ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/electrostaticMethodsPaper/electrostaticMethods.bib
Revision: 2609
Committed: Sat Mar 11 18:05:50 2006 UTC (19 years, 4 months ago) by chrisfen
File size: 67104 byte(s)
Log Message:
organizational changes

File Contents

# Content
1 %% This BibTeX bibliography file was created using BibDesk.
2 %% http://bibdesk.sourceforge.net/
3
4
5 %% Created for Chris Fennell at 2006-03-11 12:19:21 -0500
6
7
8 %% Saved with string encoding Western (ASCII)
9
10
11 @STRING{acp = "Adv. Chem. Phys."}
12
13 @STRING{cp = "Chem. Phys."}
14
15 @STRING{cpl = "Chem. Phys. Lett."}
16
17 @STRING{jacs = "J. Am. Chem. Soc."}
18
19 @STRING{jcc = "J. Comput. Chem."}
20
21 @STRING{jcp = "J. Chem. Phys."}
22
23 @STRING{jml = "J. Mol. Liq."}
24
25 @STRING{jpc = "J. Phys. Chem."}
26
27 @STRING{jpca = "J. Phys. Chem. A"}
28
29 @STRING{jpcb = "J. Phys. Chem. B"}
30
31 @STRING{mp = "Mol. Phys."}
32
33 @STRING{pccp = "Phys. Chem. Chem. Phys."}
34
35 @STRING{pnas = "Proc. Natl. Acad. Sci. USA"}
36
37 @STRING{pra = "Phys. Rev. A"}
38
39 @STRING{prb = "Phys. Rev. B"}
40
41 @STRING{pre = "Phys. Rev. E"}
42
43 @STRING{prl = "Phys. Rev. Lett."}
44
45 @STRING{rmp = "Rev. Mod. Phys."}
46
47
48 @article{deLeeuw80,
49 Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
50 Date-Added = {2006-03-07 10:26:31 -0500},
51 Date-Modified = {2006-03-07 10:30:11 -0500},
52 Journal = {Proc. R. Soc. London Ser. A},
53 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
54 Number = {1752},
55 Pages = {27-56},
56 Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
57 Volume = {373},
58 Year = {1980}}
59
60 @article{Essmann95,
61 Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
62 Date-Added = {2006-03-05 12:25:25 -0500},
63 Date-Modified = {2006-03-05 12:29:07 -0500},
64 Journal = {J. Chem. Phys.},
65 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
66 Number = {19},
67 Pages = {8577-8593},
68 Title = {A smooth particle mesh Ewald method },
69 Volume = {103},
70 Year = {1995}}
71
72 @article{Kast03,
73 Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
74 Date-Added = {2006-02-18 16:47:26 -0500},
75 Date-Modified = {2006-02-18 16:51:25 -0500},
76 Journal = {Chem. Phys. Lett.},
77 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
78 Pages = {398-404},
79 Title = {Integral equation theory for correcting truncation errors in molecular simulations},
80 Volume = {367},
81 Year = {2003}}
82
83 @article{Tobias01,
84 Author = {D.~J. Tobias},
85 Date-Added = {2006-02-15 11:28:58 -0500},
86 Date-Modified = {2006-02-15 11:32:16 -0500},
87 Journal = {Curr. Opin. Struct. Biol.},
88 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
89 Pages = {253-261},
90 Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
91 Volume = {11},
92 Year = {2001}}
93
94 @article{Zahn02,
95 Author = {D. Zahn and B. Schilling and S.~M. Kast},
96 Date-Added = {2006-02-15 09:21:27 -0500},
97 Date-Modified = {2006-02-15 09:24:07 -0500},
98 Journal = {J. Phys. Chem. B},
99 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
100 Number = {41},
101 Pages = {10725-10732},
102 Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
103 Volume = {106},
104 Year = {2002}}
105
106 @article{Wolf99,
107 Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
108 Date-Added = {2006-02-15 09:09:39 -0500},
109 Date-Modified = {2006-02-15 09:25:30 -0500},
110 Journal = {J. Chem. Phys.},
111 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
112 Number = {17},
113 Pages = {8255-8282},
114 Rating = {0},
115 Read = {No},
116 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
117 Volume = {110},
118 Year = {1999}}
119
120 @book{Berne90,
121 Address = {Malabar, Florida},
122 Author = {B.~J. Berne and R. Pecora},
123 Publisher = {Robert E. Krieger Publishing Company, Inc.},
124 Title = {Dynamic Light Scattering},
125 Year = 1990}
126
127 @article{Evans77,
128 Author = {D.~J. Evans},
129 Journal = {Mol. Phys.},
130 Pages = {317-325},
131 Title = {On the representation of orientation space},
132 Volume = 34,
133 Year = 1977}
134
135 @article{Tuckerman92,
136 Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
137 Journal = jcp,
138 Pages = {1990-2001},
139 Title = {Reversible multiple time scale molecular dynamics},
140 Volume = 97,
141 Year = 1992}
142
143 @book{Hansen86,
144 Address = {London},
145 Author = {J.~P. Hansen and I.~R. McDonald},
146 Chapter = 7,
147 Pages = {199-206},
148 Publisher = {Academic Press},
149 Title = {Theory of Simple Liquids},
150 Year = 1986}
151
152 @article{Angelani98,
153 Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
154 Journal = prl,
155 Number = 21,
156 Pages = {4648-4651},
157 Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
158 Volume = 81,
159 Year = 1998}
160
161 @article{Stillinger82,
162 Author = {F.~H. Stillinger and T.~A. Weber},
163 Journal = pra,
164 Number = 2,
165 Pages = {978-989},
166 Title = {Hidden structure in liquids},
167 Volume = 25,
168 Year = 1982}
169
170 @article{Stillinger83,
171 Author = {F.~H. Stillinger and T.~A. Weber},
172 Journal = pra,
173 Number = 4,
174 Pages = {2408-2416},
175 Title = {Dynamics of structural transitions in liquids},
176 Volume = 28,
177 Year = 1983}
178
179 @article{Weber84,
180 Author = {T.~A. Weber and F.~H. Stillinger},
181 Journal = jcp,
182 Number = 6,
183 Pages = {2742-2746},
184 Title = {The effect of density on the inherent structure in liquids},
185 Volume = 80,
186 Year = 1984}
187
188 @article{Stillinger85,
189 Author = {F.~H. Stillinger and T.~A. Weber},
190 Journal = jcp,
191 Number = 9,
192 Pages = {4767-4775},
193 Title = {Inherent structure theory of liquids in the hard-sphere limit},
194 Volume = 83,
195 Year = 1985}
196
197 @article{Stillinger98,
198 Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
199 Journal = {Nature},
200 Pages = {554-557},
201 Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
202 Volume = 393,
203 Year = 1998}
204
205 @article{Parkhurst75a,
206 Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
207 Journal = jcp,
208 Number = 6,
209 Pages = {2698-2704},
210 Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
211 Volume = 63,
212 Year = 1975}
213
214 @article{Parkhurst75b,
215 Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
216 Journal = jcp,
217 Number = 6,
218 Pages = {2705-2709},
219 Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
220 Volume = 63,
221 Year = 1975}
222
223 @article{Forester97,
224 Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
225 Journal = {J. Chem. Soc. - Faraday Transactions},
226 Pages = {613-619},
227 Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
228 Volume = 93,
229 Year = 1997}
230
231 @article{Tieleman98,
232 Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
233 Journal = {Biophys. J.},
234 Pages = {2786-2801},
235 Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
236 Volume = 74,
237 Year = 1998}
238
239 @article{Cascales98,
240 Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
241 Journal = {J. Phys. Chem. B},
242 Pages = {625-631},
243 Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
244 Volume = 102,
245 Year = 1998}
246
247 @article{Bassolino95,
248 Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
249 Journal = {J. Am. Chem. Soc.},
250 Pages = {4118-4129},
251 Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
252 Volume = 117,
253 Year = 1995}
254
255 @article{Alper95,
256 Author = {H.~E. Alper and T.~R. Stouch},
257 Journal = {J. Phys. Chem.},
258 Pages = {5724-5731},
259 Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
260 Volume = 99,
261 Year = 1995}
262
263 @article{Sok92,
264 Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
265 Journal = {J. Chem. Phys.},
266 Pages = {4699-4704},
267 Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
268 Volume = 96,
269 Year = 1992}
270
271 @article{Rabani99,
272 Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
273 Journal = prl,
274 Pages = {3649},
275 Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
276 Volume = 82,
277 Year = {1999}}
278
279 @article{Rabani97,
280 Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
281 Journal = {J. Chem. Phys.},
282 Pages = {6867-6876},
283 Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
284 Volume = 107,
285 Year = 1997}
286
287 @article{Gezelter99,
