ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/multipoleSFPaper/multipoleSFPaper.bib
Revision: 3064
Committed: Tue Oct 24 06:07:45 2006 UTC (18 years, 10 months ago) by chrisfen
File size: 107057 byte(s)
Log Message:
Imported sources

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 2006-10-23 23:35:54 -0400
6
7
8 %% Saved with string encoding Western (ASCII)
9
10
11 @string{acp = {Adv. Chem. Phys.}}
12
13 @string{ccp5 = {CCP5 Information Quarterly}}
14
15 @string{cp = {Chem. Phys.}}
16
17 @string{cpl = {Chem. Phys. Lett.}}
18
19 @string{jacs = {J. Am. Chem. Soc.}}
20
21 @string{jcc = {J. Comp. Chem.}}
22
23 @string{jcop = {J. Comp. Phys.}}
24
25 @string{jcp = {J. Chem. Phys.}}
26
27 @string{jml = {J. Mol. Liq.}}
28
29 @string{jpc = {J. Phys. Chem.}}
30
31 @string{jpca = {J. Phys. Chem. A}}
32
33 @string{jpcb = {J. Phys. Chem. B}}
34
35 @string{mp = {Mol. Phys.}}
36
37 @string{pams = {Proc. Am. Math Soc.}}
38
39 @string{pccp = {Phys. Chem. Chem. Phys.}}
40
41 @string{pnas = {Proc. Natl. Acad. Sci. USA}}
42
43 @string{pr = {Phys. Rev.}}
44
45 @string{pra = {Phys. Rev. A}}
46
47 @string{prb = {Phys. Rev. B}}
48
49 @string{pre = {Phys. Rev. E}}
50
51 @string{prl = {Phys. Rev. Lett.}}
52
53 @string{rmp = {Rev. Mod. Phys.}}
54
55
56 @book{Tolman38,
57 Address = {New York},
58 Author = {R.~C. Tolman},
59 Date-Added = {2006-09-21 15:37:16 -0400},
60 Date-Modified = {2006-09-21 15:41:28 -0400},
61 Publisher = {Oxford University Press, Inc.},
62 Title = {The Principles of Statistical Mechanics},
63 Year = {1938}}
64
65 @article{Beeman76,
66 Author = {D. Beeman},
67 Date-Added = {2006-09-20 14:44:19 -0400},
68 Date-Modified = {2006-09-20 14:45:33 -0400},
69 Journal = jcop,
70 Pages = {130-139},
71 Title = {Some Multistep Methods for Use in Molecular Dynamics Calculations},
72 Volume = {20},
73 Year = {1976}}
74
75 @inproceedings{Berendsen86,
76 Address = {North Holland, Amsterdam},
77 Author = {H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
78 Booktitle = {Molecular Dynamics Simulations of Statistical Mechanics Systems},
79 Date-Added = {2006-09-20 14:11:30 -0400},
80 Date-Modified = {2006-09-20 14:19:19 -0400},
81 Editor = {G. Ciccotti and W.~G. Hoover},
82 Pages = {43-65},
83 Series = {Proceedings of the 97th Int. ``Enrico Fermi" School of Physics},
84 Title = {Practical algorithms for dynamics simulations},
85 Year = {1986}}
86
87 @techreport{Gear66,
88 Address = {Argonne, IL},
89 Author = {C.~W. Gear},
90 Date-Added = {2006-09-20 14:00:35 -0400},
91 Date-Modified = {2006-09-20 14:05:03 -0400},
92 Institution = {Argonne National Laboratory},
93 Number = {ANL-7126},
94 Title = {The Numerical Integration of Ordinary Differential Equations of Various Orders},
95 Year = {1966}}
96
97 @article{Abascal05,
98 Author = {J.~L.~F. Abascal and E. Sanz and R. {Garc\'{i}a Fern\'{a}ndez} and C. Vega},
99 Date-Added = {2006-09-18 14:20:06 -0400},
100 Date-Modified = {2006-09-18 14:27:13 -0400},
101 Doi = {10.1063/1.1931662},
102 Journal = jcp,
103 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Abascal_Tip4p-Ice_05.pdf},
104 Number = {23},
105 Pages = {234511},
106 Title = {A potential model for the study of ices and amorphous water: \uppercase{TIP4P/I}ce},
107 Volume = {122},
108 Year = {2005}}
109
110 @article{Vega05,
111 Author = {C. Vega and E. Sanz and J.~L.~F. Abascal},
112 Date-Added = {2006-09-18 09:40:15 -0400},
113 Date-Modified = {2006-09-18 09:41:55 -0400},
114 Doi = {10.1063/1.1862245},
115 Journal = jcp,
116 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Vega_MeltTempModels_05.pdf},
117 Number = {11},
118 Pages = {114507},
119 Title = {The melting temperature of the most common models of water},
120 Volume = {122},
121 Year = {2005}}
122
123 @article{Harvey98,
124 Author = {S.~C. Harvey and R.~K.-Z. Tan and T.~E. {Cheatham III}},
125 Date-Added = {2006-09-07 00:53:34 -0400},
126 Date-Modified = {2006-09-07 00:55:37 -0400},
127 Journal = jcc,
128 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Harvey_FlyingIceCube_98.pdf},
129 Number = {7},
130 Pages = {726-740},
131 Title = {The Flying Ice Cube: \uppercase{V}elocity Rescaling in Molecular Dynamics Leads to Violation of Energy Equipartition},
132 Volume = {19},
133 Year = {1998}}
134
135 @article{Verlet68,
136 Author = {L. Verlet},
137 Date-Added = {2006-09-06 12:19:09 -0400},
138 Date-Modified = {2006-09-20 14:22:53 -0400},
139 Journal = pr,
140 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_EqCorrFunc_67.pdf},
141 Number = {1},
142 Pages = {201-214},
143 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{II. E}quilibrium Correlation Functions},
144 Volume = {165},
145 Year = {1968}}
146
147 @article{Verlet67,
148 Author = {L. Verlet},
149 Date-Added = {2006-09-06 12:16:19 -0400},
150 Date-Modified = {2006-09-20 14:22:43 -0400},
151 Journal = pr,
152 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_ClassicalFluids_67.pdf},
153 Number = {1},
154 Pages = {98-103},
155 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{I. T}hermodynamic Properties of \uppercase{L}ennard-\uppercase{J}ones Molecules},
156 Volume = {159},
157 Year = {1967}}
158
159 @article{Thompson83,
160 Author = {C.~J. Thompson},
161 Date-Added = {2006-09-06 11:59:49 -0400},
162 Date-Modified = {2006-09-06 12:02:07 -0400},
163 Journal = ccp5,
164 Pages = {20-28},
165 Title = {Use of neighbor lists in molecular dynamics},
166 Volume = {8},
167 Year = {1983}}
168
169 @article{Krautler01,
170 Author = {V. Kr\"{a}utler and W.~F. {van Gunsteren} and P.~H. H\"{u}nenberger},
171 Date-Added = {2006-09-04 00:17:15 -0400},
172 Date-Modified = {2006-09-04 00:29:36 -0400},
173 Journal = jcc,
174 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Krautler_FastSHAKE_01.pdf},
175 Number = {5},
176 Pages = {501-508},
177 Title = {A Fast \uppercase{SHAKE} Algorithm to Solve Distance Constraint Equations for Small Molecules in Molecular Dynamics Simulations},
178 Volume = {22},
179 Year = {2001}}
180
181 @article{Swope82,
182 Author = {W.~C. Swope and H.~C. Andersen and P.~H. Berens and K.~R. Wilson},
183 Date-Added = {2006-09-03 21:47:42 -0400},
184 Date-Modified = {2006-09-03 21:50:26 -0400},
185 Journal = jcp,
186 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Swope_VelocityVerlet_82.pdf},
187 Number = {1},
188 Pages = {637-649},
189 Title = {A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: \uppercase{A}pplication to small water clusters},
