Article{Banhart92, |
1173 |
|
|
author = {J. Banhart and H. Ebert and R. Kuentzler and |
1174 |
|
|
J. Voitl\"{a}nder}, |
1175 |
|
|
title = {Electronic properties of single-phased metastable |
1176 |
|
|
Ag-Cu alloys}, |
1177 |
|
|
journal = prb, |
1178 |
|
|
year = 1992, |
1179 |
|
|
volume = 46, |
1180 |
|
|
pages = {9968-9975} |
1181 |
|
|
} |
1182 |
|
|
|
1183 |
|
|
@Article{Wendt78, |
1184 |
|
|
author = {H. Wendt and F.~F. Abraham}, |
1185 |
|
|
title = {}, |
1186 |
|
|
journal = prl, |
1187 |
|
|
year = 1978, |
1188 |
|
|
volume = 41, |
1189 |
|
|
pages = 1244 |
1190 |
|
|
} |
1191 |
|
|
|
1192 |
|
|
@Article{Lewis91, |
1193 |
|
|
author = {L.~J. Lewis}, |
1194 |
|
|
title = {Atomic dynamics through the glass transition}, |
1195 |
|
|
journal = prb, |
1196 |
|
|
year = 1991, |
1197 |
|
|
volume = 44, |
1198 |
|
|
pages = {4245-4254} |
1199 |
|
|
} |
1200 |
|
|
|
1201 |
|
|
@Article{Liu92, |
1202 |
|
|
author = {R.~S. Liu and D.~W. Qi and S. Wang}, |
1203 |
|
|
title = {Subpeaks of structure factors for rapidly quenched metals}, |
1204 |
|
|
journal = prb, |
1205 |
|
|
year = 1992, |
1206 |
|
|
volume = 45, |
1207 |
|
|
pages = {451-453} |
1208 |
|
|
} |
1209 |
|
|
|
1210 |
|
|
@Book{pliny, |
1211 |
|
|
author = {Pliny}, |
1212 |
|
|
title = {Hist. Nat.}, |
1213 |
|
|
publisher = { }, |
1214 |
|
|
year = { }, |
1215 |
|
|
volume = {XXXVI} |
1216 |
|
|
} |
1217 |
|
|
|
1218 |
|
|
@Article{Anheuser94, |
1219 |
|
|
author = {K. Anheuser and J.P. Northover}, |
1220 |
|
|
title = {Silver plating of Roman and Celtic coins from Britan - a technical study}, |
1221 |
|
|
journal = {Brit. Num. J.}, |
1222 |
|
|
year = 1994, |
1223 |
|
|
volume = 64, |
1224 |
|
|
pages = 22 |
1225 |
|
|
} |
1226 |
|
|
|
1227 |
|
|
@Article{Pense92, |
1228 |
|
|
author = {A. W. Pense}, |
1229 |
|
|
title = {The Decline and Fall of the Roman Denarius}, |
1230 |
|
|
journal = {Mat. Char.}, |
1231 |
|
|
year = 1992, |
1232 |
|
|
volume = 29, |
1233 |
|
|
pages = 213 |
1234 |
|
|
} |
1235 |
|
|
|
1236 |
|
|
@Article{Ngai81, |
1237 |
|
|
author = {K.~L. Ngai and F.-S. Liu}, |
1238 |
|
|
title = {Dispersive diffusion transport and noise, |
1239 |
|
|
time-dependent diffusion coefficient, generalized |
1240 |
|
|
Einstein-Nernst relation, and dispersive |
1241 |
|
|
diffusion-controlled unimolecular and bimolecular |
1242 |
|
|
reactions}, |
1243 |
|
|
journal = prb, |
1244 |
|
|
year = 1981, |
1245 |
|
|
volume = 24, |
1246 |
|
|
pages = {1049-1065} |
1247 |
|
|
} |
1248 |
|
|
|
1249 |
|
|
@Unpublished{Truhlar00, |
1250 |
|
|
author = {D.~G. Truhlar and A. Kohen}, |
1251 |
|
|
note = {private correspondence} |
1252 |
|
|
} |
1253 |
|
|
|
1254 |
|
|
@Article{Truhlar78, |
1255 |
|
|
author = {Donald G. Truhlar}, |
1256 |
|
|
title = {Interpretation of the Activation Energy}, |
1257 |
|
|
journal = {J. Chem. Ed.}, |
1258 |
|
|
year = 1978, |
1259 |
|
|
volume = 55, |
1260 |
|
|
pages = 309 |
1261 |
|
|
} |
1262 |
|
|
|
1263 |
|
|
@Book{Tolman27, |
1264 |
|
|
author = {R. C. Tolman}, |
1265 |
|
|
title = {Statistical Mechanics with Applications to Physics and Chemistry}, |
1266 |
|
|
chapter = {}, |
1267 |
|
|
publisher = {Chemical Catalog Co.}, |
1268 |
|
|
address = {New York}, |
1269 |
|
|
year = 1927, |
1270 |
|
|
pages = {260-270} |
1271 |
|
|
} |
1272 |
|
|
|
1273 |
|
|
@Article{Tolman20, |
1274 |
|
|
author = {R. C. Tolman}, |
1275 |
|
|
title = {Statistical Mechanics Applied to Chemical Kinetics}, |
1276 |
|
|
journal = jacs, |
1277 |
|
|
year = 1920, |
1278 |
|
|
volume = 42, |
1279 |
|
|
pages = 2506 |
1280 |
|
|
} |
1281 |
|
|
|
1282 |
|
|
@Article{Nagel96, |
1283 |
|
|
author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel}, |
1284 |
|
|
title = {Supercooled Liquids and Glasses}, |
1285 |
|
|
journal = jpc, |
1286 |
|
|
year = 1996, |
1287 |
|
|
volume = 100, |
1288 |
|
|
pages = 13200 |
1289 |
|
|
} |
1290 |
|
|
|
1291 |
|
|
@InBook{Blumen86, |
1292 |
|
|
author = {A. Blumen and J. Klafter and G. Zumofen}, |
1293 |
|
|
editor = {Luciano Peitronero and E. Tosatti}, |
1294 |
|
|
title = {Fractals in Physics}, |
1295 |
|
|
chapter = {Reactions in Disordered Media Modelled by Fractals}, |
1296 |
|
|
publisher = {North-Holland}, |
1297 |
|
|
year = 1986, |
1298 |
|
|
series = {International Symposium on Fractals in Physics}, |
1299 |
|
|
address = {Amsterdam}, |
1300 |
|
|
pages = 399 |
1301 |
|
|
} |
1302 |
|
|
|
1303 |
|
|
@Article{Shlesinger84, |
1304 |
|
|
author = {M.~F. Shlesinger and E.~W. Montroll}, |
1305 |
|
|
title = {On the Williams-Watts function of dielectric relaxation}, |