288 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
289 Journal = jcp,
290 Pages = 3444,
291 Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
292 Volume = 110,
293 Year = 1999}
294
295 @article{Gezelter98,
296 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
297 Date-Modified = {2006-02-15 10:18:42 -0500},
298 Journal = jcp,
299 Pages = 4695,
300 Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
301 Volume = 109,
302 Year = 1998}
303
304 @article{Gezelter97,
305 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
306 Journal = jcp,
307 Pages = 4618,
308 Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
309 Volume = 107,
310 Year = 1997}
311
312 @article{Zwanzig83,
313 Author = {R. Zwanzig},
314 Journal = jcp,
315 Pages = {4507-4508},
316 Title = {On the relation between self-diffusion and viscosity of liquids},
317 Volume = 79,
318 Year = 1983}
319
320 @article{Zwanzig88,
321 Author = {R. Zwanzig},
322 Journal = {Proc. Natl. Acad. Sci. USA},
323 Pages = 2029,
324 Title = {Diffusion in rough potential},
325 Volume = 85,
326 Year = 1988}
327
328 @article{Stillinger95,
329 Author = {F.~H. Stillinger},
330 Journal = {Science},
331 Pages = {1935-1939},
332 Title = {A Topographic View of Supercooled Liquids and Glass Formation},
333 Volume = 267,
334 Year = 1995}
335
336 @incollection{Angell85,
337 Address = {Springfield, VA},
338 Author = {C.~A. Angell},
339 Booktitle = {Relaxations in Complex Systems},
340 Editor = {K.~Ngai and G.~B. Wright},
341 Pages = 1,
342 Publisher = {National Technical Information Service, U.S. Department of Commerce},
343 Title = {unknown},
344 Year = 1985}
345
346 @article{Bembenek96,
347 Author = {S.~D. Bembenek and B.~B. Laird},
348 Journal = jcp,
349 Pages = 5199,
350 Title = {The role of localization in glasses and supercooled liquids},
351 Volume = 104,
352 Year = 1996}
353
354 @article{Sun97a,
355 Author = {X. Sun and W.~H. Miller},
356 Date-Modified = {2006-02-15 10:33:35 -0500},
357 Journal = jcp,
358 Pages = 6346,
359 Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
360 Volume = 106,
361 Year = 1997}
362
363 @article{Spath96,
364 Author = {B.~W. Spath and W.~H. Miller},
365 Journal = jcp,
366 Pages = 95,
367 Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
368 Volume = 104,
369 Year = 1996}
370
371 @book{Warshel91,
372 Address = {New York},
373 Author = {Arieh Warshel},
374 Publisher = {Wiley},
375 Title = {Computer modeling of chemical reactions in enzymes and solutions},
376 Year = 1991}
377
378 @article{Vuilleumier97,
379 Author = {Rodolphe Vuilleumier and Daniel Borgis},
380 Journal = jpc,
381 Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
382 Volume = {in press},
383 Year = 1997}
384
385 @article{Kob95a,
386 Author = {W. Kob and H.~C. Andersen},
387 Journal = pre,
388 Pages = {4626-4641},
389 Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
390 Volume = 51,
391 Year = 1995}
392
393 @article{Kob95b,
394 Author = {W. Kob and H.~C. Andersen},
395 Journal = pre,
396 Pages = {4134-4153},
397 Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
398 Volume = 52,
399 Year = 1995}
400
401 @inproceedings{Gotze89,
402 Address = {Amsterdam},
403 Author = {W. G{\"{o}}tze},
404 Booktitle = {Liquids, Freezing and Glass Transitions},
405 Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
406 Pages = {287-503},
407 Publisher = {North-Holland},
408 Title = {Aspects of Structural Glass Transitions},
409 Volume = {I},
410 Year = 1989}
411
412 @article{Sun97b,
413 Author = {X. Sun and W.~H. Miller},
414 Date-Modified = {2006-02-15 10:33:29 -0500},
415 Journal = jcp,
416 Pages = 916,
417 Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
418 Year = 1997}
419
420 @article{Keshavamurthy94,
421 Author = {S. Keshavamurthy and W.~H. Miller},
422 Journal = cpl,
423 Pages = 189,
424 Title = {ivr},
425 Volume = 218,
426 Year = 1994}
427
428 @article{Billing75,
429 Author = {G.~D. Billing},
430 Journal = cpl,
431 Pages = 391,
432 Title = {ehrenfest},
433 Volume = 30,
434 Year = 1975}
435
436 @article{Chang90,
437 Author = {Y.-T. Chang and W.~H. Miller},
438 Journal = jpc,
439 Pages = {5884-5888},
440 Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
441 Volume = 94,
442 Year = 1990}
443
444 @article{Shor94,
445 Author = {P.W. Shor},
446 Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
447 Pages = {124-134},
448 Title = {Algorithms for quantum computation: discrete logarithms and factoring},
449 Year = 1994}
450
451 @article{Feynman82,
452 Author = {R.~P. Feynman},
453 Journal = {Int. J. Theor. Phys.},
454 Pages = {467-488},
455 Title = {Simulating physics with computers},
456 Volume = 21,
457 Year = 1982}
458
459 @article{Grover97,
460 Author = {L.~K. Grover},
461 Journal = prl,
462 Pages = {4709-4712},
463 Title = {Quantum computers can search arbitrarily large databases by a single query},
464 Volume = 79,
465 Year = 1997}
466
467 @article{Chuang98,
468 Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
469 Journal = prl,
470 Pages = {3408-3411},
471 Title = {Experimental Implementation of Fast Quantum Searching},
472 Volume = 80,
473 Year = 1998}
474
475 @article{Monroe95,
476 Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
477 Journal = prl,
478 Pages = 4714,
479 Title = {Demonstration of a fundamental quantum logic gate},
480 Volume = 75,
481 Year = 1995}
482
483 @article{Lent93,
484 Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
485 Journal = {Nanotechnology},
486 Pages = {49-57},
487 Title = {Quantum Cellular Automata},
488 Volume = 4,
489 Year = 1993}
490
491 @article{Barenco95,
492 Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
493 Journal = {Phys. Rev. A},
494 Pages = {3457-3467},
495 Title = {elementary gates for quantum computation},
496 Volume = 52,
497 Year = 1995}
498
499 @article{Reinot97,
500 Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
501 Date-Modified = {2006-02-15 10:31:21 -0500},
502 Journal = jcp,
503 Pages = {457-466},
504 Title = {Electronic dephasing and electron-phonon coupling of aluminum phthalocyanine tetrasulphonate in hyperquenched and annealed glassy films of ethanol and methanol over a broad temperature range},
505 Volume = 106,
506 Year = 1997}
507
508 @article{Laflamme96,
509 Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
510 Journal = prl,
511 Pages = 77,
512 Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
513 Volume = 98,
514 Year = 1996}
515
516 @article{Shor95,
517 Author = {P.~W. Shor},
518 Journal = {Phys. Rev. A},
519 Pages = {2493-2496},
520 Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
521 Volume = 52,
522 Year = 1995}
523
524 @article{Calderbank96,
525 Author = {A.~R. Calderbank and P.~W. Shor},
526 Journal = {Phys. Rev. A},
527 Pages = {1098-1105},
528 Title = {Good quantum error-correcting codes exist},
529 Volume = 54,
530 Year = 1996}
531
532 @article{Steane96,
533 Author = {A.~M. Steane},
534 Journal = prl,
535 Pages = {793-797},
536 Title = {Error correcting codes in quantum theory},
537 Volume = 77,
538 Year = 1996}
539
540 @article{Gezelter95,
541 Author = {J.~D. Gezelter and W.~H. Miller},
542 Journal = jcp,
543 Pages = {7868-7876},
544 Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
545 Volume = 103,
546 Year = 1995}
547
548 @article{Chakrabarti92,
549 Author = {A.~C. Chakrabarti and D.~W. Deamer},
550 Journal = {Biochimica et Biophysica Acta},
551 Pages = {171-177},
552 Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
553 Volume = 1111,
554 Year = 1992}
555
556 @article{Paula96,
557 Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
558 Journal = {Biophys. J.},
559 Pages = {339-348},
560 Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
561 Volume = 70,
562 Year = 1996}
563
564 @article{Little96,
565 Author = {H.~J. Little},
566 Journal = {Pharmacology \& Therapeutics},
567 Pages = {37-58},
568 Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
569 Volume = 69,
570 Year = 1996}
571
572 @article{McKinnon92,
573 Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
574 Journal = jpc,
575 Pages = {10497-10506},
576 Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
577 Volume = 96,
578 Year = 1992}
579
580 @article{Venable93,
581 Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
582 Journal = {Science},
583 Pages = {223-226},