190 Volume = {76},
191 Year = {1982}}
192
193 @article{Trotter59,
194 Author = {H.~F. Trotter},
195 Date-Added = {2006-09-03 18:05:35 -0400},
196 Date-Modified = {2006-09-03 18:07:32 -0400},
197 Journal = pams,
198 Pages = {545-551},
199 Title = {On the product of Semi-Groups of Operators},
200 Volume = {10},
201 Year = {1959}}
202
203 @article{Barojas73,
204 Author = {J. Barojas and D. Levesque and B. Quentrec},
205 Date-Added = {2006-09-03 14:32:02 -0400},
206 Date-Modified = {2006-09-03 14:34:00 -0400},
207 Journal = pra,
208 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Barojas_EulerSwitch_73.pdf},
209 Number = {3},
210 Pages = {1092-1105},
211 Title = {Simulation of Diatomic Homonuclear Liquids},
212 Volume = {7},
213 Year = {1973}}
214
215 @article{Mezei92,
216 Author = {M. Mezei},
217 Date-Added = {2006-08-28 07:48:49 -0400},
218 Date-Modified = {2006-08-28 07:50:59 -0400},
219 Doi = {10.1002/jcc.540130515},
220 Journal = jcc,
221 Number = {5},
222 Pages = {651-656},
223 Title = {Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water},
224 Volume = {13},
225 Year = {1992}}
226
227 @article{Pauling35,
228 Author = {L. Pauling},
229 Date-Added = {2006-08-27 22:01:49 -0400},
230 Date-Modified = {2006-08-27 22:03:59 -0400},
231 Journal = jacs,
232 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ResidualEntropy/Pauling_ResidEntropy_33.pdf},
233 Pages = {2680-2684},
234 Title = {The Structure and Entropy of Ice and of Other Crystals with Some Randomness of Atomic Arrangement},
235 Volume = {57},
236 Year = {1935}}
237
238 @article{Nada03,
239 Author = {H. Nada and J.~P.~J.~M. {van der Eerden}},
240 Date-Added = {2006-08-27 21:44:08 -0400},
241 Date-Modified = {2006-08-27 21:47:37 -0400},
242 Doi = {10.1063/1.1562610},
243 Journal = jcp,
244 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Nada_6siteH2O_03.pdf},
245 Number = {16},
246 Pages = {7401-7413},
247 Title = {An intermolecular potential model for the simulation of ice and water near the melting point: \uppercase{A} six-site model of \uppercase{H}$_2$\uppercase{O}},
248 Volume = {118},
249 Year = {2003}}
250
251 @article{Kindt96,
252 Author = {J.~T. Kindt and C.~A. Schmuttenmaer},
253 Date-Added = {2006-08-27 13:55:26 -0400},
254 Date-Modified = {2006-08-27 13:56:35 -0400},
255 Journal = jpc,
256 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kindt_FarIRDielectricOfPolarLiquids_96.pdf},
257 Number = {24},
258 Pages = {10373-10379},
259 Title = {Far-Infrared Dielectric Properties of Polar Liquids Probed by Femtosecond Terahertz Pulse Spectroscopy},
260 Volume = {100},
261 Year = {1996}}
262
263 @article{Freddolino06,
264 Author = {P.~L. Freddolino and A.~S. Arkhipov and S.~B. Larson and A. McPherson and K. Schulten},
265 Date-Added = {2006-08-24 16:11:43 -0400},
266 Date-Modified = {2006-08-24 16:14:03 -0400},
267 Doi = {10.1016/j.str.2005.11.014},
268 Journal = {Structure},
269 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Freddolino_VirusSimulation_06.pdf},
270 Pages = {437-449},
271 Title = {Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus},
272 Volume = {14},
273 Year = {2006}}
274
275 @article{Gillen72,
276 Author = {K.~T. Gillen and D.~C. Douglas and M.~J.~R. Hoch},
277 Date-Added = {2006-08-24 10:40:48 -0400},
278 Date-Modified = {2006-08-24 10:41:10 -0400},
279 Journal = jcp,
280 Pages = {5117-5119},
281 Title = {Self-Diffusion in Liquid Water to $-31^\circ$~\uppercase{C}},
282 Volume = 57,
283 Year = 1972}
284
285 @book{Rothschild84,
286 Address = {New York},
287 Author = {W.~G. Rothschild},
288 Date-Added = {2006-08-24 10:35:25 -0400},
289 Date-Modified = {2006-08-24 10:35:25 -0400},
290 Publisher = {John Wiley \& Sons, Inc.},
291 Title = {Dynamics of Molecular Liquids},
292 Year = 1984}
293
294 @article{Krynicki66,
295 Author = {K. Krynicki},
296 Date-Added = {2006-08-24 10:34:29 -0400},
297 Date-Modified = {2006-08-24 10:35:05 -0400},
298 Journal = {Physica},
299 Pages = {167-178},
300 Title = {PROTON SPIN-LATTICE RELAXATION IN PURE WATER BETWEEN 0$^\circ$\uppercase{C} AND 100$^\circ$\uppercase{C}},
301 Volume = 32,
302 Year = 1966}
303
304 @book{Eisenberg69,
305 Address = {Oxford},
306 Author = {D. Eisenberg and W. Kauzmann},
307 Date-Added = {2006-08-24 10:33:59 -0400},
308 Date-Modified = {2006-08-24 10:33:59 -0400},
309 Publisher = {Oxford University Press},
310 Title = {The Structure and Properties of Water},
311 Year = 1969}
312
313 @article{Mills73,
314 Author = {R. Mills},
315 Date-Added = {2006-08-24 10:24:33 -0400},
316 Date-Modified = {2006-08-24 10:25:04 -0400},
317 Journal = jpc,
318 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Mills_Diffuse_73.pdf},
319 Number = 5,
320 Pages = {685-688},
321 Title = {Self-Diffusion in Normal and Heavy Water in the Range 1-45$^\circ$},
322 Volume = 77,
323 Year = 1973}
324
325 @article{Barriol64,
326 Author = {J. Barriol and A. Weisbecker},
327 Date-Added = {2006-08-24 10:23:25 -0400},
328 Date-Modified = {2006-08-24 10:23:39 -0400},
329 Journal = {Compt. Rend. Acad. Sc. Paris},
330 Pages = {4643-4645},
331 Title = {Contribution \`{a} l'\'{e}tude di\'{e}lectrique des liquides associ\'{e}s par liaisons hydrog\'{e}ne},
332 Volume = 259,
333 Year = 1964}
334
335 @article{Badyal00,
336 Author = {Y.~S. Badyal and M.~-L. Saboungi and D.~L. Price and S.~D. Shastri and D.~R. Haeffner and A.~K. Soper},
337 Date-Added = {2006-08-24 10:21:10 -0400},
338 Date-Modified = {2006-08-24 10:22:49 -0400},
339 Journal = jcp,
340 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Badyal_ElectronDistributionInH2O_00.pdf},
341 Number = 21,
342 Pages = {9206-9208},
343 Title = {Electron distribution in water},
344 Volume = 112,
345 Year = 2000}
346
347 @article{Gubskaya02,
348 Author = {A.~V. Gubskaya and P.~G. Kusalik},
349 Date-Added = {2006-08-24 10:17:41 -0400},
350 Date-Modified = {2006-08-24 10:18:37 -0400},
351 Journal = jcp,
352 Number = 11,
353 Pages = {5290-5302},
354 Title = {The total molecular dipole moment for liquid water},
355 Volume = 117,
356 Year = 2002}
357
358 @article{Sprik91,
359 Author = {M. Sprik},
360 Date-Added = {2006-08-24 10:10:41 -0400},
361 Date-Modified = {2006-08-24 10:17:06 -0400},
362 Journal = jcp,
363 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Sprik_HBondingAndStaticDielectricInH2O_91.pdf},