1306 |
|
|
journal = {Proc. Natl. Acad. Sci. USA}, |
1307 |
|
|
year = 1984, |
1308 |
|
|
volume = 81, |
1309 |
|
|
pages = {1280-1283} |
1310 |
|
|
} |
1311 |
|
|
|
1312 |
|
|
@Article{Klafter86, |
1313 |
|
|
author = {J. Klafter and M.~F. Shlesinger}, |
1314 |
|
|
title = {On the relationship among three theories of |
1315 |
|
|
relaxation in disordered systems}, |
1316 |
|
|
journal = {Proc. Natl. Acad. Sci. USA}, |
1317 |
|
|
year = 1986, |
1318 |
|
|
volume = 83, |
1319 |
|
|
pages = {848-851} |
1320 |
|
|
} |
1321 |
|
|
|
1322 |
|
|
@Article{Li2001, |
1323 |
tim |
2691 |
author = {Z. Li and M. Lieberman and W. Hill}, |
1324 |
|
|
title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine |
1325 |
tim |
2685 |
Monolayers: umbrella vs. octopus design strategies |
1326 |
|
|
for formation of oriented {\sc sam}s}, |
1327 |
tim |
2691 |
journal = {Langmuir}, |
1328 |
|
|
year = 2001, |
1329 |
tim |
2685 |
volume = 17, |
1330 |
|
|
pages = {4887-4894} |
1331 |
|
|
} |
1332 |
|
|
|
1333 |
|
|
@Article{Evans1993, |
1334 |
|
|
author = {J.~W. Evans}, |
1335 |
|
|
title = {Random and Cooperative Sequential Adsorption}, |
1336 |
|
|
journal = rmp, |
1337 |
|
|
year = 1993, |
1338 |
|
|
volume = 65, |
1339 |
|
|
pages = {1281-1329} |
1340 |
|
|
} |
1341 |
|
|
|
1342 |
|
|
|
1343 |
|
|
@Article{Dwyer1977, |
1344 |
tim |
2691 |
author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei}, |
1345 |
|
|
title = {}, |
1346 |
|
|
journal = {Surf. Sci.}, |
1347 |
|
|
year = 1977, |
1348 |
|
|
volume = 64, |
1349 |
|
|
pages = 617 |
1350 |
tim |
2685 |
} |
1351 |
|
|
|
1352 |
|
|
@Article{Macritche1978, |
1353 |
tim |
2691 |
author = {F. MacRitche}, |
1354 |
|
|
title = {}, |
1355 |
|
|
journal = {Adv. Protein Chem.}, |
1356 |
|
|
year = 1978, |
1357 |
|
|
volume = 32, |
1358 |
|
|
pages = 283 |
1359 |
tim |
2685 |
} |
1360 |
|
|
|
1361 |
|
|
@Article{Feder1980, |
1362 |
tim |
2691 |
author = {J. Feder}, |
1363 |
|
|
title = {}, |
1364 |
|
|
journal = {J. Theor. Biol.}, |
1365 |
|
|
year = 1980, |
1366 |
|
|
volume = 87, |
1367 |
|
|
pages = 237 |
1368 |
tim |
2685 |
} |
1369 |
|
|
|
1370 |
|
|
@Article{Ramsden1993, |
1371 |
tim |
2691 |
author = {J.~J. Ramsden}, |
1372 |
|
|
title = {}, |
1373 |
|
|
journal = prl, |
1374 |
|
|
year = 1993, |
1375 |
|
|
volume = 71, |
1376 |
|
|
pages = 295 |
1377 |
tim |
2685 |
} |
1378 |
|
|
|
1379 |
|
|
|
1380 |
|
|
@Article{Egelhoff1989, |
1381 |
tim |
2691 |
author = {W.~F. Egelhoff and I. Jacob}, |
1382 |
|
|
title = {}, |
1383 |
|
|
journal = prl, |
1384 |
|
|
year = 1989, |
1385 |
|
|
volume = 62, |
1386 |
|
|
pages = 921 |
1387 |
tim |
2685 |
} |
1388 |
|
|
|
1389 |
|
|
|
1390 |
|
|
@Article{Viot1992a, |
1391 |
tim |
2691 |
author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, |
1392 |
|
|
title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC |
1393 |
tim |
2685 |
PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR}, |
1394 |
tim |
2691 |
journal = jpc, |
1395 |
|
|
year = 1992, |
1396 |
|
|
volume = 97, |
1397 |
|
|
pages = {5212-5218} |
1398 |
tim |
2685 |
} |
1399 |
|
|
|
1400 |
|
|
@Article{Viot1992b, |
1401 |
tim |
2691 |
author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, |
1402 |
|
|
title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION |
1403 |
tim |
2685 |
OF VERY ELONGATED PARTICLES}, |
1404 |
tim |
2691 |
journal = {Physica A}, |
1405 |
|
|
year = 1992, |
1406 |
|
|
volume = 191, |
1407 |
|
|
pages = {248-252} |
1408 |
tim |
2685 |
} |
1409 |
|
|
|
1410 |
|
|
@Article{Dobson1987, |
1411 |
|
|
author = {B.~W. Dobson}, |
1412 |
|
|
title = {}, |
1413 |
|
|
journal = prb, |
1414 |
|
|
year = 1987, |
1415 |
|
|
volume = 36, |
1416 |
|
|
pages = 1068 |
1417 |
|
|
} |
1418 |
|
|
|
1419 |
|
|
@Article{Boyer1995, |
1420 |
|
|
author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot}, |
1421 |
|
|
title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL |
1422 |
|
|
ADSORPTION}, |
1423 |
|
|
journal = jcp, |
1424 |
|
|
year = 1995, |
1425 |
|
|
volume = 103, |
1426 |
|
|
pages = 1607 |
1427 |
|
|
} |
1428 |
|
|
|
1429 |
|
|
@Article{Viot1992c, |
1430 |
|
|
author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, |
1431 |
|
|
title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC |
1432 |
|
|
PARTICLES}, |
1433 |
|
|
journal = {Physica A}, |
1434 |
|
|
year = 1992, |
1435 |
|
|
volume = 191, |
1436 |
|
|
pages = {248-252} |
1437 |
|
|
} |
1438 |
|
|
|
1439 |
|
|
@Article{Ricci1994, |
1440 |
|
|