584 Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
585 Volume = 262,
586 Year = 1993}
587
588 @article{Essmann99,
589 Author = {U. Essmann and M.~L. Berkowitz},
590 Journal = {Biophys. J.},
591 Pages = {2081-2089},
592 Title = {Dynamical properties of phospholipid bilayers from computer simulation},
593 Volume = 76,
594 Year = 1999}
595
596 @article{Tu98,
597 Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
598 Journal = {Biophys. J.},
599 Pages = {2123-2134},
600 Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
601 Volume = 75,
602 Year = 1998}
603
604 @article{Pomes96,
605 Author = {R. Pomes and B. Roux},
606 Journal = {Biophys. J.},
607 Pages = {19-39},
608 Title = {Structure and dynamics of a proton wire: A theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
609 Volume = 71,
610 Year = 1996}
611
612 @article{Duwez60,
613 Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
614 Journal = {J. Appl. Phys.},
615 Pages = {1136-1137},
616 Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
617 Volume = 31,
618 Year = 1960}
619
620 @article{Peker93,
621 Author = {A. Peker and W.~L. Johnson},
622 Journal = {Appl. Phys. Lett.},
623 Pages = {2342-2344},
624 Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
625 Volume = 63,
626 Year = 1993}
627
628 @article{ChoiYim97,
629 Author = {H. Choi-Yim and W.~L. Johnson},
630 Journal = {Appl. Phys. Lett.},
631 Pages = {3808-3810},
632 Title = {Bulk metallic glass matrix composites},
633 Volume = 71,
634 Year = 1997}
635
636 @article{Sun96,
637 Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
638 Journal = {J. Mater. Res.},
639 Pages = {2738-2743},
640 Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
641 Volume = 11,
642 Year = 1996}
643
644 @article{Heller93,
645 Author = {H. Heller and M. Schaefer and K. Schulten},
646 Journal = jpc,
647 Pages = {8343-8360},
648 Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
649 Volume = 97,
650 Year = 1993}
651
652 @article{Kushick76,
653 Author = {J. Kushick and B.~J. Berne},
654 Journal = jcp,
655 Pages = {1362-1367},
656 Title = {Computer Simulation of anisotropic molecular fluids},
657 Volume = 64,
658 Year = 1976}
659
660 @article{Berardi96,
661 Author = {R. Berardi and S. Orlandi and C Zannoni},
662 Journal = cpl,
663 Pages = {357-362},
664 Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
665 Volume = 261,
666 Year = 1996}
667
668 @article{Berardi99,
669 Author = {R. Berardi and S. Orlandi and C. Zannoni},
670 Journal = {Int. J. Mod. Phys. C},
671 Pages = {477-484},
672 Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
673 Volume = 10,
674 Year = 1999}
675
676 @article{Pasterny00,
677 Author = {K. Pasterny and E. Gwozdz and A. Brodka},
678 Date-Modified = {2006-02-15 10:29:47 -0500},
679 Journal = {J. Mol. Liq.},
680 Pages = {173-184},
681 Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
682 Volume = 85,
683 Year = 2000}
684
685 @article{Jorgensen83,
686 Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
687 Journal = jcp,
688 Pages = {926-935},
689 Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
690 Volume = 79,
691 Year = 1983}
692
693 @article{Berardi98,
694 Author = {R. Berardi and C. Fava and C. Zannoni},
695 Journal = cpl,
696 Pages = {8-14},
697 Title = {A Gay-Berne potential for dissimilar biaxial particles},
698 Volume = 297,
699 Year = 1998}
700
701 @article{Luckhurst90,
702 Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
703 Journal = {Liquid Crystals},
704 Pages = {451-464},
705 Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the Gay-Berne model mesogen},
706 Volume = 8,
707 Year = 1990}
708
709 @article{Gay81,
710 Author = {J.~G. Gay and B.~J. Berne},
711 Journal = jcp,
712 Pages = {3316-3319},
713 Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
714 Volume = 74,
715 Year = 1981}
716
717 @article{Berne72,
718 Author = {B.~J. Berne and P. Pechukas},
719 Journal = jcp,
720 Pages = {4213-4216},
721 Title = {Gaussian Model Potentials for Molecular Interactions},
722 Volume = 56,
723 Year = 1972}
724
725 @article{Perram96,
726 Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
727 Journal = pre,
728 Pages = {6565-6572},
729 Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
730 Volume = 54,
731 Year = 1996}
732
733 @article{Cornell95,
734 Author = {W.~D. Cornell and P. Cieplak and C.~I. Bayly and I.~R. Gould and K.~M. {Merz, Jr.} and D.~M. Ferguson and D.~C. Spellmeyer and T. Fox and J.~W. Caldwell and P.~A. Kollman},
735 Journal = jacs,
736 Pages = {5179-5197},
737 Title = {A second generation force field for the simulation of proteins and nucleic acids},
738 Volume = 117,
739 Year = 1995}
740
741 @article{Brooks83,
742 Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
743 Journal = {J. Comp. Chem.},
744 Pages = {187-217},
745 Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
746 Volume = 4,
747 Year = 1983}
748
749 @incollection{MacKerell98,
750 Address = {New York},
751 Author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and and M. Karplus},
752 Booktitle = {The Encyclopedia of Computational Chemistry},
753 Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
754 Pages = {271-277},
755 Publisher = {John Wiley \& Sons},
756 Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
757 Volume = 1,
758 Year = 1998}
759
760 @incollection{Jorgensen98a,
761 Address = {New York},
762 Author = {W.~L. Jorgensen},
763 Booktitle = {The Encyclopedia of Computational Chemistry},
764 Date-Modified = {2006-02-15 10:21:45 -0500},
765 Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
766 Pages = {1986-1989},
767 Publisher = {John Wiley \& Sons},
768 Title = {OPLS Force Fields},
769 Volume = 3,
770 Year = 1998}
771
772 @article{Rabani00,
773 Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
774 Date-Modified = {2006-02-15 10:30:55 -0500},
775 Journal = prl,
776 Pages = 467,
777 Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
778 Volume = 85,
779 Year = 2000}
780
781 @book{Cevc87,
782 Address = {New York},
783 Author = {G. Cevc and D. Marsh},
784 Publisher = {John Wiley \& Sons},
785 Title = {Phospholipid Bilayers},
786 Year = 1987}
787
788 @article{Janiak79,
789 Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
790 Journal = {J. Biol. Chem.},
791 Pages = {6068-6078},
792 Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
793 Volume = 254,
794 Year = 1979}
795
796 @book{Tobias90,
797 Address = {Tucson},
798 Author = {Sheila Tobias},
799 Publisher = {Research Corp.},
800 Title = {They're not Dumb. They're Different: Stalking the Second Tier},
801 Year = 1990}
802
803 @article{Mazur92,
804 Author = {E. Mazur},
805 Journal = {Optics and Photonics News},
806 Pages = 38,
807 Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing?},
808 Volume = 3,
809 Year = 1992}
810
811 @book{Mazur97,
812 Address = {New Jersey},
813 Author = {Eric Mazur},
814 Publisher = {Prentice Hall},
815 Title = {Peer Instruction: A User's Manual},
816 Year = 1997}
817
818 @article{Wigner55,
819 Author = {E.~P. Wigner},
820 Journal = {Annals of Mathematics},
821 Pages = {548-564},
822 Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
823 Volume = 62,
824 Year = 1955}
825
826 @article{Gaukel98,
827 Author = {C. Gaukel and H.~R. Schober},
828 Journal = {Solid State Comm.},
829 Pages = {1-5},
830 Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
831 Volume = 107,
832 Year = 1998}
833
834 @article{Qi99,
835 Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
836 Journal = prb,
837 Number = 5,
838 Pages = {3527-3533},
839 Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
840 Volume = 59,
841 Year = 1999}
842
843 @article{Khorunzhy97,
844 Author = {A. Khorunzhy and G.~J. Rodgers},
845 Journal = {J. Math. Phys.},
846 Pages = {3300-3320},
847 Title = {Eigenvalue distribution of large dilute random matrices},
848 Volume = 38,
849 Year = 1997}
850
851 @article{Rodgers88,
852 Author = {G.~J. Rodgers and A. Bray},
853 Journal = {Phys. Rev. B},
854 Pages = 355703562,
855 Title = {Density of States of a Sparse Random Matrix},
856 Volume = 37,
857 Year = 1988}
858
859 @article{Rodgers90,
860 Author = {G.~J. Rodgers and C. {De Dominicis}},
861 Journal = {J. Phys. A: Math. Gen.},
862 Pages = {1567-1573},
863 Title = {Density of states of sparse random matrices},
864 Volume = 23,
865 Year = 1990}
866