364 Number = 9,
365 Pages = {6762-6769},
366 Title = {Hydrogen bonding and the static dielectric constant in liquid water},
367 Volume = 95,
368 Year = 1991}
369
370 @article{Nezbeda02,
371 Author = {M. Lisal and J. Kolafa and I. Nezbeda},
372 Date-Added = {2006-08-24 10:08:19 -0400},
373 Date-Modified = {2006-08-24 10:08:37 -0400},
374 Journal = jcp,
375 Number = 19,
376 Pages = {8892-8897},
377 Title = {An examination of the five-site potential (\uppercase{TIP5P}) for water},
378 Volume = 117,
379 Year = 2002}
380
381 @article{Rahman72,
382 Author = {A. Rahman and F.~H. Stillinger},
383 Date-Added = {2006-08-24 10:03:48 -0400},
384 Date-Modified = {2006-08-24 10:09:05 -0400},
385 Journal = jcp,
386 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Ice_Simulations/Rahman_ProtonDistributionInIce_72.pdf},
387 Number = 9,
388 Pages = {4009-4017},
389 Title = {Proton Distribution in Ice and the \uppercase{K}irkwood Correlation Factor},
390 Volume = 57,
391 Year = 1972}
392
393 @article{Bernal33,
394 Author = {J.~D. Bernal and R.~H. Fowler},
395 Date-Added = {2006-08-24 09:58:00 -0400},
396 Date-Modified = {2006-08-24 09:59:43 -0400},
397 Journal = jcp,
398 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Bernal_TheoryOfWater_33.pdf},
399 Number = {8},
400 Pages = {515-548},
401 Title = {A Theory of Water and Ionic Solution with Particular Reference to Hydrogen and Hydroxyl Ions},
402 Volume = {1},
403 Year = {1933}}
404
405 @article{Hoover86,
406 Author = {W.~G. Hoover},
407 Date-Added = {2006-08-24 09:53:21 -0400},
408 Date-Modified = {2006-08-24 09:53:21 -0400},
409 Journal = pra,
410 Number = 3,
411 Pages = {2499-2500},
412 Title = {Constant-pressure equations of motion},
413 Volume = 34,
414 Year = 1986}
415
416 @article{Fennell06,
417 Author = {C.~J. Fennell and J.~D. Gezelter},
418 Date-Added = {2006-08-24 09:49:57 -0400},
419 Date-Modified = {2006-08-24 09:49:57 -0400},
420 Doi = {10.1063/1.2206581},
421 Journal = jcp,
422 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_PairwiseSummationMethods_06.pdf},
423 Number = {23},
424 Pages = {234104(12)},
425 Rating = {5},
426 Read = {Yes},
427 Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
428 Volume = {124},
429 Year = {2006}}
430
431 @article{Evans77b,
432 Author = {D.~J. Evans and S. Murad},
433 Date-Added = {2006-08-22 14:23:16 -0400},
434 Date-Modified = {2006-08-22 14:23:16 -0400},
435 Journal = mp,
436 Pages = {327-331},
437 Title = {Singularity-free algorithm for molecular dynamics simulation of rigid polyatomics},
438 Volume = 34,
439 Year = 1977}
440
441 @article{Aguado03,
442 Author = {A. Aguado and P.~A. Madden},
443 Date-Added = {2006-08-16 10:42:15 -0400},
444 Date-Modified = {2006-08-16 10:43:56 -0400},
445 Doi = {10.1063/1.1605941},
446 Journal = jcp,
447 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Aguado_MultipoleEwald_03.pdf},
448 Number = {14},
449 Pages = {7471-7483},
450 Title = {Ewald summation of electrostatic multipole interactions up to the quadrupolar level},
451 Volume = {119},
452 Year = {2003}}
453
454 @article{Smith98,
455 Author = {W. Smith},
456 Date-Added = {2006-08-16 10:02:44 -0400},
457 Date-Modified = {2006-10-23 23:29:30 -0400},
458 Journal = {CCP5 Information Quarterly},
459 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Smith_PointMultipoleEwald_98.pdf},
460 Pages = {18-30},
461 Title = {Point multipoles in the \uppercase{E}wald summation (Revisited)},
462 Volume = {46},
463 Year = {1998}}
464
465 @book{Stone02,
466 Address = {Oxford},
467 Author = {A.~J. Stone},
468 Date-Added = {2006-08-14 18:14:32 -0400},
469 Date-Modified = {2006-10-23 13:56:08 -0400},
470 Publisher = {Oxford University Press, Inc.},
471 Title = {The Theory of Intermolecular Forces},
472 Year = {2002}}
473
474 @book{Hirschfelder67,
475 Address = {New York},
476 Author = {J.~O. Hirschfelder and C.~F. Curtiss and R.~B. Bird},
477 Date-Added = {2006-08-14 10:15:21 -0400},
478 Date-Modified = {2006-10-23 13:55:15 -0400},
479 Publisher = {John Wiley \& Sons, Inc.},
480 Title = {Molecular Theory of Gases and Liquids},
481 Year = {1967}}
482
483 @article{Ryckaert77,
484 Author = {J.-P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
485 Date-Added = {2006-08-06 17:05:44 -0400},
486 Date-Modified = {2006-09-27 10:08:56 -0400},
487 Doi = {10.1016/0021-9991(77)90098-5},
488 Journal = jcop,
489 Month = {March},
490 Number = {3},
491 Pages = {327-341},
492 Title = {Numerical integration of the cartesian equations of motion of a system with constraints: \uppercase{m}olecular dynamics of {\it n}-alkanes},
493 Volume = {23},
494 Year = {1977}}
495
496 @article{Impey82,
497 Author = {R.~W. Impey and P.~A. Madden and I.~R. McDonald},
498 Date-Added = {2006-08-03 08:42:21 -0400},
499 Date-Modified = {2006-08-03 08:44:06 -0400},
500 Journal = mp,
501 Number = {3},
502 Pages = {513-539},
503 Title = {Spectroscopic and transport properties of water: \uppercase{M}odel calculations and the interpretation of experimental results},
504 Volume = {46},
505 Year = {1982}}
506
507 @article{Laasonen93,
508 Author = {K. Laasonen and M. Sprik and M. Parrinello and R. Car},
509 Date-Added = {2006-08-02 08:23:46 -0400},
510 Date-Modified = {2006-08-02 13:09:18 -0400},
511 Journal = jcp,
512 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Laasonen_AbInitioLiquidWater_93.pdf},
513 Number = {11},
514 Pages = {9080-9089},
515 Title = {``{\it \uppercase{A}b initio}" liquid water},
516 Volume = {99},
517 Year = {1993}}
518
519 @article{Donchev06,
520 Author = {A.~G. Donchev and N.~G. Galkin and A.~A. Illarionov and O.~V. Khoruzhii and M.~A. Olevanov and M.~V. Subbotin and V.~I. Tarasov},
521 Date-Added = {2006-08-02 08:15:11 -0400},
522 Date-Modified = {2006-08-02 08:16:16 -0400},
523 Doi = {www.pnas.org/cgi/doi/10.1073/pnas.0602982103},
524 Journal = pnas,
525 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Donchev_QuantumWater_06.pdf},
526 Number = {23},
527 Pages = {8613-8617},
528 Title = {Water properties from first principles: \uppercase{S}imulations by a general-purpose quantum mechanical polarizable force field},
529 Volume = {103},
530 Year = {2006}}
531
532 @article{Malmberg56,
533 Author = {G.~G. Malmberg and A.~A. Maryott},
534 Date-Added = {2006-08-01 17:19:00 -0400},
535 Date-Modified = {2006-08-02 13:16:04 -0400},
536 Journal = {J. Res. Natl. Bur. Stand.},
537 Number = {1},