author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot}, |
1441 |
tim |
2691 |
title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND |
1442 |
tim |
2685 |
EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS}, |
1443 |
|
|
journal = jcp, |
1444 |
|
|
year = 1994, |
1445 |
|
|
volume = 101, |
1446 |
|
|
pages = 9164 |
1447 |
|
|
} |
1448 |
|
|
|
1449 |
|
|
@Article{Semmler1998, |
1450 |
tim |
2691 |
author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec}, |
1451 |
|
|
title = {Diffusional Deposition of Charged Latex Particles on |
1452 |
tim |
2685 |
Water-Solid Interfaces at Low Ionic Strength}, |
1453 |
tim |
2691 |
journal = {Langmuir}, |
1454 |
|
|
year = 1998, |
1455 |
|
|
volume = 14, |
1456 |
|
|
pages = {5127-5132} |
1457 |
tim |
2685 |
} |
1458 |
|
|
|
1459 |
|
|
@Article{Solomon1986, |
1460 |
tim |
2691 |
author = {H. Solomon and H. Weiner}, |
1461 |
|
|
title = {A REVIEW OF THE PACKING PROBLEM}, |
1462 |
|
|
journal = {Comm. Statistics A}, |
1463 |
|
|
year = 1986, |
1464 |
|
|
volume = 15, |
1465 |
|
|
pages = {2571-2607} |
1466 |
tim |
2685 |
} |
1467 |
|
|
|
1468 |
|
|
@Article{Bonnier1993, |
1469 |
tim |
2691 |
author = {B. Bonnier and M. Hontebeyrie and C. Meyers}, |
1470 |
|
|
title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING |
1471 |
tim |
2685 |
D-DIMENSIONAL CUBES}, |
1472 |
tim |
2691 |
journal = {Physica A}, |
1473 |
|
|
year = 1993, |
1474 |
|
|
volume = 198, |
1475 |
|
|
pages = {1-10} |
1476 |
tim |
2685 |
} |
1477 |
|
|
|
1478 |
|
|
@Book{Frenkel1996, |
1479 |
tim |
2691 |
author = {D. Frenkel and B. Smit}, |
1480 |
|
|
title = {Understanding Molecular Simulation : From Algorithms |
1481 |
tim |
2685 |
to Applications}, |
1482 |
tim |
2691 |
publisher = {Academic Press}, |
1483 |
|
|
year = 1996, |
1484 |
|
|
address = {New York} |
1485 |
tim |
2685 |
|
1486 |
|
|
|
1487 |
|
|
} |
1488 |
|
|
|
1489 |
|
|
@Article{Dullweber1997, |
1490 |
tim |
2691 |
author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, |
1491 |
|
|
title = {Symplectic splitting methods for rigid body molecular |
1492 |
tim |
2685 |
dynamics}, |
1493 |
tim |
2691 |
journal = jcp, |
1494 |
|
|
year = 1997, |
1495 |
|
|
volume = 107, |
1496 |
|
|
number = 15, |
1497 |
|
|
pages = {5840-5851} |
1498 |
tim |
2685 |
} |
1499 |
|
|
|
1500 |
|
|
@Article{Siepmann1998, |
1501 |
tim |
2691 |
author = {M. Martin and J.~I. Siepmann}, |
1502 |
|
|
title = {Transferable Potentials for Phase Equilibria. 1. United-Atom |
1503 |
tim |
2685 |
Description of n-Alkanes}, |
1504 |
tim |
2691 |
journal = jpcB, |
1505 |
|
|
year = 1998, |
1506 |
|
|
volume = 102, |
1507 |
|
|
pages = {2569-2577} |
1508 |
tim |
2685 |
} |
1509 |
|
|
|
1510 |
|
|
@Article{Marrink01, |
1511 |
tim |
2691 |
author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark}, |
1512 |
|
|
title = {Simulations of the Spontaneous Aggregation of Phospholipids |
1513 |
tim |
2685 |
into Bilayers}, |
1514 |
tim |
2691 |
journal = jacs, |
1515 |
|
|
year = 2001, |
1516 |
|
|
volume = 123, |
1517 |
|
|
pages = {8638-8639} |
1518 |
tim |
2685 |
} |
1519 |
|
|
|
1520 |
|
|
@Article{liu96:new_model, |
1521 |
tim |
2691 |
author = {Y. Liu and T. Ichiye}, |
1522 |
|
|
title = {Soft sticky dipole potential for liquid water: a new model}, |
1523 |
|
|
journal = jpc, |
1524 |
|
|
year = 1996, |
1525 |
|
|
volume = 100, |
1526 |
|
|
pages = {2723-2730} |
1527 |
tim |
2685 |
} |
1528 |
|
|
|
1529 |
|
|
@Article{liu96:monte_carlo, |
1530 |
tim |
2691 |
author = {Y. Liu and T. Ichiye}, |
1531 |
|
|
title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation}, |
1532 |
|
|
journal = {Chemical Physics Letters}, |
1533 |
|
|
year = 1996, |
1534 |
|
|
volume = 256, |
1535 |
|
|
pages = {334-340} |
1536 |
tim |
2685 |
} |
1537 |
|
|
|
1538 |
|
|
@Article{chandra99:ssd_md, |
1539 |
tim |
2691 |
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} |
1546 |
tim |
2685 |
} |
1547 |
|
|
|
1548 |
|
|
@Book{allen87:csl, |
1549 |
tim |
2691 |
author = {M.~P. Allen and D.~J. Tildesley}, |
1550 |
|
|
title = {Computer Simulations of Liquids}, |
1551 |
|
|
publisher = {Oxford University Press}, |
1552 |
|
|
year = 1987, |
1553 |
|
|
address = {New York} |
1554 |
tim |
2685 |
} |
1555 |
|
|
|
1556 |
|
|
@Book{leach01:mm, |
1557 |
tim |
2691 |
author = {A. Leach}, |
1558 |
|
|
title = {Molecular Modeling: Principles and Applications}, |
1559 |
|
|
publisher = {Pearson Educated Limited}, |
1560 |
|
|
year = 2001, |
1561 |
|
|
address = {Harlow, England}, |
1562 |
|
|
edition = {2nd} |
1563 |
tim |
2685 |
} |
1564 |
|
|