867 @inproceedings{Barker80,
868 Author = {J.~A. Barker},
869 Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
870 Editor = {D. Ceperley},
871 Pages = {45-6},
872 Series = {NRCC Workshop Proceedings},
873 Title = {Reaction field method for polar fluids},
874 Volume = 9,
875 Year = 1980}
876
877 @article{Smith82,
878 Author = {W. Smith},
879 Journal = {CCP5 Quarterly},
880 Pages = {13-25},
881 Title = {Point multipoles in the Ewald summation},
882 Volume = 4,
883 Year = 1982}
884
885 @article{Daw84,
886 Author = {M.~S. Daw and M.~I. Baskes},
887 Journal = prb,
888 Number = 12,
889 Pages = {6443-6453},
890 Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
891 Volume = 29,
892 Year = 1984}
893
894 @article{Sutton90,
895 Author = {A.~P. Sutton and J. Chen},
896 Date-Modified = {2006-02-15 10:33:48 -0500},
897 Journal = {Phil. Mag. Lett.},
898 Pages = {139-146},
899 Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
900 Volume = 61,
901 Year = 1990}
902
903 @article{Lu97,
904 Author = {J. Lu and J.~A. Szpunar},
905 Journal = {Phil. Mag. A},
906 Pages = {1057-1066},
907 Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
908 Volume = {75},
909 Year = {1997}}
910
911 @article{Shlesinger99,
912 Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
913 Journal = {Am. J. Phys.},
914 Pages = {1253-1259},
915 Title = {Above, below, and beyond Brownian motion},
916 Volume = 67,
917 Year = 1999}
918
919 @article{Klafter96,
920 Author = {J. Klafter and M. Shlesinger and G. Zumofen},
921 Journal = {Physics Today},
922 Pages = {33-39},
923 Title = {Beyond Brownian Motion},
924 Volume = 49,
925 Year = 1996}
926
927 @article{Blumen83,
928 Author = {A. Blumen and J. Klafter and G. Zumofen},
929 Journal = {Phys. Rev. B},
930 Pages = {3429-3435},
931 Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
932 Volume = 27,
933 Year = 1983}
934
935 @article{Klafter94,
936 Author = {J. Klafter and G. Zumofen},
937 Journal = jpc,
938 Pages = {7366-7370},
939 Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
940 Volume = 98,
941 Year = 1994}
942
943 @article{Dzugutov92,
944 Author = {M. Dzugutov},
945 Journal = pra,
946 Pages = {R2984-R2987},
947 Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
948 Volume = 46,
949 Year = 1992}
950
951 @article{Moore94,
952 Author = {P. Moore and T. Keyes},
953 Journal = jcp,
954 Pages = 6709,
955 Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
956 Volume = 100,
957 Year = 1994}
958
959 @article{Seeley89,
960 Author = {G. Seeley and T. Keyes},
961 Journal = jcp,
962 Pages = {5581-5586},
963 Title = {Normal-mode analysis of liquid-state dynamics},
964 Volume = 91,
965 Year = 1989}
966
967 @article{Madan90,
968 Author = {B. Madan and T. Keyes and G. Seeley},
969 Journal = jcp,
970 Pages = {7565-7569},
971 Title = {Diffusion in supercooled liquids via normal mode analysis},
972 Volume = 92,
973 Year = 1990}
974
975 @article{Madan91,
976 Author = {B. Madan and T. Keyes and G. Seeley},
977 Journal = jcp,
978 Pages = {6762-6769},
979 Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
980 Volume = 94,
981 Year = 1991}
982
983 @article{Buchner92,
984 Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
985 Journal = jcp,
986 Pages = {8522-8535},
987 Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
988 Volume = 97,
989 Year = 1992}
990
991 @article{Wan94,
992 Author = {Yi. Wan and R.~M. Stratt},
993 Journal = jcp,
994 Pages = {5123-5138},
995 Title = {Liquid theory for the instantaneous normal modes of a liquid},
996 Volume = 100,
997 Year = 1994}
998
999 @article{Stratt95,
1000 Author = {R.~M. Stratt},
1001 Journal = {Acc. Chem. Res.},
1002 Pages = {201-207},
1003 Title = {The instantaneous normal modes of liquids},
1004 Volume = 28,
1005 Year = 1995}
1006
1007 @article{Nitzan95,
1008 Author = {G.~V. Vijayadamodar and A. Nitzan},
1009 Journal = jcp,
1010 Pages = {2169-2177},
1011 Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
1012 Volume = 103,
1013 Year = 1995}
1014
1015 @article{Ribeiro98,
1016 Author = {M.~C.~C. Ribeiro and P.~A. Madden},
1017 Journal = jcp,
1018 Pages = {3256-3263},
1019 Title = {Unstable Modes in Ionic Melts},
1020 Volume = 108,
1021 Year = 1998}
1022
1023 @article{Keyes98,
1024 Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
1025 Date-Modified = {2006-02-15 10:22:13 -0500},
1026 Journal = jcp,
1027 Pages = {4693-4694},
1028 Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
1029 Volume = 109,
1030 Year = 1998}
1031
1032 @article{Alemany98,
1033 Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
1034 Journal = jcp,
1035 Pages = {5175-5176},
1036 Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
1037 Volume = 109,
1038 Year = 1998}
1039
1040 @article{Belonoshko00,
1041 Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
1042 Journal = prb,
1043 Pages = {3838-3844},
1044 Title = {Quasi ab initio molecular dynamic study of Cu melting},
1045 Volume = 61,
1046 Year = 2000}
1047
1048 @article{Banhart92,
1049 Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1050 Journal = prb,
1051 Pages = {9968-9975},
1052 Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1053 Volume = 46,
1054 Year = 1992}
1055
1056 @article{Wendt78,
1057 Author = {H. Wendt and F.~F. Abraham},
1058 Journal = prl,
1059 Pages = 1244,
1060 Volume = 41,
1061 Year = 1978}
1062
1063 @article{Lewis91,
1064 Author = {L.~J. Lewis},
1065 Journal = prb,
1066 Pages = {4245-4254},
1067 Title = {Atomic dynamics through the glass transition},
1068 Volume = 44,
1069 Year = 1991}
1070
1071 @article{Liu92,
1072 Author = {R.~S. Liu and D.~W. Qi and S. Wang},
1073 Journal = prb,
1074 Pages = {451-453},
1075 Title = {Subpeaks of structure factors for rapidly quenched metals},
1076 Volume = 45,
1077 Year = 1992}
1078
1079 @article{Anheuser94,
1080 Author = {K. Anheuser and J.P. Northover},
1081 Journal = {Brit. Num. J.},
1082 Pages = 22,
1083 Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
1084 Volume = 64,
1085 Year = 1994}
1086
1087 @article{Pense92,
1088 Author = {A. W. Pense},
1089 Journal = {Mat. Char.},
1090 Pages = 213,
1091 Title = {The Decline and Fall of the Roman Denarius},
1092 Volume = 29,
1093 Year = 1992}
1094
1095 @article{Ngai81,
1096 Author = {K.~L. Ngai and F.-S. Liu},
1097 Journal = prb,
1098 Pages = {1049-1065},
1099 Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1100 Volume = 24,
1101 Year = 1981}
1102
1103 @unpublished{Truhlar00,
1104 Author = {D.~G. Truhlar and A. Kohen},
1105 Date-Modified = {2006-02-15 16:35:52 -0500},
1106 Note = {private correspondence},
1107 Year = {2000}}
1108
1109 @article{Truhlar78,
1110 Author = {Donald G. Truhlar},
1111 Journal = {J. Chem. Ed.},
1112 Pages = 309,
1113 Title = {Interpretation of the Activation Energy},
1114 Volume = 55,
1115 Year = 1978}
1116
1117 @book{Tolman27,
1118 Address = {New York},
1119 Author = {R. C. Tolman},
1120 Pages = {260-270},
1121 Publisher = {Chemical Catalog Co.},
1122 Title = {Statistical Mechanics with Applications to Physics and Chemistry},
1123 Year = 1927}
1124
1125 @article{Tolman20,
1126 Author = {R. C. Tolman},
1127 Journal = jacs,
1128 Pages = 2506,
1129 Title = {Statistical Mechanics Applied to Chemical Kinetics},
1130 Volume = 42,
1131 Year = 1920}
1132
1133 @article{Ediger96,
1134 Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
1135 Date-Modified = {2006-02-15 10:16:35 -0500},
1136 Journal = jpc,
1137 Pages = 13200,
1138 Title = {Supercooled Liquids and Glasses},
1139 Volume = 100,
1140 Year = 1996}
1141
1142 @inbook{Blumen86,
1143 Address = {Amsterdam},
1144 Author = {A. Blumen and J. Klafter and G. Zumofen},
1145 Chapter = {Reactions in Disordered Media Modelled by Fractals},
1146 Editor = {Luciano Peitronero and E. Tosatti},
1147 Pages = 399,
1148 Publisher = {North-Holland},
1149 Series = {International Symposium on Fractals in Physics},
1150 Title = {Fractals in Physics},
1151 Year = 1986}
1152
1153 @article{Shlesinger84,
1154 Author = {M.~F. Shlesinger and E.~W. Montroll},
1155 Journal = {Proc. Natl. Acad. Sci. USA},
1156 Pages = {1280-1283},
1157 Title = {On the Williams-Watts function of dielectric relaxation},
1158 Volume = 81,
1159 Year = 1984}
1160
1161 @article{Klafter86,
1162 Author = {J. Klafter and M.~F. Shlesinger},
1163 Journal = {Proc. Natl. Acad. Sci. USA},
1164 Pages = {848-851},