538 Pages = {1-8},
539 Title = {Dielectric constant of Water from 0$^\circ$ to 100$^\circ$\uppercase{C}},
540 Volume = {56},
541 Year = {1956}}
542
543 @article{Neumann80,
544 Author = {M. Neumann and O. Steinhauser},
545 Date-Added = {2006-08-01 17:17:52 -0400},
546 Date-Modified = {2006-08-01 17:18:51 -0400},
547 Journal = mp,
548 Number = {2},
549 Pages = {437-454},
550 Title = {The influence of boundary conditions used in machine simulations on the structure of polar systems},
551 Volume = {39},
552 Year = {1980}}
553
554 @article{Neumann83,
555 Author = {M. Neumann},
556 Date-Added = {2006-08-01 17:16:51 -0400},
557 Date-Modified = {2006-08-01 17:17:45 -0400},
558 Journal = mp,
559 Number = {4},
560 Pages = {841-858},
561 Title = {Dipole moment fluctuation formulas in computer simulations of polar systems},
562 Volume = {50},
563 Year = {1983}}
564
565 @article{Kell75,
566 Author = {G.~S. Kell},
567 Date-Added = {2006-08-01 16:05:09 -0400},
568 Date-Modified = {2006-08-02 13:17:29 -0400},
569 Journal = {J. Chem. Eng. Data},
570 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kell_CompressibilityAndExpansivityOfH2O_75.pdf},
571 Number = {1},
572 Pages = {91-105},
573 Title = {Density, Thermal Expansivity, and Compressibility of Liquid Water from 0$^\circ$ to 150$^\circ$\uppercase{C}: \uppercase{C}orrelations and Tables for Atmospheric Pressure and Saturation Reviewed and Expressed on 1968 Temperature Scale},
574 Volume = {20},
575 Year = {1975}}
576
577 @article{Wagner02,
578 Author = {W. Wagner and A. Pru{\ss}},
579 Date-Added = {2006-08-01 16:02:31 -0400},
580 Date-Modified = {2006-08-02 13:16:50 -0400},
581 Journal = {J. Phys. Chem. Ref. Data},
582 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Wagner_ThermodynamicPropertiesOfH2O_03.pdf},
583 Number = {2},
584 Pages = {387-535},
585 Title = {The \uppercase{IAPWS} Formulation 1995 for the Thermodynamic Properties of Ordinary Water Substance for General and Scientific Use},
586 Volume = {31},
587 Year = {2002}}
588
589 @article{Neumann84,
590 Author = {M. Neumann and O. Steinhauser and G.~S. Pawley},
591 Date-Added = {2006-07-31 10:22:39 -0400},
592 Date-Modified = {2006-07-31 10:24:17 -0400},
593 Journal = mp,
594 Number = {1},
595 Pages = {97-113},
596 Title = {Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations},
597 Volume = {52},
598 Year = {1984}}
599
600 @article{Neumann85,
601 Author = {M. Neumann},
602 Date-Added = {2006-07-31 10:19:17 -0400},
603 Date-Modified = {2006-08-02 13:17:58 -0400},
604 Journal = jcp,
605 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/DielectricConst./Neumann_H2ODielConst_85.pdf},
606 Number = {12},
607 Pages = {5663-5672},
608 Title = {The dielectric constant of water. \uppercase{C}omputer simulations with the \uppercase{MCY} potential},
609 Volume = {82},
610 Year = {1985}}
611
612 @book{Berry00,
613 Address = {New York},
614 Author = {R. Stephen Berry and Stuart A. Rice and John Ross},
615 Date-Added = {2006-07-30 14:49:40 -0400},
616 Date-Modified = {2006-07-30 14:53:08 -0400},
617 Edition = {Second},
618 Editor = {Donald G. Truhlar},
619 Publisher = {Oxford University Press, Inc.},
620 Series = {Topics in Physical Chemistry},
621 Title = {Physical Chemistry},
622 Year = {2000}}
623
624 @article{Sorenson00,
625 Author = {J.~M. Sorenson and G. Hura and R.~M. Glaeser and T. Head-Gordon},
626 Date-Added = {2006-07-21 11:41:31 -0400},
627 Date-Modified = {2006-07-21 11:44:44 -0400},
628 Journal = jcp,
629 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayRadial_2000.pdf},
630 Number = {20},
631 Pages = {9149-9161},
632 Title = {What can x-ray scattering tell us about the radial distribution functions of water?},
633 Volume = {113},
634 Year = {2000}}
635
636 @book{CRC80,
637 Address = {Boca Raton, FL},
638 Date-Added = {2006-07-21 09:20:17 -0400},
639 Date-Modified = {2006-07-21 09:20:17 -0400},
640 Edition = 60,
641 Editor = {R.~C. Weast},
642 Publisher = {CRC Press, Inc.},
643 Title = {CRC Handbook of Chemistry and Physics},
644 Year = 1980}
645
646 @article{Shi06,
647 Author = {Q. Shi and S. Izvekov and G.~A. Voth},
648 Date-Added = {2006-07-20 15:28:29 -0400},
649 Date-Modified = {2006-07-20 15:29:45 -0400},
650 Doi = {10.1021/jp062700h},
651 Journal = jpcb,
652 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Shi_MixedAtomisticCGIonChannel_06.pdf},
653 Title = {Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel},
654 Year = {2006}}
655
656 @article{Weis06,
657 Author = {J.-J. Weis and D. Levesque},
658 Date-Added = {2006-07-20 15:22:45 -0400},
659 Date-Modified = {2006-07-20 15:24:22 -0400},
660 Doi = {10.1063/1.2215614},
661 Journal = jcp,
662 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Weis_OrientationalOrderHardSphereDipole_06.pdf},
663 Number = {3},
664 Pages = {034504},
665 Title = {Orientational order in high density dipolar hard sphere fluids},
666 Volume = {125},
667 Year = {2006}}
668
669 @article{Rick04,
670 Author = {S.~W. Rick},
671 Date-Added = {2006-07-18 10:49:48 -0400},
672 Date-Modified = {2006-08-19 19:34:36 -0400},
673 Doi = {10.1063/1.1652434},
674 Journal = jcp,
675 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Rick_TIP5P-E_04.pdf},
676 Number = {13},
677 Pages = {6085-6093},
678 Title = {A reoptimization of the five-site water potential (\uppercase{TIP5P}) for use with \uppercase{E}wald sums},
679 Volume = {120},
680 Year = {2004}}
681
682 @article{Horn04,
683 Author = {H.~W. Horn and W.~C. Swope and J.~W. Pitera and J.~D. Madura and T.~J. Dick and G.~L. Hura and T. Head-Gordon},
684 Date-Added = {2006-07-18 10:18:42 -0400},
685 Date-Modified = {2006-07-18 14:21:48 -0400},
686 Doi = {10.1063/1.1683075},
687 Journal = jcp,
688 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Horn_TIP4P-Ew_04.pdf},
689 Number = {20},
690 Pages = {9665-9678},
691 Title = {Development of an improved four-site water model for biomolecular simulations: \uppercase{TIP4P-E}w},
692 Volume = {120},
693 Year = {2004}}
694
695 @article{Brodka04,
696 Author = {A. Br\'{o}dka},
697 Date-Added = {2006-04-26 09:41:52 -0400},
698 Date-Modified = {2006-07-18 14:29:43 -0400},
699 Doi = {10.1016/j.cplett.2004.10.086},
700 Journal = cpl,
701 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
702 Pages = {62-67},
703 Title = {\uppercase{E}wald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