|
1565 |
|
|
|
1566 |
|
|
@Article{katsaras00, |
1567 |
tim |
2691 |
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}, |
1568 |
|
|
title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples}, |
1569 |
|
|
journal = {Physical Review E}, |
1570 |
|
|
year = 2000, |
1571 |
|
|
volume = 61, |
1572 |
|
|
number = 5, |
1573 |
|
|
pages = {5668-5677} |
1574 |
tim |
2685 |
} |
1575 |
|
|
|
1576 |
|
|
@Article{sengupta00, |
1577 |
tim |
2691 |
author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras}, |
1578 |
|
|
title = {Novel structural Features of the ripple phase of phospholipids}, |
1579 |
|
|
journal = {Europhysics Letters}, |
1580 |
|
|
year = 2000, |
1581 |
|
|
volume = 49, |
1582 |
|
|
number = 6, |
1583 |
|
|
pages = {722-728} |
1584 |
tim |
2685 |
} |
1585 |
|
|
|
1586 |
|
|
@Article{venable00, |
1587 |
tim |
2691 |
author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, |
1588 |
|
|
title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles}, |
1589 |
|
|
journal = jcp, |
1590 |
|
|
year = 2000, |
1591 |
|
|
volume = 112, |
1592 |
|
|
number = 10, |
1593 |
|
|
pages = {4822-4832} |
1594 |
tim |
2685 |
} |
1595 |
|
|
|
1596 |
|
|
@Article{lindahl00, |
1597 |
tim |
2691 |
author = {E. Lindahl and O. Edholm}, |
1598 |
|
|
title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations}, |
1599 |
|
|
journal = {Biophysical Journal}, |
1600 |
|
|
year = 2000, |
1601 |
|
|
volume = 79, |
1602 |
|
|
pages = {426-433}, |
1603 |
|
|
month = {July} |
1604 |
tim |
2685 |
} |
1605 |
|
|
|
1606 |
|
|
|
1607 |
|
|
@Article{saiz02, |
1608 |
tim |
2691 |
author = {L. Saiz and M. Klein}, |
1609 |
|
|
title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations}, |
1610 |
|
|
journal = jcp, |
1611 |
|
|
year = 2002, |
1612 |
|
|
volume = 116, |
1613 |
|
|
number = 7, |
1614 |
|
|
pages = {3052-3057} |
1615 |
tim |
2685 |
} |
1616 |
|
|
|
1617 |
|
|
@Article{stevens95, |
1618 |
tim |
2691 |
author = {M.~J. Stevens and G.~S. Grest}, |
1619 |
|
|
title = {Phase coexistence of a Stockmayer fluid in an aplied field}, |
1620 |
|
|
journal = {Physical Review E}, |
1621 |
|
|
year = 1995, |
1622 |
|
|
volume = 51, |
1623 |
|
|
number = 6, |
1624 |
|
|
pages = {5976-5983} |
1625 |
tim |
2685 |
} |
1626 |
|
|
|
1627 |
|
|
@Article{darden93:pme, |
1628 |
tim |
2691 |
author = {T. Darden and D. York and L. Pedersen}, |
1629 |
|
|
title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems}, |
1630 |
|
|
journal = {Journal of Chemical Physics}, |
1631 |
|
|
year = 1993, |
1632 |
|
|
volume = 98, |
1633 |
|
|
number = 12, |
1634 |
|
|
pages = {10089-10092} |
1635 |
tim |
2685 |
} |
1636 |
|
|
|
1637 |
|
|
|
1638 |
|
|
|
1639 |
|
|
@Article{goetz98, |
1640 |
tim |
2691 |
author = {R. Goetz and R. Lipowsky}, |
1641 |
|
|
title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, |
1642 |
|
|
journal = {Journal of Chemical Physics}, |
1643 |
|
|
year = 1998, |
1644 |
|
|
volume = 108, |
1645 |
|
|
number = 17, |
1646 |
|
|
pages = 7397 |
1647 |
tim |
2685 |
} |
1648 |
|
|
|
1649 |
|
|
@Article{marrink01:undulation, |
1650 |
tim |
2691 |
author = {S.~J. Marrink and A.~E. Mark}, |
1651 |
|
|
title = {Effect of undulations on surface tension in simulated bilayers}, |
1652 |
|
|
journal = {Journal of Physical Chemistry B}, |
1653 |
|
|
year = 2001, |
1654 |
|
|
volume = 105, |
1655 |
|
|
pages = {6122-6127} |
1656 |
tim |
2685 |
} |
1657 |
|
|
|
1658 |
|
|
@Article{lindahl00:undulation, |
1659 |
tim |
2691 |
author = {E. Lindahl and O. Edholm}, |
1660 |
|
|
title = {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation}, |
1661 |
|
|
journal = {Biophysical Journal}, |
1662 |
|
|
year = 2000, |
1663 |
|
|
volume = 79, |
1664 |
|
|
pages = {426-433} |
1665 |
tim |
2685 |
} |
1666 |
|
|
|
1667 |
|
|
@Article{metropolis:1949, |
1668 |
tim |
2691 |
author = {N. Metropolis and S. Ulam}, |
1669 |
|
|
title = {The $\mbox{Monte Carlo}$ Method}, |
1670 |
|
|
journal = {J. Am. Stat. Ass.}, |
1671 |
|
|
year = 1949, |
1672 |
|
|
volume = 44, |
1673 |
|
|
pages = {335-341} |
1674 |
tim |
2685 |
} |
1675 |
|
|
|
1676 |
|
|
@Article{metropolis:1953, |
1677 |
tim |
2691 |
author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller}, |
1678 |
|
|
title = {Equation of State Calculations by Fast Computing Machines}, |
1679 |
|
|
journal = {J. Chem. Phys.}, |
1680 |
|
|
year = 1953, |
1681 |
|
|
volume = 21, |
1682 |
|
|
pages = {1087-1092} |
1683 |
tim |
2685 |
} |
1684 |
|
|
|
1685 |
|
|
@Article{born:1912, |
1686 |
tim |
2691 |
author = {M. Born and Th. Von~Karman}, |