1165 Title = {On the relationship among three theories of relaxation in disordered systems},
1166 Volume = 83,
1167 Year = 1986}
1168
1169 @article{Li01,
1170 Author = {Z. Li and M. Lieberman and W. Hill},
1171 Date-Modified = {2006-02-15 10:25:36 -0500},
1172 Journal = {Langmuir},
1173 Pages = {4887-4894},
1174 Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
1175 Volume = 17,
1176 Year = 2001}
1177
1178 @article{Evans93,
1179 Author = {J.~W. Evans},
1180 Date-Modified = {2006-02-15 10:17:03 -0500},
1181 Journal = rmp,
1182 Pages = {1281-1329},
1183 Title = {Random and Cooperative Sequential Adsorption},
1184 Volume = 65,
1185 Year = 1993}
1186
1187 @article{Dwyer1977,
1188 Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1189 Journal = {Surf. Sci.},
1190 Pages = 617,
1191 Volume = 64,
1192 Year = 1977}
1193
1194 @article{Macritche78,
1195 Author = {F. MacRitche},
1196 Date-Modified = {2006-02-15 10:27:37 -0500},
1197 Journal = {Adv. Protein Chem.},
1198 Pages = 283,
1199 Volume = 32,
1200 Year = 1978}
1201
1202 @article{Feder80,
1203 Author = {J. Feder},
1204 Date-Modified = {2006-02-15 10:17:21 -0500},
1205 Journal = {J. Theor. Biol.},
1206 Pages = 237,
1207 Volume = 87,
1208 Year = 1980}
1209
1210 @article{Ramsden93,
1211 Author = {J.~J. Ramsden},
1212 Date-Modified = {2006-02-15 10:31:03 -0500},
1213 Journal = prl,
1214 Pages = 295,
1215 Volume = 71,
1216 Year = 1993}
1217
1218 @article{Egelhoff89,
1219 Author = {W.~F. Egelhoff and I. Jacob},
1220 Date-Modified = {2006-02-15 10:16:54 -0500},
1221 Journal = prl,
1222 Pages = 921,
1223 Volume = 62,
1224 Year = 1989}
1225
1226 @article{Viot92a,
1227 Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1228 Date-Modified = {2006-02-15 10:12:51 -0500},
1229 Journal = jpc,
1230 Pages = {5212-5218},
1231 Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1232 Volume = 97,
1233 Year = 1992}
1234
1235 @article{Viot92b,
1236 Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1237 Date-Modified = {2006-02-15 10:12:57 -0500},
1238 Journal = {Physica A},
1239 Pages = {248-252},
1240 Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
1241 Volume = 191,
1242 Year = 1992}
1243
1244 @article{Dobson1987,
1245 Author = {B.~W. Dobson},
1246 Journal = prb,
1247 Pages = 1068,
1248 Volume = 36,
1249 Year = 1987}
1250
1251 @article{Boyer95,
1252 Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1253 Date-Modified = {2006-02-15 10:15:52 -0500},
1254 Journal = jcp,
1255 Pages = 1607,
1256 Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
1257 Volume = 103,
1258 Year = 1995}
1259
1260 @article{Viot92c,
1261 Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1262 Date-Modified = {2006-02-15 10:13:03 -0500},
1263 Journal = {Physica A},
1264 Pages = {248-252},
1265 Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
1266 Volume = 191,
1267 Year = 1992}
1268
1269 @article{Ricci94,
1270 Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
1271 Date-Modified = {2006-02-15 10:31:32 -0500},
1272 Journal = jcp,
1273 Pages = 9164,
1274 Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1275 Volume = 101,
1276 Year = 1994}
1277
1278 @article{Semmler98,
1279 Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1280 Date-Modified = {2006-02-15 10:14:46 -0500},
1281 Journal = {Langmuir},
1282 Pages = {5127-5132},
1283 Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
1284 Volume = 14,
1285 Year = 1998}
1286
1287 @article{Solomon86,
1288 Author = {H. Solomon and H. Weiner},
1289 Date-Modified = {2006-02-15 10:10:38 -0500},
1290 Journal = {Comm. Statistics A},
1291 Pages = {2571-2607},
1292 Title = {A REVIEW OF THE PACKING PROBLEM},
1293 Volume = 15,
1294 Year = 1986}
1295
1296 @article{Bonnier93,
1297 Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
1298 Date-Modified = {2006-02-15 10:08:35 -0500},
1299 Journal = {Physica A},
1300 Pages = {1-10},
1301 Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
1302 Volume = 198,
1303 Year = 1993}
1304
1305 @book{Frenkel96,
1306 Address = {New York},
1307 Author = {D. Frenkel and B. Smit},
1308 Date-Modified = {2006-02-15 10:18:08 -0500},
1309 Publisher = {Academic Press},
1310 Title = {Understanding Molecular Simulation : From Algorithms to Applications},
1311 Year = 1996}
1312
1313 @article{Dullweber1997,
1314 Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
1315 Journal = jcp,
1316 Number = 15,
1317 Pages = {5840-5851},
1318 Title = {Symplectic splitting methods for rigid body molecular dynamics},
1319 Volume = 107,
1320 Year = 1997}
1321
1322 @article{Martin98,
1323 Author = {M. Martin and J.~I. Siepmann},
1324 Date-Modified = {2006-02-15 10:15:05 -0500},
1325 Journal = jpcB,
1326 Pages = {2569-2577},
1327 Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
1328 Volume = 102,
1329 Year = 1998}
1330
1331 @article{Marrink01a,
1332 Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
1333 Date-Modified = {2006-02-15 10:28:09 -0500},
1334 Journal = jacs,
1335 Pages = {8638-8639},
1336 Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
1337 Volume = 123,
1338 Year = 2001}
1339
1340 @article{Liu96b,
1341 Author = {Y. Liu and T. Ichiye},
1342 Date-Modified = {2006-02-15 10:27:07 -0500},
1343 Journal = jpc,
1344 Pages = {2723-2730},
1345 Title = {Soft sticky dipole potential for liquid water: a new model},
1346 Volume = 100,
1347 Year = 1996}
1348
1349 @article{Liu96a,
1350 Author = {Y. Liu and T. Ichiye},
1351 Date-Modified = {2006-02-15 10:27:01 -0500},
1352 Journal = {Chemical Physics Letters},
1353 Pages = {334-340},
1354 Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1355 Volume = 256,
1356 Year = 1996}
1357
1358 @article{Chandra99,
1359 Author = {A. Chandra and T. Ichiye},
1360 Date-Modified = {2006-02-15 10:09:36 -0500},
1361 Journal = {Journal of Chemical Physics},
1362 Number = 6,
1363 Pages = {2701-2709},
1364 Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1365 Volume = 111,
1366 Year = 1999}
1367
1368 @book{Allen87,
1369 Address = {New York},
1370 Author = {M.~P. Allen and D.~J. Tildesley},
1371 Date-Modified = {2006-02-15 10:08:08 -0500},
1372 Publisher = {Oxford University Press},
1373 Title = {Computer Simulations of Liquids},
1374 Year = 1987}
1375
1376 @book{Leach01,
1377 Address = {Harlow, England},
1378 Author = {A.~R. Leach},
1379 Date-Modified = {2006-02-15 10:25:19 -0500},
1380 Edition = {2nd},
1381 Publisher = {Pearson Educated Limited},
1382 Title = {Molecular Modeling: Principles and Applications},
1383 Year = 2001}
1384
1385 @article{Katsaras00,
1386 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},
1387 Date-Modified = {2006-02-15 10:21:52 -0500},
1388 Journal = {Physical Review E},
1389 Number = 5,
1390 Pages = {5668-5677},
1391 Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
1392 Volume = 61,
1393 Year = 2000}
1394
1395 @article{Sengupta00,
1396 Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
1397 Date-Modified = {2006-02-15 10:32:00 -0500},
1398 Journal = {Europhysics Letters},
1399 Number = 6,
1400 Pages = {722-728},
1401 Title = {Novel structural Features of the ripple phase of phospholipids},
1402 Volume = 49,
1403 Year = 2000}
1404
1405 @article{Venable00,
1406 Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1407 Date-Modified = {2006-02-15 10:11:19 -0500},
1408 Journal = jcp,
1409 Number = 10,
1410 Pages = {4822-4832},
1411 Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1412 Volume = 112,
1413 Year = 2000}
1414
1415 @article{Lindahl00,
1416 Author = {E. Lindahl and O. Edholm},
1417 Date-Modified = {2006-02-15 10:26:05 -0500},
1418 Journal = {Biophysical Journal},
1419 Month = {July},
1420 Pages = {426-433},
1421 Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1422 Volume = 79,
1423 Year = 2000}
1424
1425 @article{Saiz02,
1426 Author = {L. Saiz and M. Klein},
1427 Date-Modified = {2006-02-15 10:31:50 -0500},
1428 Journal = jcp,
1429 Number = 7,
1430 Pages = {3052-3057},
1431 Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
1432 Volume = 116,
1433 Year = 2002}
1434
1435 @article{Stevens95,
1436 Author = {M.~J. Stevens and G.~S. Grest},
1437 Date-Modified = {2006-02-15 10:10:47 -0500},
1438 Journal = {Physical Review E},
1439 Number = 6,
1440 Pages = {5976-5983},
1441 Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
1442 Volume = 51,
1443 Year = 1995}
1444
1445 @article{Darden93,