704 Volume = {400},
705 Year = {2004}}
706
707 @article{deJoannis02,
708 Author = {J. {de Joannis} and A. Arnold and C. Holm},
709 Date-Added = {2006-04-26 09:40:15 -0400},
710 Date-Modified = {2006-07-18 14:35:47 -0400},
711 Doi = {10.1063/1.149195},
712 Journal = jcp,
713 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
714 Number = {6},
715 Pages = {2503-2512},
716 Title = {Electrostatics in periodic slab geometries. \uppercase{II}},
717 Volume = {117},
718 Year = {2002}}
719
720 @article{Kawata01,
721 Author = {M. Kawata and M. Mikami},
722 Date-Added = {2006-04-26 09:38:01 -0400},
723 Date-Modified = {2006-07-18 14:31:24 -0400},
724 Journal = cpl,
725 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
726 Pages = {157-164},
727 Title = {Rapid calculation of two-dimensional \uppercase{E}wald summation},
728 Volume = {340},
729 Year = {2001}}
730
731 @article{Arnold02,
732 Author = {A. Arnold and J. {de Joannis} and C. Holm},
733 Date-Added = {2006-04-26 09:36:09 -0400},
734 Date-Modified = {2006-07-18 14:29:18 -0400},
735 Doi = {10.1063/1.149195},
736 Journal = jcp,
737 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
738 Number = {6},
739 Pages = {2496-2502},
740 Title = {Electrostatics in periodic slab geometries. \uppercase{I}},
741 Volume = {117},
742 Year = {2002}}
743
744 @article{Kolafa92,
745 Author = {J. Kolafa and J.~W. Perram},
746 Date-Added = {2006-03-21 09:41:58 -0500},
747 Date-Modified = {2006-07-18 14:41:10 -0400},
748 Journal = {Mol. Simul.},
749 Pages = {351-368},
750 Title = {Cutoff Errors in the \uppercase{E}wald Summation Formulae for Point Charge Systems},
751 Volume = {9},
752 Year = {1992}}
753
754 @article{Karasawa89,
755 Author = {N. Karasawa and W.~A. {Goddard III}},
756 Date-Added = {2006-03-21 09:11:44 -0500},
757 Date-Modified = {2006-03-21 09:13:00 -0500},
758 Journal = jpc,
759 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
760 Pages = {7320-7327},
761 Title = {Acceleration of Convergence for Lattice Sums},
762 Volume = {93},
763 Year = {1989}}
764
765 @article{Roux99,
766 Author = {B. Roux and T. Simonson},
767 Date-Added = {2006-03-19 20:10:18 -0500},
768 Date-Modified = {2006-03-19 20:12:10 -0500},
769 Journal = {Biophys. Chem.},
770 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
771 Pages = {1-20},
772 Title = {Implicit solvent models},
773 Volume = {78},
774 Year = {1999}}
775
776 @article{Rokhlin85,
777 Author = {V. Rokhlin},
778 Date-Added = {2006-03-19 20:02:25 -0500},
779 Date-Modified = {2006-09-05 22:30:02 -0400},
780 Doi = {10.1016/0021-9991(85)90002-6},
781 Journal = jcop,
782 Month = {September},
783 Number = {2},
784 Pages = {187-207},
785 Title = {Rapid solution of integral equations of classical potential theory},
786 Volume = {60},
787 Year = {1985}}
788
789 @article{Grossfield00,
790 Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
791 Date-Added = {2006-03-19 19:52:19 -0500},
792 Date-Modified = {2006-03-19 19:54:14 -0500},
793 Journal = {Proteins},
794 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
795 Pages = {211-223},
796 Title = {Dipole Lattice Membrane Model for Protein Calculations},
797 Volume = {41},
798 Year = {2000}}
799
800 @article{Born20,
801 Author = {M. Born},
802 Date-Added = {2006-03-19 18:05:01 -0500},
803 Date-Modified = {2006-03-19 18:07:42 -0500},
804 Journal = {Z. Physik},
805 Pages = {45-48},
806 Title = {Volumen und hydratationswame der ionen},
807 Volume = {1},
808 Year = {1920}}
809
810 @article{Luty96,
811 Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
812 Date-Added = {2006-03-18 20:59:19 -0500},
813 Date-Modified = {2006-03-18 21:00:33 -0500},
814 Journal = jpc,
815 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
816 Number = {7},
817 Pages = {2581-2587},
818 Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
819 Volume = {100},
820 Year = {1996}}
821
822 @article{Rhee89,
823 Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
824 Date-Added = {2006-03-18 20:48:07 -0500},
825 Date-Modified = {2006-07-18 14:33:26 -0400},
826 Journal = {Phys. Rev. B},
827 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
828 Number = {1},
829 Pages = {36-42},
830 Title = {\uppercase{E}wald methods in molecular dynamics for systems of finite extent in one of three dimensions},
831 Volume = {40},
832 Year = {1989}}
833
834 @article{Hunenberger99a,
835 Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
836 Date-Added = {2006-03-18 20:14:24 -0500},
837 Date-Modified = {2006-07-18 15:03:36 -0400},
838 Journal = jcp,
839 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
840 Number = {4},
841 Pages = {1856-1872},
842 Title = {\uppercase{E}wald artifacts in computer simulations of ionic solvation and ion -- ion interaction: \uppercase{A} continuum electrostatics study},
843 Volume = {110},
844 Year = {1999}}
845
846 @article{Roberts95,
847 Author = {J.~E. Roberts and J. Schnitker},
848 Date-Added = {2006-03-18 20:12:23 -0500},
849 Date-Modified = {2006-07-18 15:11:50 -0400},
850 Journal = jpc,
851 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
852 Pages = {1322-1331},
853 Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: $\mbox{A}$ Systematic Study},
854 Volume = {99},
855 Year = {1995}}
856
857 @article{Roberts94,
858 Author = {J.~E. Roberts and J. Schnitker},
859 Date-Added = {2006-03-18 20:10:37 -0500},
860 Date-Modified = {2006-03-18 20:12:19 -0500},
861 Journal = jcp,
862 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
863 Number = {6},
864 Pages = {5024-5031},
865 Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
866 Volume = {101},
867 Year = {1994}}
868
869 @article{Yeh99,
870 Author = {I.-C. Yeh and M.~L. Berkowitz},
871 Date-Added = {2006-03-18 19:24:27 -0500},
872 Date-Modified = {2006-07-18 14:34:09 -0400},
873 Journal = jcp,
874 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
875 Number = {7},
876 Pages = {3155-3162},
877 Title = {\uppercase{E}wald summation for systems with slab geometry},
878 Volume = {111},
879 Year = {1999}}
880
881 @article{Parry76,
882 Author = {D.~E. Parry},
883 Date-Added = {2006-03-18 19:11:01 -0500},
884 Date-Modified = {2006-07-18 15:09:52 -0400},
885 Journal = {Surf. Sci.},
886 Pages = {195},
887 Title = {Errata: $\mbox{T}$he electrostatic potential in the surface region of an ionic crystal},
888 Volume = {54},
889 Year = {1976}}
890
891 @article{Parry75,