1687 |
|
|
title = {Uber Schwingungen in Raumgittern}, |
1688 |
|
|
journal = {Physik Z.}, |
1689 |
|
|
year = 1912, |
1690 |
|
|
volume = 13, |
1691 |
|
|
number = {297-309} |
1692 |
tim |
2685 |
} |
1693 |
|
|
|
1694 |
|
|
@Book{chandler:1987, |
1695 |
tim |
2691 |
author = {David Chandler}, |
1696 |
|
|
title = {Introduction to Modern Statistical Mechanics}, |
1697 |
|
|
publisher = {Oxford University Press}, |
1698 |
|
|
year = 1987 |
1699 |
tim |
2685 |
} |
1700 |
|
|
|
1701 |
|
|
|
1702 |
|
|
@Article{pearlman:1995, |
1703 |
tim |
2691 |
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}, |
1704 |
|
|
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}, |
1705 |
|
|
journal = {Computer Physics Communications}, |
1706 |
|
|
year = 1995, |
1707 |
|
|
volume = 91, |
1708 |
|
|
pages = {1-41} |
1709 |
tim |
2685 |
} |
1710 |
|
|
|
1711 |
|
|
@Book{Goldstein01, |
1712 |
tim |
2691 |
author = {H. Goldstein and C. Poole and J. Safko}, |
1713 |
|
|
title = {Classical Mechanics}, |
1714 |
|
|
publisher = {Addison Wesley}, |
1715 |
|
|
year = 2001, |
1716 |
|
|
address = {San Francisco}, |
1717 |
|
|
edition = {3rd} |
1718 |
tim |
2685 |
} |
1719 |
|
|
|
1720 |
|
|
@Article{Bratko85, |
1721 |
tim |
2691 |
author = {D. Bratko and L. Blum and A. Luzar}, |
1722 |
|
|
title = {A simple model for the intermolecular potential of water}, |
1723 |
|
|
journal = jcp, |
1724 |
|
|
year = 1985, |
1725 |
|
|
volume = 83, |
1726 |
|
|
number = 12, |
1727 |
|
|
pages = {6367-6370} |
1728 |
tim |
2685 |
} |
1729 |
|
|
|
1730 |
|
|
@Article{Bratko95, |
1731 |
tim |
2691 |
author = {L. Blum and F. Vericat and D. Bratko}, |
1732 |
|
|
title = {Towards an analytical model of water: The octupolar model}, |
1733 |
|
|
journal = jcp, |
1734 |
|
|
year = 1995, |
1735 |
|
|
volume = 102, |
1736 |
|
|
number = 3, |
1737 |
|
|
pages = {1461-1462} |
1738 |
tim |
2685 |
} |
1739 |
|
|
|
1740 |
|
|
@Article{Ichiye03, |
1741 |
tim |
2691 |
author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks |
1742 |
tim |
2685 |
and T. Ichiye}, |
1743 |
tim |
2691 |
title = {A temperature of maximum density in soft sticky dipole |
1744 |
tim |
2685 |
water}, |
1745 |
tim |
2691 |
journal = cpl, |
1746 |
|
|
year = 2003, |
1747 |
|
|
volume = 376, |
1748 |
|
|
pages = {646-652}, |
1749 |
tim |
2685 |
} |
1750 |
|
|
|
1751 |
|
|
|
1752 |
|
|
@Article{Soper86, |
1753 |
tim |
2691 |
author = {A.~K. Soper and M.~G. Phillips}, |
1754 |
|
|
title = {A new determination of the structure of water at 298K}, |
1755 |
|
|
journal = cp, |
1756 |
|
|
year = 1986, |
1757 |
|
|
volume = 107, |
1758 |
|
|
number = 1, |
1759 |
|
|
pages = {47-60}, |
1760 |
tim |
2685 |
} |
1761 |
|
|
|
1762 |
|
|
@Article{plimpton95, |
1763 |
tim |
2691 |
author = {S. Plimpton}, |
1764 |
|
|
title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics}, |
1765 |
|
|
journal = {J. Comp. Phys.}, |
1766 |
|
|
year = 1995, |
1767 |
|
|
volume = 117, |
1768 |
|
|
pages = {1-19}, |
1769 |
tim |
2685 |
} |
1770 |
|
|
|
1771 |
|
|
@Article{plimpton93, |
1772 |
tim |
2691 |
author = {S.~J. Plimpton and B.~A. Hendrickson}, |
1773 |
|
|
title = {Parallel Molecular Dynamics with the Embedded Atom Method}, |
1774 |
|
|
journal = {MRS Proceedings}, |
1775 |
|
|
year = 1993, |
1776 |
|
|
volume = 291, |
1777 |
|
|
pages = 37 |
1778 |
tim |
2685 |
} |
1779 |
|
|
|
1780 |
|
|
|
1781 |
|
|
@Article{Ercolessi02, |
1782 |
tim |
2691 |
author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi}, |
1783 |
|
|
title = {Bending strain-driven modification of surface resconstructions: Au(111)}, |
1784 |
|
|
journal = prb, |
1785 |
|
|
year = 2002, |
1786 |
|
|
volume = 65, |
1787 |
|
|
pages = 241406 |
1788 |
tim |
2685 |
} |
1789 |
|
|
|
1790 |
|
|
@Article{Ercolessi88, |
1791 |
tim |
2691 |
author = {F. Ercolessi and M. Parrinello and E. Tosatti}, |
1792 |
|
|
title = {Simulation of Gold in the Glue Model.}, |
1793 |
|
|
journal = {Philosophical Magazine A}, |
1794 |
|
|
year = 1988, |
1795 |
|
|
volume = 58, |
1796 |
|
|
pages = {213-226} |
1797 |
tim |
2685 |
} |
1798 |
|
|
|
1799 |
|
|
@Article{Finnis84, |
1800 |
tim |
2691 |
author = {M.~W Finnis and J.~E. Sinclair }, |
1801 |
|
|
title = {A Simple Empirical N-Body Potential for Transition-Metals}, |
1802 |
|
|
journal = {Phil. Mag. A}, |
1803 |
|
|
year = 1984, |
1804 |
|
|
volume = 50, |
1805 |
|
|
pages = {45-55} |
1806 |
tim |
2685 |
} |
1807 |
|
|
|
1808 |
|
|
@Article{FBD86, |
1809 |
|
|
author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw}, |