1446 Author = {T. Darden and D. York and L. Pedersen},
1447 Date-Modified = {2006-02-15 10:09:52 -0500},
1448 Journal = {Journal of Chemical Physics},
1449 Number = 12,
1450 Pages = {10089-10092},
1451 Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
1452 Volume = 98,
1453 Year = 1993}
1454
1455 @article{Goetz98,
1456 Author = {R. Goetz and R. Lipowsky},
1457 Date-Modified = {2006-02-15 10:18:26 -0500},
1458 Journal = {Journal of Chemical Physics},
1459 Number = 17,
1460 Pages = 7397,
1461 Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
1462 Volume = 108,
1463 Year = 1998}
1464
1465 @article{Marrink01b,
1466 Author = {S.~J. Marrink and A.~E. Mark},
1467 Date-Modified = {2006-02-15 10:28:01 -0500},
1468 Journal = {Journal of Physical Chemistry B},
1469 Pages = {6122-6127},
1470 Title = {Effect of undulations on surface tension in simulated bilayers},
1471 Volume = 105,
1472 Year = 2001}
1473
1474 @article{Metropolis49,
1475 Author = {N. Metropolis and S. Ulam},
1476 Date-Modified = {2006-02-15 10:29:03 -0500},
1477 Journal = {J. Am. Stat. Ass.},
1478 Pages = {335-341},
1479 Title = {The $\mbox{Monte Carlo}$ Method},
1480 Volume = 44,
1481 Year = 1949}
1482
1483 @article{Metropolis53,
1484 Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1485 Date-Modified = {2006-03-09 10:44:24 -0500},
1486 Journal = {J. Chem. Phys.},
1487 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
1488 Pages = {1087-1092},
1489 Title = {Equation of State Calculations by Fast Computing Machines},
1490 Volume = 21,
1491 Year = 1953}
1492
1493 @article{Born12,
1494 Author = {M. Born and Th. Von~Karman},
1495 Date-Modified = {2006-02-15 10:08:50 -0500},
1496 Journal = {Physik Z.},
1497 Number = {297-309},
1498 Title = {Uber Schwingungen in Raumgittern},
1499 Volume = 13,
1500 Year = 1912}
1501
1502 @book{Chandler87,
1503 Author = {David Chandler},
1504 Date-Modified = {2006-02-15 10:09:20 -0500},
1505 Publisher = {Oxford University Press},
1506 Title = {Introduction to Modern Statistical Mechanics},
1507 Year = 1987}
1508
1509 @article{Pearlman95,
1510 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},
1511 Date-Modified = {2006-02-15 10:30:13 -0500},
1512 Journal = {Computer Physics Communications},
1513 Pages = {1-41},
1514 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},
1515 Volume = 91,
1516 Year = 1995}
1517
1518 @book{Goldstein01,
1519 Address = {San Francisco},
1520 Author = {H. Goldstein and C. Poole and J. Safko},
1521 Edition = {3rd},
1522 Publisher = {Addison Wesley},
1523 Title = {Classical Mechanics},
1524 Year = 2001}
1525
1526 @article{Bratko85,
1527 Author = {D. Bratko and L. Blum and A. Luzar},
1528 Journal = jcp,
1529 Number = 12,
1530 Pages = {6367-6370},
1531 Title = {A simple model for the intermolecular potential of water},
1532 Volume = 83,
1533 Year = 1985}
1534
1535 @article{Bratko95,
1536 Author = {L. Blum and F. Vericat and D. Bratko},
1537 Journal = jcp,
1538 Number = 3,
1539 Pages = {1461-1462},
1540 Title = {Towards an analytical model of water: The octupolar model},
1541 Volume = 102,
1542 Year = 1995}
1543
1544 @article{Tan03,
1545 Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
1546 Journal = cpl,
1547 Pages = {646-652},
1548 Title = {A temperature of maximum density in soft sticky dipole water},
1549 Volume = 376,
1550 Year = 2003}
1551
1552 @article{Soper86,
1553 Author = {A.~K. Soper and M.~G. Phillips},
1554 Journal = cp,
1555 Number = 1,
1556 Pages = {47-60},
1557 Title = {A new determination of the structure of water at 298K},
1558 Volume = 107,
1559 Year = 1986}
1560
1561 @article{Plimpton95,
1562 Author = {S. Plimpton},
1563 Date-Modified = {2006-02-15 10:30:31 -0500},
1564 Journal = {J. Comp. Phys.},
1565 Pages = {1-19},
1566 Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
1567 Volume = 117,
1568 Year = 1995}
1569
1570 @article{Tartaglino02,
1571 Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
1572 Date-Modified = {2006-02-15 10:34:04 -0500},
1573 Journal = prb,
1574 Pages = 241406,
1575 Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
1576 Volume = 65,
1577 Year = 2002}
1578
1579 @article{Ercolessi88,
1580 Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
1581 Journal = {Philosophical Magazine A},
1582 Pages = {213-226},
1583 Title = {Simulation of Gold in the Glue Model.},
1584 Volume = 58,
1585 Year = 1988}
1586
1587 @article{Finnis84,
1588 Author = {M.~W Finnis and J.~E. Sinclair},
1589 Journal = {Phil. Mag. A},
1590 Pages = {45-55},
1591 Title = {A Simple Empirical N-Body Potential for Transition-Metals},
1592 Volume = 50,
1593 Year = 1984}
1594
1595 @article{Foiles86,
1596 Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
1597 Date-Modified = {2006-02-15 10:17:44 -0500},
1598 Journal = prb,
1599 Number = 12,
1600 Pages = 7983,
1601 Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1602 Volume = 33,
1603 Year = 1986}
1604
1605 @article{Daw93,
1606 Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
1607 Date-Modified = {2006-02-15 10:16:13 -0500},
1608 Journal = {Mat. Sci. Rep.},
1609 Pages = {251-310},
1610 Title = {The embededd-atom method},
1611 Volume = 9,
1612 Year = 1993}
1613
1614 @article{Johnson89,
1615 Author = {R.~A. Johnson},
1616 Date-Modified = {2006-02-15 10:21:36 -0500},
1617 Journal = prb,
1618 Number = 17,
1619 Pages = 12554,
1620 Title = {Alloy models with the embedded-atom method},
1621 Volume = 39,
1622 Year = 1989}
1623
1624 @article{Kol97,
1625 Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
1626 Date-Modified = {2006-02-15 10:24:53 -0500},
1627 Journal = jcp,
1628 Number = 7,
1629 Pages = {2580-2588},
1630 Title = {A symplectic method for rigid-body molecular simulation},
1631 Volume = 107,
1632 Year = 1997}
1633
1634 @article{Hoover85,
1635 Author = {W.~G. Hoover},
1636 Date-Modified = {2006-02-15 10:21:18 -0500},
1637 Journal = pra,
1638 Pages = 1695,
1639 Title = {Canonical dynamics: Equilibrium phase-space distributions},
1640 Volume = 31,
1641 Year = 1985}
1642
1643 @article{Roux91,
1644 Author = {B. Roux and M. Karplus},
1645 Journal = jpc,
1646 Number = 15,
1647 Pages = {4856-4868},
1648 Title = {Ion transport in a Gramicidin-like channel: dynamics and mobility},
1649 Volume = 95,
1650 Year = 1991}
1651
1652 @article{Marrink94,
1653 Author = {S.~J Marrink and H.~J.~C. Berendsen},
1654 Journal = jpc,
1655 Number = 15,
1656 Pages = {4155-4168},
1657 Title = {Simulation of water transport through a lipid membrane},
1658 Volume = 98,
1659 Year = 1994}
1660
1661 @article{Daw89,
1662 Author = {Murray~S. Daw},
1663 Journal = {Physical Review B},
1664 Pages = {7441-7452},
1665 Title = {Model of metallic cohesion: The embedded-atom method},
1666 Volume = 39,
1667 Year = 1989}
1668
1669 @inbook{Voter95b,
1670 Author = {A.~F. Voter},
1671 Chapter = 4,
1672 Date-Modified = {2006-02-15 10:35:07 -0500},
1673 Editor = {J.~H. Westbrook and R.~L. Fleischer},
1674 Pages = 77,
1675 Publisher = {John Wiley and Sons Ltd},
1676 Title = {Intermetallic Compounds: Principles and Practice},
1677 Volume = 1,
1678 Year = 1995}
1679
1680 @article{Marrink02,
1681 Author = {S.~J. Marrink and D.~P. Teileman},
1682 Date-Modified = {2006-02-15 10:28:20 -0500},
1683 Journal = {Biophysical Journal},
1684 Pages = {2386-2392},
1685 Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1686 Volume = 83,
1687 Year = 2002}
1688
1689 @article{Sum03,
1690 Author = {A.~K. Sum and J.~J. de~Pablo},
1691 Date-Modified = {2006-02-15 10:11:01 -0500},
1692 Journal = {Biophysical Journal},
1693 Pages = {3636-3645},
1694 Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
1695 Volume = 85,
1696 Year = 2003}
1697
1698 @article{Gomez03,
1699 Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
1700 Date-Modified = {2006-02-15 10:17:14 -0500},
1701 Journal = {Eur. Biophys. J.},
1702 Pages = {217-227},
1703 Title = {Setting up and optimization of membrane protein simulations},
1704 Volume = 31,
1705 Year = 2002}
1706
1707 @article{Smondyrev99,
1708 Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1709 Date-Modified = {2006-02-15 10:10:29 -0500},
1710 Journal = {Biophysical Journal},
1711 Pages = {2472-2478},
1712 Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1713 Volume = 76,
1714 Year = 1999}
1715
1716 @article{Nina02,
1717 Author = {M. Nina and T. Simonson},