892 Author = {D.~E. Parry},
893 Date-Added = {2006-03-18 19:08:40 -0500},
894 Date-Modified = {2006-03-18 19:16:14 -0500},
895 Journal = {Surf. Sci.},
896 Pages = {433-440},
897 Title = {The electrostatic potential in the surface region of an ionic crystal},
898 Volume = {49},
899 Year = {1975}}
900
901 @article{deLeeuw79,
902 Author = {S.~W. {de Leeuw} and J.~W. Perram},
903 Date-Added = {2006-03-18 19:05:18 -0500},
904 Date-Modified = {2006-03-18 19:07:48 -0500},
905 Journal = mp,
906 Pages = {1313-1327},
907 Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
908 Volume = {37},
909 Year = {1979}}
910
911 @article{Heyes77,
912 Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
913 Date-Added = {2006-03-18 19:02:16 -0500},
914 Date-Modified = {2006-03-18 19:04:48 -0500},
915 Journal = {J. Chem. Soc., Faraday Trans. II},
916 Number = {7},
917 Pages = {1485-1496},
918 Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
919 Volume = {73},
920 Year = {1977}}
921
922 @article{Spohr97,
923 Author = {E. Spohr},
924 Date-Added = {2006-03-18 18:51:02 -0500},
925 Date-Modified = {2006-03-18 18:52:21 -0500},
926 Journal = jcp,
927 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
928 Number = {16},
929 Pages = {6342-6348},
930 Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
931 Volume = {107},
932 Year = {1997}}
933
934 @article{York94,
935 Author = {D. York and W. Yang},
936 Date-Added = {2006-03-18 11:52:58 -0500},
937 Date-Modified = {2006-07-18 14:34:21 -0400},
938 Journal = jcp,
939 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
940 Number = {4},
941 Pages = {3298-3300},
942 Title = {The fast Fourier Poisson method for calculating \uppercase{E}wald sums},
943 Volume = {101},
944 Year = {1994}}
945
946 @article{Shimada93,
947 Author = {J. Shimada and H. Kaneko and T. Takada},
948 Date-Added = {2006-03-18 11:10:38 -0500},
949 Date-Modified = {2006-03-18 11:12:10 -0500},
950 Journal = jcc,
951 Pages = {867-78},
952 Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
953 Volume = {14},
954 Year = {1993}}
955
956 @article{Luty94,
957 Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
958 Date-Added = {2006-03-18 10:37:17 -0500},
959 Date-Modified = {2006-07-18 14:31:50 -0400},
960 Journal = {Mol. Simul.},
961 Pages = {11-20},
962 Title = {A comparison of particle-particle particle-mesh and \uppercase{E}wald methods for calculating electrostatic interactions in periodic systems},
963 Volume = {14},
964 Year = {1994}}
965
966 @book{Hockney81,
967 Address = {New York},
968 Author = {R.~W. Hockney and J.~W. Eastwood},
969 Date-Added = {2006-03-18 10:33:19 -0500},
970 Date-Modified = {2006-03-18 10:35:04 -0500},
971 Publisher = {McGraw-Hill},
972 Title = {Computer Simulation Using Particles},
973 Year = {1981}}
974
975 @article{Sagui99,
976 Author = {C. Sagui and T.~A. Darden},
977 Date-Added = {2006-03-17 18:27:01 -0500},
978 Date-Modified = {2006-07-18 15:12:58 -0400},
979 Journal = {Annu. Rev. Biophys. Biomol. Struct.},
980 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_electrostaticInBiomolecules_99.pdf},
981 Pages = {155-179},
982 Title = {Molecular Dynamics Simulations of Biomolecules: $\mbox{L}$ong-Range Electrostatic Effects},
983 Volume = {28},
984 Year = {1999}}
985
986 @article{Perram88,
987 Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
988 Date-Added = {2006-03-17 13:42:04 -0500},
989 Date-Modified = {2006-03-17 13:59:01 -0500},
990 Journal = mp,
991 Pages = {875-893},
992 Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
993 Volume = {65},
994 Year = {1988}}
995
996 @article{Woodcock71,
997 Author = {L.~V. Woodcock and K. Singer},
998 Date-Added = {2006-03-17 11:14:17 -0500},
999 Date-Modified = {2006-07-18 14:46:33 -0400},
1000 Journal = {Trans. Faraday Soc.},
1001 Pages = {12-30},
1002 Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by $\mbox{Monte Carlo}$ Computation},
1003 Volume = {67},
1004 Year = {1971}}
1005
1006 @article{Smith81,
1007 Author = {E.~R. Smith},
1008 Date-Added = {2006-03-16 13:47:17 -0500},
1009 Date-Modified = {2006-03-16 13:48:34 -0500},
1010 Journal = {Proc. R. Soc. London Ser. A},
1011 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
1012 Pages = {475-505},
1013 Title = {Electrostatic Energy in Ionic Crystals},
1014 Volume = {375},
1015 Year = {1981}}
1016
1017 @article{Weber00,
1018 Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
1019 Date-Added = {2006-03-16 09:49:22 -0500},
1020 Date-Modified = {2006-07-18 15:18:48 -0400},
1021 Doi = {10.1021/jp9937757},
1022 Journal = jpcb,
1023 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
1024 Number = {15},
1025 Pages = {3668-3675},
1026 Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under \uppercase{E}wald Boundary Conditions: $\mbox{I}$nfluence of Artificial Periodicity on Peptide Conformation},
1027 Volume = {104},
1028 Year = {2000}}
1029
1030 @article{Hunenberger99b,
1031 Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
1032 Date-Added = {2006-03-16 09:45:10 -0500},
1033 Date-Modified = {2006-07-18 15:03:59 -0400},
1034 Journal = {Biophys. Chem.},
1035 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
1036 Pages = {69-88},
1037 Title = {Effect of artificial periodicity in simulations of biomolecules under \uppercase{E}wald boundary conditions: \uppercase{A} continuum electrostatics study},
1038 Volume = {78},
1039 Year = {1999}}
1040
1041 @article{Petersen95,
1042 Author = {H.~G. Petersen},
1043 Date-Added = {2006-03-16 08:43:02 -0500},
1044 Date-Modified = {2006-07-18 14:33:13 -0400},
1045 Journal = jcp,
1046 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
1047 Month = {September},
1048 Number = {9},
1049 Pages = {3668-3679},
1050 Title = {Accuracy and efficiency of the particle mesh \uppercase{E}wald method},
1051 Volume = {103},
1052 Year = {1995}}
1053
1054 @article{Luty95,
1055 Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
1056 Date-Added = {2006-03-16 08:39:13 -0500},
1057 Date-Modified = {2006-03-16 08:41:15 -0500},
1058 Journal = jcp,
1059 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
1060 Number = {8},
1061 Pages = {3014-3021},
1062 Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
1063 Volume = {103},
1064 Year = {1995}}
1065
1066 @article{Barker73,
1067 Author = {J.~A. Barker and R.~O. Watts},
1068 Date-Added = {2006-03-15 18:58:17 -0500},