1810 |
|
|
title = {Embedded-atom-method functions for the fcc metals |
1811 |
|
|
$\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, |
1812 |
|
|
journal = prb, |
1813 |
|
|
year = 1986, |
1814 |
|
|
volume = 33, |
1815 |
|
|
number = 12, |
1816 |
|
|
pages = 7983 |
1817 |
|
|
} |
1818 |
|
|
|
1819 |
|
|
@Article{johnson89, |
1820 |
tim |
2691 |
author = {R.~A. Johnson}, |
1821 |
|
|
title = {Alloy models with the embedded-atom method}, |
1822 |
|
|
journal = prb, |
1823 |
|
|
year = 1989, |
1824 |
|
|
volume = 39, |
1825 |
|
|
number = 17, |
1826 |
|
|
pages = 12554 |
1827 |
tim |
2685 |
} |
1828 |
|
|
|
1829 |
|
|
@Article{Laird97, |
1830 |
tim |
2691 |
author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler}, |
1831 |
|
|
title = {A symplectic method for rigid-body molecular simulation}, |
1832 |
|
|
journal = jcp, |
1833 |
|
|
year = 1997, |
1834 |
|
|
volume = 107, |
1835 |
|
|
number = 7, |
1836 |
|
|
pages = {2580-2588} |
1837 |
tim |
2685 |
} |
1838 |
|
|
|
1839 |
|
|
|
1840 |
|
|
@Article{hoover85, |
1841 |
tim |
2691 |
author = {W.~G. Hoover}, |
1842 |
|
|
title = {Canonical dynamics: Equilibrium phase-space distributions}, |
1843 |
|
|
journal = pra, |
1844 |
|
|
year = 1985, |
1845 |
|
|
volume = 31, |
1846 |
|
|
pages = 1695 |
1847 |
tim |
2685 |
} |
1848 |
|
|
|
1849 |
|
|
@Article{Roux91, |
1850 |
tim |
2691 |
author = {B. Roux and M. Karplus}, |
1851 |
|
|
title = {Ion transport in a Gramicidin-like channel: dynamics and mobility}, |
1852 |
|
|
journal = jpc, |
1853 |
|
|
year = 1991, |
1854 |
|
|
volume = 95, |
1855 |
|
|
number = 15, |
1856 |
|
|
pages = {4856-4868} |
1857 |
tim |
2685 |
} |
1858 |
|
|
|
1859 |
|
|
|
1860 |
|
|
@Article{Marrink94, |
1861 |
tim |
2691 |
author = {S.~J Marrink and H.~J.~C. Berendsen}, |
1862 |
|
|
title = {Simulation of water transport through a lipid membrane}, |
1863 |
|
|
journal = jpc, |
1864 |
|
|
year = 1994, |
1865 |
|
|
volume = 98, |
1866 |
|
|
number = 15, |
1867 |
|
|
pages = {4155-4168} |
1868 |
tim |
2685 |
} |
1869 |
|
|
|
1870 |
|
|
|
1871 |
|
|
@Article{Daw89, |
1872 |
tim |
2691 |
author = {Murray~S. Daw}, |
1873 |
|
|
title = {Model of metallic cohesion: The embedded-atom method}, |
1874 |
|
|
journal = {Physical Review B}, |
1875 |
|
|
year = 1989, |
1876 |
|
|
volume = 39, |
1877 |
|
|
pages = {7441-7452} |
1878 |
tim |
2685 |
} |
1879 |
|
|
|
1880 |
|
|
@InBook{voter, |
1881 |
tim |
2691 |
author = {A.~F. Voter}, |
1882 |
|
|
editor = {J.~H. Westbrook and R.~L. Fleischer}, |
1883 |
|
|
title = {Intermetallic Compounds: Principles and Practice}, |
1884 |
|
|
chapter = 4, |
1885 |
|
|
publisher = {John Wiley and Sons Ltd}, |
1886 |
|
|
year = 1995, |
1887 |
|
|
volume = 1, |
1888 |
|
|
pages = 77 |
1889 |
tim |
2685 |
} |
1890 |
|
|
|
1891 |
|
|
@Article{marrink:2002, |
1892 |
tim |
2691 |
author = {S.~J. Marrink and D.~P. Teileman}, |
1893 |
|
|
title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition}, |
1894 |
|
|
journal = {Biophysical Journal}, |
1895 |
|
|
year = 2002, |
1896 |
|
|
volume = 83, |
1897 |
|
|
pages = {2386-2392} |
1898 |
tim |
2685 |
} |
1899 |
|
|
|
1900 |
|
|
@Article{sum:2003, |
1901 |
tim |
2691 |
author = {A.~K. Sum and J.~J. de~Pablo}, |
1902 |
|
|
title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, |
1903 |
|
|
journal = {Biophysical Journal}, |
1904 |
|
|
year = 2003, |
1905 |
|
|
volume = 85, |
1906 |
|
|
pages = {3636-3645} |
1907 |
tim |
2685 |
} |
1908 |
|
|
|
1909 |
|
|
@Article{gomez:2003, |
1910 |
tim |
2691 |
author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom}, |
1911 |
|
|
title = {Setting up and optimization of membrane protein simulations}, |
1912 |
|
|
journal = {Eur. Biophys. J.}, |
1913 |
|
|
year = 2002, |
1914 |
|
|
volume = 31, |
1915 |
|
|
pages = {217-227} |
1916 |
tim |
2685 |
} |
1917 |
|
|
|
1918 |
|
|
|
1919 |
|
|
@Article{smondyrev:1999, |
1920 |
tim |
2691 |
author = {A.~M. Smondyrev and M.~L. Berkowitz}, |
1921 |
|
|
title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}}, |
1922 |
|
|
journal = {Biophysical Journal}, |
1923 |
|
|
year = 1999, |
1924 |
|
|
volume = 76, |
1925 |
|
|
pages = {2472-2478} |
1926 |
tim |
2685 |
} |
1927 |
|
|
|
1928 |
|
|
@Article{nina:2002, |
1929 |
tim |
2691 |
author = {M. Nina and T. Simonson}, |
1930 |
|
|
title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments}, |
1931 |
|
|
journal = {J. Phys. Chem. B}, |
1932 |
|
|
year = 2002, |
1933 |
|
|
volume = 106, |
1934 |
|
|
pages = {3696-3705} |
1935 |
tim |
2685 |
} |
1936 |
|
|
|
1937 |