1718 Date-Modified = {2006-02-15 10:29:27 -0500},
1719 Journal = {J. Phys. Chem. B},
1720 Pages = {3696-3705},
1721 Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1722 Volume = 106,
1723 Year = 2002}
1724
1725 @article{Norberg00,
1726 Author = {J. Norberg and L. Nilsson},
1727 Date-Modified = {2006-02-15 10:29:36 -0500},
1728 Journal = {Biophysical Journal},
1729 Pages = {1537-1553},
1730 Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1731 Volume = 79,
1732 Year = 2000}
1733
1734 @article{Patra03,
1735 Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1736 Date-Modified = {2006-02-15 10:29:58 -0500},
1737 Journal = {Biophysical Journal},
1738 Pages = {3636-3645},
1739 Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1740 Volume = 84,
1741 Year = 2003}
1742
1743 @article{Marrink04,
1744 Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
1745 Date-Modified = {2006-02-15 10:28:28 -0500},
1746 Journal = {J. Phys. Chem. B},
1747 Pages = {750-760},
1748 Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
1749 Volume = 108,
1750 Year = 2004}
1751
1752 @article{Andersen83,
1753 Author = {H.~C. Andersen},
1754 Date-Modified = {2006-02-15 10:08:20 -0500},
1755 Journal = {Journal of Computational Physics},
1756 Pages = {24-34},
1757 Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1758 Volume = 52,
1759 Year = 1983}
1760
1761 @article{Hura00,
1762 Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1763 Date-Modified = {2006-02-15 10:21:28 -0500},
1764 Journal = {J. Chem. Phys.},
1765 Pages = {9140-9148},
1766 Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1767 Volume = 113,
1768 Year = 2000}
1769
1770 @article{Ryckaert77,
1771 Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1772 Date-Modified = {2006-02-15 10:31:44 -0500},
1773 Journal = {Journal of Computational Physics},
1774 Pages = {327-341},
1775 Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1776 Volume = 23,
1777 Year = 1977}
1778
1779 @inbook{Fowles99,
1780 Author = {G.~R. Fowles and G.~L. Cassiday},
1781 Chapter = 10,
1782 Date-Modified = {2006-02-15 10:18:00 -0500},
1783 Edition = {6th},
1784 Publisher = {Saunders College Publishing},
1785 Title = {Analytical Mechanics},
1786 Year = 1999}
1787
1788 @article{Petrache00,
1789 Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
1790 Date-Modified = {2006-02-15 10:30:24 -0500},
1791 Journal = {Biophysical Journal},
1792 Pages = {3172-3192},
1793 Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1794 Volume = 79,
1795 Year = 2000}
1796
1797 @article{Egberts88,
1798 Author = {E. Egberts and H.~J.~C. Berendsen},
1799 Date-Modified = {2006-02-15 10:16:43 -0500},
1800 Journal = {J. Chem. Phys.},
1801 Pages = {3718-3732},
1802 Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
1803 Volume = 89,
1804 Year = 1988}
1805
1806 @article{Holz00,
1807 Author = {M. Holz and S.~R. Heil and A. Sacco},
1808 Journal = {Phys. Chem. Chem. Phys.},
1809 Pages = {4740-4742},
1810 Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1811 Volume = 2,
1812 Year = 2000}
1813
1814 @incollection{Zannoni94,
1815 Author = {C. Zannoni},
1816 Booktitle = {The Molecular Dynamics of Liquid Crstals},
1817 Chapter = 6,
1818 Date-Modified = {2006-02-15 10:12:36 -0500},
1819 Editor = {G.~R. Luckhurst and C.~A. Veracini},
1820 Pages = {139-169},
1821 Publisher = {Kluwer Academic Publishers},
1822 Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1823 Year = 1994}
1824
1825 @article{Melchionna93,
1826 Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
1827 Date-Modified = {2006-02-15 10:28:54 -0500},
1828 Journal = {Molecular Physics},
1829 Pages = {533-544},
1830 Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
1831 Volume = 78,
1832 Year = 1993}
1833
1834 @article{Fennell04,
1835 Author = {C.~J. Fennell and J.~D. Gezelter},
1836 Date-Modified = {2006-02-15 09:08:04 -0500},
1837 Journal = jcp,
1838 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
1839 Number = 19,
1840 Pages = {9175-9184},
1841 Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1842 Volume = 120,
1843 Year = 2004}
1844
1845 @article{Klein01,
1846 Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
1847 Date-Modified = {2006-02-15 10:27:22 -0500},
1848 Journal = {J. Phys. Chem. B},
1849 Pages = {4464-4470},
1850 Title = {A Coarse Grain Model for Phospholipid Simulations},
1851 Volume = 105,
1852 Year = 2001}
1853
1854 @article{Marrink03,
1855 Author = {S.~J. Marrink and A.~E. Mark},
1856 Date-Modified = {2006-02-15 10:28:41 -0500},
1857 Journal = {J. Am. Chem. Soc.},
1858 Pages = {15233-15242},
1859 Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1860 Volume = 125,
1861 Year = 2003}
1862
1863 @article{Fletcher64,
1864 Author = {R. Fletcher and C.~M. Reeves},
1865 Date-Modified = {2006-02-15 10:17:34 -0500},
1866 Journal = {Comput. J.},
1867 Number = 2,
1868 Pages = {149-154},
1869 Title = {Function minimization by conjugate gradients},
1870 Volume = 7,
1871 Year = 1964}
1872
1873 @article{Polak69,
1874 Author = {E. Polak and G. Ribiere},
1875 Date-Modified = {2006-02-15 10:14:00 -0500},
1876 Journal = {Rev. Fr. Inform. Rech. Oper.},
1877 Pages = {35-43},
1878 Title = {Note sur la convergence de methodes de directions conjugees},
1879 Volume = {16-R1},
1880 Year = 1969}
1881
1882 @article{Voter87,
1883 Author = {A.~F. Voter and S.~P. Chen},
1884 Date-Modified = {2006-02-15 10:35:19 -0500},
1885 Journal = {Mat. Res. Soc. Symp. Proc.},
1886 Pages = {175},
1887 Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
1888 Volume = {82},
1889 Year = {1987}}
1890
1891 @article{Hendrickson95,
1892 Author = {Bruce Hendrickson and Steve Plimpton},
1893 Date-Modified = {2006-02-15 10:19:11 -0500},
1894 Journal = {Journal of Parallel and Distributed Computing},
1895 Pages = {15-25},
1896 Title = {Parallel Many-body Simulations without All-to-All Communication},
1897 Volume = {27},
1898 Year = {1995}}
1899
1900 @inproceedings{Paradyn93,
1901 Address = {Pittsburgh, PA},
1902 Author = {S.~J. Plimpton and B.~A. Hendrickson},
1903 Booktitle = {Materials Theory and Modelling},
1904 Date-Modified = {2006-02-15 10:30:42 -0500},
1905 Editor = {J. Broughton and P. Bristowe and J. Newsam},
1906 Pages = 37,
1907 Publisher = {Materials Research Society},
1908 Series = {MRS Proceedings},
1909 Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
1910 Volume = 291,
1911 Year = 1993}
1912
1913 @article{Voter95a,
1914 Author = {A.~F. Voter},
1915 Date-Modified = {2006-02-15 10:35:27 -0500},
1916 Journal = {Intermetallic Compounds: Principles and Practice},
1917 Pages = {77},
1918 Title = {The Embedded-Atom Method},
1919 Volume = {1},
1920 Year = {1995}}
1921
1922 @article{Heller90,
1923 Author = {H. Heller and H. Grubmuller and K. Schulten},
1924 Date-Modified = {2006-02-15 10:19:02 -0500},
1925 Journal = {Molecular Simulation},
1926 Pages = {133},
1927 Title = {Molecular dynamics simulation on a parallel computer},
1928 Volume = {5},
1929 Year = {1990}}
1930
1931 @book{Fox88,
1932 Address = {Englewood Cliffs, NJ},
1933 Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
1934 Publisher = {Prentice-Hall},
1935 Title = {Solving Promblems on Concurrent Processors},
1936 Volume = {I},
1937 Year = 1988}
1938
1939 @article{Berendsen95,
1940 Author = {H.~J.~C. Berendsen and D. van~der~Spoel and R. van~Drunen},
1941 Date-Modified = {2006-02-15 10:20:47 -0500},
1942 Journal = {Comp. Phys. Comm.},
1943 Pages = {43-56},
1944 Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
1945 Volume = 91,
1946 Year = 1995}
1947
1948 @article{Lindahl01,
1949 Author = {E. Lindahl and B. Hess and D. van~der~Spoel},
1950 Date-Modified = {2006-02-15 10:25:51 -0500},
1951 Journal = {J. Mol. Mod.},
1952 Pages = {306-317},
1953 Title = {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
1954 Volume = 7,
1955 Year = 2001}
1956
1957 @article{Smith96,
1958 Author = {W. Smith and T. Forester},
1959 Date-Modified = {2006-02-15 10:10:14 -0500},
1960 Journal = {J. Molec. Graphics.},
1961 Number = 3,
1962 Pages = {136-141},
1963 Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package},
1964 Volume = 14,
1965 Year = 1996}
1966
1967 @article{Ponder87,
1968 Author = {J.~W. Ponder and F.~M. Richards},
1969 Date-Modified = {2006-02-15 10:13:45 -0500},
1970 Journal = {J. Comp. Chem.},
1971 Number = 7,
1972 Pages = {1016-1024},