1069 Date-Modified = {2006-07-18 14:44:12 -0400},
1070 Journal = mp,
1071 Pages = {789-792},
1072 Title = {$\mbox{Monte Carlo}$ studies of the dielectric properties of water-like models},
1073 Volume = {26},
1074 Year = {1973}}
1075
1076 @article{Adams79,
1077 Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
1078 Date-Added = {2006-03-15 17:46:36 -0500},
1079 Date-Modified = {2006-03-15 17:48:04 -0500},
1080 Journal = mp,
1081 Number = {2},
1082 Pages = {387-400},
1083 Title = {The computer simulation of polar liquids},
1084 Volume = {38},
1085 Year = {1979}}
1086
1087 @article{Rahman71,
1088 Author = {A. Rahman and F.~H. Stillinger},
1089 Date-Added = {2006-03-15 17:04:53 -0500},
1090 Date-Modified = {2006-03-15 17:07:29 -0500},
1091 Journal = jcp,
1092 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
1093 Month = {October},
1094 Number = {7},
1095 Pages = {3336-3359},
1096 Title = {Molecular Dynamics Study of Liquid Water},
1097 Volume = {55},
1098 Year = {1971}}
1099
1100 @article{Andrea83,
1101 Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
1102 Date-Added = {2006-03-15 15:16:12 -0500},
1103 Date-Modified = {2006-03-15 15:18:10 -0500},
1104 Journal = jcp,
1105 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
1106 Number = {9},
1107 Pages = {4576-4584},
1108 Title = {The role of long ranged forces in determining the structure and properties of liquid water},
1109 Volume = {79},
1110 Year = {1983}}
1111
1112 @article{Brush66,
1113 Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
1114 Date-Added = {2006-03-13 16:55:39 -0500},
1115 Date-Modified = {2006-07-18 14:48:59 -0400},
1116 Journal = jcp,
1117 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
1118 Month = {September},
1119 Number = {6},
1120 Pages = {2102-2118},
1121 Title = {$\mbox{Monte Carlo}$ Study of a One-Component Plasma. \uppercase{I}},
1122 Volume = {45},
1123 Year = {1966}}
1124
1125 @article{Ewald21,
1126 Author = {P.~P. Ewald},
1127 Date-Added = {2006-03-13 13:32:04 -0500},
1128 Date-Modified = {2006-03-16 22:39:27 -0500},
1129 Journal = {Ann. Physik},
1130 Pages = {253-287},
1131 Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
1132 Volume = {64},
1133 Year = {1921}}
1134
1135 @article{Jones56,
1136 Author = {R.~E. Jones and D.~H. Templeton},
1137 Date-Added = {2006-03-13 13:25:58 -0500},
1138 Date-Modified = {2006-07-18 14:24:50 -0400},
1139 Journal = jcp,
1140 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
1141 Number = {5},
1142 Pages = {1062-1063},
1143 Title = {Optimum Atomic Shape for \uppercase{B}ertaut Series},
1144 Volume = {25},
1145 Year = {1956}}
1146
1147 @article{Heyes81,
1148 Author = {D.~M. Heyes},
1149 Date-Added = {2006-03-13 13:12:45 -0500},
1150 Date-Modified = {2006-03-13 13:14:27 -0500},
1151 Journal = jcp,
1152 Keywords = {Empty Keywords},
1153 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
1154 Number = {3},
1155 Pages = {1924-1929},
1156 Title = {Electrostatic potentials and fields in infinite point charge lattices},
1157 Volume = {74},
1158 Year = {1981}}
1159
1160 @article{Steinbach94,
1161 Author = {P.~J. Steinbach and B.~R. Brooks},
1162 Date-Added = {2006-03-12 19:26:45 -0500},
1163 Date-Modified = {2006-09-05 22:30:22 -0400},
1164 Doi = {10.1002/jcc.540150702},
1165 Journal = jcc,
1166 Number = {7},
1167 Pages = {667-683},
1168 Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
1169 Volume = {15},
1170 Year = {1994}}
1171
1172 @article{deLeeuw80,
1173 Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
1174 Date-Added = {2006-03-07 10:26:31 -0500},
1175 Date-Modified = {2006-07-18 14:52:02 -0400},
1176 Journal = {Proc. R. Soc. London Ser. A},
1177 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
1178 Number = {1752},
1179 Pages = {27-56},
1180 Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. \uppercase{I. L}attice Sums and Dielectric Constants},
1181 Volume = {373},
1182 Year = {1980}}
1183
1184 @article{Essmann95,
1185 Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
1186 Date-Added = {2006-03-05 12:25:25 -0500},
1187 Date-Modified = {2006-07-18 14:30:21 -0400},
1188 Journal = jcp,
1189 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
1190 Number = {19},
1191 Pages = {8577-8593},
1192 Title = {A smooth particle mesh \uppercase{E}wald method},
1193 Volume = {103},
1194 Year = {1995}}
1195
1196 @article{Kast03,
1197 Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
1198 Date-Added = {2006-02-18 16:47:26 -0500},
1199 Date-Modified = {2006-02-18 16:51:25 -0500},
1200 Journal = cpl,
1201 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
1202 Pages = {398-404},
1203 Title = {Integral equation theory for correcting truncation errors in molecular simulations},
1204 Volume = {367},
1205 Year = {2003}}
1206
1207 @article{Tobias01,
1208 Author = {D.~J. Tobias},
1209 Date-Added = {2006-02-15 11:28:58 -0500},
1210 Date-Modified = {2006-07-18 15:21:08 -0400},
1211 Journal = {Curr. Opin. Struct. Biol.},
1212 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
1213 Pages = {253-261},
1214 Title = {Electrostatics calculations: $\mbox{R}$ecent methodological advances and applications to membranes},
1215 Volume = {11},
1216 Year = {2001}}
1217
1218 @article{Zahn02,
1219 Author = {D. Zahn and B. Schilling and S.~M. Kast},
1220 Date-Added = {2006-02-15 09:21:27 -0500},
1221 Date-Modified = {2006-07-18 15:19:05 -0400},
1222 Journal = jpcb,
1223 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
1224 Number = {41},
1225 Pages = {10725-10732},
1226 Title = {Enhancement of the \uppercase{W}olf Damped Coulomb Potential: $\mbox{S}$tatic, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
1227 Volume = {106},
1228 Year = {2002}}
1229
1230 @article{Wolf99,
1231 Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
1232 Date-Added = {2006-02-15 09:09:39 -0500},
1233 Date-Modified = {2006-07-17 12:28:56 -0400},
1234 Journal = jcp,
1235 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
1236 Number = {17},
1237 Pages = {8255-8282},
1238 Rating = {0},
1239 Read = {No},
1240 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
1241 Volume = {110},
1242 Year = {1999}}
1243
1244 @book{Berne90,
1245 Address = {Malabar, Florida},
1246 Author = {B.~J. Berne and R. Pecora},
1247 Publisher = {Robert E. Krieger Publishing Company, Inc.},
1248 Title = {Dynamic Light Scattering},
1249 Year = 1990}