|
|
@Article{norberg:2000, |
1938 |
tim |
2691 |
author = {J. Norberg and L. Nilsson}, |
1939 |
|
|
title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, |
1940 |
|
|
journal = {Biophysical Journal}, |
1941 |
|
|
year = 2000, |
1942 |
|
|
volume = 79, |
1943 |
|
|
pages = {1537-1553} |
1944 |
tim |
2685 |
} |
1945 |
|
|
|
1946 |
|
|
@Article{patra:2003, |
1947 |
tim |
2691 |
author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen}, |
1948 |
|
|
title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions}, |
1949 |
|
|
journal = {Biophysical Journal}, |
1950 |
|
|
year = 2003, |
1951 |
|
|
volume = 84, |
1952 |
|
|
pages = {3636-3645} |
1953 |
tim |
2685 |
} |
1954 |
|
|
|
1955 |
|
|
@Article{marrink04, |
1956 |
tim |
2691 |
author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, |
1957 |
|
|
title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, |
1958 |
|
|
journal = {J. Phys. Chem. B}, |
1959 |
|
|
year = 2004, |
1960 |
|
|
volume = 108, |
1961 |
|
|
pages = {750-760} |
1962 |
tim |
2685 |
} |
1963 |
|
|
|
1964 |
|
|
@Article{andersen83, |
1965 |
tim |
2691 |
author = {H.~C. Andersen}, |
1966 |
|
|
title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, |
1967 |
|
|
journal = {Journal of Computational Physics}, |
1968 |
|
|
year = 1983, |
1969 |
|
|
volume = 52, |
1970 |
|
|
pages = {24-34} |
1971 |
tim |
2685 |
} |
1972 |
|
|
|
1973 |
|
|
@Article{hura00, |
1974 |
tim |
2691 |
author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon}, |
1975 |
|
|
title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions}, |
1976 |
|
|
journal = {J. Chem. Phys.}, |
1977 |
|
|
year = 2000, |
1978 |
|
|
volume = 113, |
1979 |
|
|
pages = {9140-9148} |
1980 |
tim |
2685 |
} |
1981 |
|
|
|
1982 |
|
|
|
1983 |
|
|
@Article{ryckaert77, |
1984 |
tim |
2691 |
author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen}, |
1985 |
|
|
title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes}, |
1986 |
|
|
journal = {Journal of Computational Physics}, |
1987 |
|
|
year = 1977, |
1988 |
|
|
volume = 23, |
1989 |
|
|
pages = {327-341} |
1990 |
tim |
2685 |
} |
1991 |
|
|
|
1992 |
|
|
|
1993 |
|
|
@InBook{fowles99:lagrange, |
1994 |
tim |
2691 |
author = {G.~R. Fowles and G.~L. Cassiday}, |
1995 |
|
|
title = {Analytical Mechanics}, |
1996 |
|
|
chapter = 10, |
1997 |
|
|
publisher = {Saunders College Publishing}, |
1998 |
|
|
year = 1999, |
1999 |
|
|
edition = {6th} |
2000 |
tim |
2685 |
} |
2001 |
|
|
|
2002 |
|
|
@Article{petrache00, |
2003 |
tim |
2691 |
author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, |
2004 |
|
|
title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, |
2005 |
|
|
journal = {Biophysical Journal}, |
2006 |
|
|
year = 2000, |
2007 |
|
|
volume = 79, |
2008 |
|
|
pages = {3172-3192} |
2009 |
tim |
2685 |
} |
2010 |
|
|
|
2011 |
|
|
@Article{egberts88, |
2012 |
tim |
2691 |
author = {E. Egberts and H.~J.~C. Berendsen}, |
2013 |
|
|
title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail}, |
2014 |
|
|
journal = {J. Chem. Phys.}, |
2015 |
|
|
year = 1988, |
2016 |
|
|
volume = 89, |
2017 |
|
|
pages = {3718-3732} |
2018 |
tim |
2685 |
} |
2019 |
|
|
|
2020 |
tim |
2691 |
@Article{Holz00, |
2021 |
|
|
author = {M. Holz and S.~R. Heil and A. Sacco}, |
2022 |
|
|
title = {Temperature-dependent self-diffusion coefficients of |
2023 |
|
|
water and six selected molecular liquids for calibration |
2024 |
|
|
in accurate $^1${\sc h} {\sc nmr pfg} measurements}, |
2025 |
|
|
journal = {Phys. Chem. Chem. Phys.}, |
2026 |
|
|
year = 2000, |
2027 |
|
|
volume = 2, |
2028 |
tim |
2685 |
pages = {4740-4742}, |
2029 |
|
|
} |
2030 |
|
|
|
2031 |
|
|
@InCollection{zannoni94, |
2032 |
tim |
2691 |
author = {C. Zannoni}, |
2033 |
|
|
title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals}, |
2034 |
|
|
booktitle = {The Molecular Dynamics of Liquid Crstals}, |
2035 |
|
|
pages = {139-169}, |
2036 |
|
|
publisher = {Kluwer Academic Publishers}, |
2037 |
|
|
year = 1994, |
2038 |
|
|
editor = {G.~R. Luckhurst and C.~A. Veracini}, |
2039 |
|
|
chapter = 6 |
2040 |
tim |
2685 |
} |
2041 |
|
|
|
2042 |
|
|
|
2043 |
|
|
@Article{melchionna93, |
2044 |
tim |
2691 |
author = {S. Melchionna and G. Ciccotti and B.~L. Holian}, |
2045 |
|
|
title = {Hoover {\sc npt} dynamics for systems varying in shape and size}, |
2046 |
|
|
journal = {Molecular Physics}, |
2047 |
|
|
year = 1993, |
2048 |
|
|
volume = 78, |
2049 |
|
|
pages = {533-544} |
2050 |
tim |
2685 |
} |
2051 |
|
|
|
2052 |
|
|
@Article{fennell04, |