1973 Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
1974 Volume = 8,
1975 Year = 1987}
1976
1977 @article{Berendsen87,
1978 Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
1979 Journal = jpc,
1980 Pages = {6269-6271},
1981 Title = {The Missing Term in Effective Pair Potentials},
1982 Volume = 91,
1983 Year = 1987}
1984
1985 @incollection{Berendsen81,
1986 Address = {Dordrecht},
1987 Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
1988 Booktitle = {Intermolecular Forces},
1989 Editor = {B. Pullman},
1990 Pages = 331,
1991 Publisher = {Reidel},
1992 Title = {Simple Point Charge Water},
1993 Year = 1981}
1994
1995 @article{Mahoney00,
1996 Author = {M.~W. Mahoney and W.~L. Jorgensen},
1997 Journal = jcp,
1998 Number = 20,
1999 Pages = {8910-8922},
2000 Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
2001 Volume = 112,
2002 Year = 2000}
2003
2004 @article{Meineke05,
2005 Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2006 Date-Modified = {2006-03-05 12:37:31 -0500},
2007 Journal = {J. Comp. Chem.},
2008 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
2009 Pages = {252-271},
2010 Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2011 Volume = 26,
2012 Year = 2005}
2013
2014 @article{Baez95a,
2015 Author = {L.~A. B\`{a}ez and P. Clancy},
2016 Journal = mp,
2017 Number = 3,
2018 Pages = {385-396},
2019 Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
2020 Volume = 86,
2021 Year = 1995}
2022
2023 @article{Baez95b,
2024 Author = {L.~A. B\`{a}ez and P. Clancy},
2025 Journal = jcp,
2026 Number = 22,
2027 Pages = {9744-9755},
2028 Title = {Phase equilibria in extended simple point charge ice-water systems},
2029 Volume = 103,
2030 Year = 1995}
2031
2032 @article{Davidson84,
2033 Author = {E.~R. Davidson and K. Morokuma},
2034 Journal = jcp,
2035 Number = 8,
2036 Pages = {3741-3742},
2037 Title = {A proposed antiferroelectric structure for proton ordered ice Ih},
2038 Volume = 81,
2039 Year = 1984}
2040
2041 @article{Sanz04,
2042 Author = {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
2043 Journal = prl,
2044 Number = 25,
2045 Pages = 255701,
2046 Title = {Phase Diagram of Water from Computer Simulation},
2047 Volume = 92,
2048 Year = 2004}
2049
2050 @article{Onsager36,
2051 Author = {L. Onsager},
2052 Journal = jacs,
2053 Pages = {1486-1493},
2054 Title = {Electric Moments of Molecules in Liquids},
2055 Volume = 58,
2056 Year = 1936}
2057
2058 @article{Matsumoto02,
2059 Author = {M. Matsumoto and S. Saito and I. Ohimine},
2060 Journal = {Nature (London)},
2061 Pages = {409-413},
2062 Title = {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
2063 Volume = 416,
2064 Year = 2002}
2065
2066 @article{Yamada02,
2067 Author = {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
2068 Journal = prl,
2069 Number = 19,
2070 Pages = 195701,
2071 Title = {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
2072 Volume = 88,
2073 Year = 2002}
2074
2075 @article{Wallqvist95,
2076 Author = {A. Wallqvist and B.~J. Berne},
2077 Journal = jpc,
2078 Pages = {2885-2892},
2079 Title = {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
2080 Volume = 99,
2081 Year = 1995}
2082
2083 @article{Vlot99,
2084 Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
2085 Journal = jcp,
2086 Number = 1,
2087 Pages = {55-61},
2088 Title = {Free energy calculations on systems of rigid molecules: An application to the TIP4P model of H$_2$O},
2089 Volume = 110,
2090 Year = 1999}
2091
2092 @article{Gao00,
2093 Author = {G.~T. Gao and X.~C. Zeng and H. Tanaka},
2094 Journal = jcp,
2095 Number = 19,
2096 Pages = {8534-8538},
2097 Title = {The melting temperature of proton-disordered hexagonal ice: A computer simulation of 4-site transferable intermolecular potential model of water},
2098 Volume = 112,
2099 Year = 2000}
2100
2101 @article{Bizid87,
2102 Author = {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
2103 Journal = jcp,
2104 Number = 4,
2105 Pages = {2225-2230},
2106 Title = {Structure of high-density amorphous water. I. X-ray diffraction study},
2107 Volume = 87,
2108 Year = 1987}
2109
2110 @article{Quintana92,
2111 Author = {J. Quintana and A.~D.~J. Haymet},
2112 Journal = cpl,
2113 Number = 3,
2114 Pages = {273-277},
2115 Title = {The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models},
2116 Volume = 189,
2117 Year = 1992}
2118
2119 @article{Mezei92,
2120 Author = {M. Mezei},
2121 Journal = {J. Comput. Chem.},
2122 Pages = 651,
2123 Title = {Don't Remember},
2124 Volume = 13,
2125 Year = 1992}
2126
2127 @article{Widom63,
2128 Author = {B. Widom},
2129 Journal = jcp,
2130 Pages = 2808,
2131 Title = {Particle insertion},
2132 Volume = 39,
2133 Year = 1963}
2134
2135 @article{Clancy94,
2136 Author = {L.~A. B\'{a}ez and P. Clancy},
2137 Journal = jcp,
2138 Number = 11,
2139 Pages = {9837-9840},
2140 Title = {Existence of a density maximum in extended simple point charge water},
2141 Volume = 101,
2142 Year = 1994}
2143
2144 @article{Jorgensen98b,
2145 Author = {W.~L. Jorgensen and C. Jenson},
2146 Journal = jcc,
2147 Number = 10,
2148 Pages = {1179-1186},
2149 Title = {Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density},
2150 Volume = 19,
2151 Year = 1998}
2152
2153 @article{Mahoney01,
2154 Author = {M.~W. Mahoney and W.~L. Jorgensen},
2155 Journal = jcp,
2156 Number = 1,
2157 Pages = {363-366},
2158 Title = {Diffusion constant of the TIP5P model of liquid water},
2159 Volume = 114,
2160 Year = 2001}
2161
2162 @article{Rahman75,
2163 Author = {A. Rahman and F.~H. Stillinger and H.~L. Lemberg},
2164 Journal = jcp,
2165 Number = 12,
2166 Pages = {5223-5230},
2167 Title = {Study of a central force model for liquid water by molecular dynamics},
2168 Volume = 63,
2169 Year = 1975}
2170
2171 @article{Spoel98,
2172 Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
2173 Date-Modified = {2006-03-05 12:38:54 -0500},
2174 Journal = jcp,
2175 Number = 24,
2176 Pages = {10220-10230},
2177 Title = {A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field},
2178 Volume = 108,
2179 Year = 1998}
2180
2181 @article{Gallagher03,
2182 Author = {K.~R. Gallagher and K.~A. Sharp},
2183 Journal = jacs,
2184 Pages = 9853,
2185 Title = {A New Angle on Heat Capacity Changes in Hydrophobic Solvation},
2186 Volume = 125,
2187 Year = 2003}
2188
2189 @article{Frenkel84,
2190 Author = {D. Frenkel and A.~J.~C. Ladd},
2191 Journal = jcp,
2192 Number = 7,
2193 Pages = {3188-3193},
2194 Title = {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
2195 Volume = 81,
2196 Year = 1984}
2197
2198 @article{Hermens88,
2199 Author = {J. Hermans and A. Pathiaseril and A. Anderson},
2200 Journal = jacs,
2201 Pages = {5982-5986},
2202 Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
2203 Volume = 110,
2204 Year = 1988}
2205
2206 @article{Meijer90,
2207 Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2208 Journal = jcp,
2209 Number = 12,
2210 Pages = {7570-7575},
2211 Title = {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
2212 Volume = 92,
2213 Year = 1990}
2214
2215 @article{Li96,
2216 Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
2217 Journal = {Science},
2218 Pages = {666-669},
2219 Title = {Emergence of Preferred Structures in a Simple Model of Protein Folding},
2220 Volume = 273,
2221 Year = 1996}
2222
2223 @article{Stillinger74,
2224 Author = {F.~H. Stillinger and A. Rahman},
2225 Journal = jcp,
2226 Number = 4,
2227 Pages = {1545-1557},
2228 Title = {Improved simulation of liquid water by molecular dynamics},
2229 Volume = 60,
2230 Year = 1974}
2231
2232 @article{Caldwell95,
2233 Author = {J.~W. Caldwell and P.~A. Kollman},
2234 Journal = jpc,
2235 Number = 16,
2236 Pages = {6208-6219},
2237 Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2238 Volume = 99,
2239 Year = 1995}
2240
2241 @article{Urbic00,
2242 Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2243 Date-Modified = {2006-02-15 10:34:30 -0500},
2244 Journal = jcp,
2245 Number = 6,
2246 Pages = {2843-2848},
2247 Title = {A two-dimensional model of water: Therory and computer simulations},
2248 Volume = 112,
2249 Year = 2000}
2250
2251 @article{Yang04,
2252 Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2253 Journal = prl,
2254 Number = 14,
2255 Pages = 146102,
2256 Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2257 Volume = 92,
2258 Year = 2004}