2053 |
tim |
2691 |
author = {C.~J. Fennell and J.~D. Gezelter}, |
2054 |
|
|
title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models}, |
2055 |
|
|
journal = {J. Chem. Phys}, |
2056 |
|
|
year = {in press 2004} |
2057 |
tim |
2685 |
} |
2058 |
|
|
|
2059 |
|
|
@Article{klein01, |
2060 |
tim |
2691 |
author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, |
2061 |
|
|
title = {A coarse Grain Model for Phospholipid Simulations}, |
2062 |
|
|
journal = {J. Phys. Chem. B}, |
2063 |
|
|
year = 2001, |
2064 |
|
|
volume = 105, |
2065 |
|
|
pages = {4464-4470} |
2066 |
tim |
2685 |
} |
2067 |
|
|
|
2068 |
|
|
|
2069 |
|
|
@Article{marrink03:vesicles, |
2070 |
tim |
2691 |
author = {S.~J. Marrink and A.~E. Mark}, |
2071 |
|
|
title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles}, |
2072 |
|
|
journal = {J. Am. Chem. Soc.}, |
2073 |
|
|
year = 2003, |
2074 |
|
|
volume = 125, |
2075 |
|
|
pages = {15233-15242} |
2076 |
tim |
2685 |
} |
2077 |
|
|
|
2078 |
tim |
2691 |
@Book{gamma94, |
2079 |
|
|
author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, |
2080 |
|
|
title = {Design Patterns: Elements of Reusable Object-Oriented Software}, |
2081 |
|
|
chapter = 7, |
2082 |
|
|
publisher = {Perason Education}, |
2083 |
|
|
year = 1994, |
2084 |
|
|
address = {London}, |
2085 |
|
|
} |
2086 |
|
|
|
2087 |
|
|
@Book{alexander, |
2088 |
|
|
author = {C. Alexander}, |
2089 |
|
|
title = {A Pattern Language: Towns, Buildings, Construction}, |
2090 |
|
|
publisher = {Oxford University Press}, |
2091 |
|
|
year = 1987, |
2092 |
|
|
address = {New York} |
2093 |
|
|
} |
2094 |
|
|
|
2095 |
|
|
@Article{wilson, |
2096 |
|
|
author = {G.~V. Wilson }, |
2097 |
|
|
title = {Where's the Real Bottleneck in Scientific Computing?}, |
2098 |
|
|
journal = {American Scientist}, |
2099 |
|
|
year = 2006, |
2100 |
|
|
volume = 94 |
2101 |
|
|
} |
2102 |
|
|
|
2103 |
|
|
@article{Meineke05, |
2104 |
|
|
Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter}, |
2105 |
|
|
Date-Modified = {2006-03-05 12:37:31 -0500}, |
2106 |
|
|
Journal = {J. Comp. Chem.}, |
2107 |
|
|
Pages = {252-271}, |
2108 |
|
|
Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics}, |
2109 |
|
|
Volume = 26, |
2110 |
|
|
Year = 2005 |
2111 |
|
|
} |
2112 |
tim |
2693 |
|
2113 |
|
|
@article{Matthey05, |
2114 |
tim |
2694 |
Author = {T. Matthey, T. Cickovski and \textit{et al}}, |
2115 |
tim |
2693 |
Date-Modified = {2006-03-05 12:37:31 -0500}, |
2116 |
|
|
Journal = {ACM Transactions on Mathematical Software}, |
2117 |
|
|
Pages = {237-265}, |
2118 |
|
|
Title = {ProtoMol, an Object-Oriented Framework for Prototyping Novel Algorithms for Molecular Dynamics}, |
2119 |
|
|
Volume = 20, |
2120 |
|
|
Year = 2004 |
2121 |
|
|
} |
2122 |
tim |
2694 |
|
2123 |
|
|
@Book{tolman79, |
2124 |
|
|
author = {R.~C. Tolman}, |
2125 |
|
|
title = {The Principles of Statistical Mechanics}, |
2126 |
|
|
chapter = 2, |
2127 |
|
|
publisher = {Dover Publications, Inc.}, |
2128 |
|
|
year = 1979, |
2129 |
|
|
address = {New York}, |
2130 |
|
|
pages = {19-22} |
2131 |
|
|
} |
2132 |
|
|
|
2133 |
|
|
@Book{Marion90, |
2134 |
|
|
author = {J.~B. Marion}, |
2135 |
|
|
title = {Classical Dynamics of Particles and Systems}, |
2136 |
|
|
publisher = {Academic Press}, |
2137 |
|
|
year = 1990, |
2138 |
|
|
address = {New York}, |
2139 |
|
|
edition = {2rd} |
2140 |
|
|
} |
2141 |
|
|
|
2142 |
|
|
@Book{Leimkuhler04, |
2143 |
|
|
author = {B. Leimkuhler and S. Reich}, |
2144 |
|
|
title = {Simulating Hamiltonian Dynamics}, |
2145 |
|
|
publisher = {Cambridge University Press}, |
2146 |
|
|
year = 2004, |
2147 |
tim |
2730 |
address = {Cambridge} |
2148 |
tim |
2694 |
} |
2149 |
tim |
2706 |
|
2150 |
|
|
@Article{Gray03, |
2151 |
|
|
author = {J.~J Gray,S. Moughon, C. Wang }, |
2152 |
|
|
title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations}, |
2153 |
|
|
journal = {jmb}, |
2154 |
|
|
year = 2003, |
2155 |
|
|
volume = 331, |
2156 |
|
|
pages = {281-299} |
2157 |
|
|
} |
2158 |
|
|
|
2159 |
|
|
@Article{McLachlan93, |
2160 |
|
|
author = {R.~I McLachlan}, |
2161 |
|
|
title = {Explicit Lie-Poisson integration and the Euler equations}, |
2162 |
|
|
journal = {prl}, |
2163 |
|
|
year = 1993, |
2164 |
|
|
volume = 71, |
2165 |
|
|
pages = {3043-3046} |
2166 |
|
|
} |
2167 |
tim |
2718 |
@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 |
tim |
2730 |
pages = {6356-6360} |
2175 |
tim |
2718 |
} |
2176 |
tim |
2730 |
|
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 |
|
|
} |