1250
1251 @article{Evans77,
1252 Author = {D.~J. Evans},
1253 Journal = mp,
1254 Pages = {317-325},
1255 Title = {On the representation of orientation space},
1256 Volume = 34,
1257 Year = 1977}
1258
1259 @article{Tuckerman92,
1260 Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
1261 Journal = jcp,
1262 Pages = {1990-2001},
1263 Title = {Reversible multiple time scale molecular dynamics},
1264 Volume = 97,
1265 Year = 1992}
1266
1267 @book{Hansen86,
1268 Address = {London},
1269 Author = {J.~P. Hansen and I.~R. McDonald},
1270 Chapter = 7,
1271 Pages = {199-206},
1272 Publisher = {Academic Press},
1273 Title = {Theory of Simple Liquids},
1274 Year = 1986}
1275
1276 @article{Angelani98,
1277 Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
1278 Date-Modified = {2006-07-18 14:59:40 -0400},
1279 Journal = prl,
1280 Number = 21,
1281 Pages = {4648-4651},
1282 Title = {Connected Network of Minima as a Model Glass: \uppercase{L}ong Time Dynamics},
1283 Volume = 81,
1284 Year = 1998}
1285
1286 @article{Stillinger82,
1287 Author = {F.~H. Stillinger and T.~A. Weber},
1288 Journal = pra,
1289 Number = 2,
1290 Pages = {978-989},
1291 Title = {Hidden structure in liquids},
1292 Volume = 25,
1293 Year = 1982}
1294
1295 @article{Stillinger83,
1296 Author = {F.~H. Stillinger and T.~A. Weber},
1297 Journal = pra,
1298 Number = 4,
1299 Pages = {2408-2416},
1300 Title = {Dynamics of structural transitions in liquids},
1301 Volume = 28,
1302 Year = 1983}
1303
1304 @article{Weber84,
1305 Author = {T.~A. Weber and F.~H. Stillinger},
1306 Journal = jcp,
1307 Number = 6,
1308 Pages = {2742-2746},
1309 Title = {The effect of density on the inherent structure in liquids},
1310 Volume = 80,
1311 Year = 1984}
1312
1313 @article{Stillinger85,
1314 Author = {F.~H. Stillinger and T.~A. Weber},
1315 Journal = jcp,
1316 Number = 9,
1317 Pages = {4767-4775},
1318 Title = {Inherent structure theory of liquids in the hard-sphere limit},
1319 Volume = 83,
1320 Year = 1985}
1321
1322 @article{Stillinger98,
1323 Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
1324 Journal = {Nature},
1325 Pages = {554-557},
1326 Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
1327 Volume = 393,
1328 Year = 1998}
1329
1330 @article{Parkhurst75a,
1331 Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
1332 Date-Modified = {2006-07-18 14:50:48 -0400},
1333 Journal = jcp,
1334 Number = 6,
1335 Pages = {2698-2704},
1336 Title = {Dense liquids. \uppercase{I. T}he effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
1337 Volume = 63,
1338 Year = 1975}
1339
1340 @article{Parkhurst75b,
1341 Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
1342 Date-Modified = {2006-07-18 14:51:04 -0400},
1343 Journal = jcp,
1344 Number = 6,
1345 Pages = {2705-2709},
1346 Title = {Dense liquids. \uppercase{II. T}he effect of density and temperature on viscosity of tetramethylsilane and benzene},
1347 Volume = 63,
1348 Year = 1975}
1349
1350 @article{Forester97,
1351 Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
1352 Journal = {J. Chem. Soc. - Faraday Transactions},
1353 Pages = {613-619},
1354 Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
1355 Volume = 93,
1356 Year = 1997}
1357
1358 @article{Tieleman98,
1359 Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
1360 Journal = {Biophys. J.},
1361 Pages = {2786-2801},
1362 Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
1363 Volume = 74,
1364 Year = 1998}
1365
1366 @article{Cascales98,
1367 Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
1368 Date-Modified = {2006-07-18 15:01:21 -0400},
1369 Journal = jpcb,
1370 Pages = {625-631},
1371 Title = {Anaesthetic mechanism on a model biological membrane: \uppercase{A} molecular dynamics simulation study},
1372 Volume = 102,
1373 Year = 1998}
1374
1375 @article{Bassolino95,
1376 Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
1377 Journal = jacs,
1378 Pages = {4118-4129},
1379 Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
1380 Volume = 117,
1381 Year = 1995}
1382
1383 @article{Alper95,
1384 Author = {H.~E. Alper and T.~R. Stouch},
1385 Journal = jpc,
1386 Pages = {5724-5731},
1387 Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
1388 Volume = 99,
1389 Year = 1995}
1390
1391 @article{Sok92,
1392 Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
1393 Journal = jcp,
1394 Pages = {4699-4704},
1395 Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
1396 Volume = 96,
1397 Year = 1992}
1398
1399 @article{Rabani99,
1400 Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1401 Journal = prl,
1402 Pages = {3649},
1403 Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
1404 Volume = 82,
1405 Year = {1999}}
1406
1407 @article{Rabani97,
1408 Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1409 Date-Modified = {2006-07-18 15:11:37 -0400},
1410 Journal = jcp,
1411 Pages = {6867-6876},
1412 Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: $\mbox{C}$age correlations},
1413 Volume = 107,
1414 Year = 1997}
1415
1416 @article{Gezelter99,
1417 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1418 Journal = jcp,
1419 Pages = 3444,
1420 Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
1421 Volume = 110,
1422 Year = 1999}
1423
1424 @article{Gezelter98,
1425 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1426 Date-Modified = {2006-02-15 10:18:42 -0500},
1427 Journal = jcp,
1428 Pages = 4695,
1429 Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
1430 Volume = 109,
1431 Year = 1998}
1432
1433 @article{Gezelter97,
1434 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1435 Journal = jcp,
1436 Pages = 4618,
1437 Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
1438 Volume = 107,
1439 Year = 1997}
1440
1441 @article{Zwanzig83,
1442 Author = {R. Zwanzig},
1443 Journal = jcp,
1444 Pages = {4507-4508},
1445 Title = {On the relation between self-diffusion and viscosity of liquids},
1446 Volume = 79,
1447 Year = 1983}
1448
1449 @article{Stillinger95,
1450 Author = {F.~H. Stillinger},
1451 Journal = {Science},
1452 Pages = {1935-1939},
1453 Title = {A Topographic View of Supercooled Liquids and Glass Formation},
1454 Volume = 267,
1455 Year = 1995}
1456
1457 @article{Bembenek96,
1458 Author = {S.~D. Bembenek and B.~B. Laird},
1459 Journal = jcp,
1460 Pages = 5199,
1461 Title = {The role of localization in glasses and supercooled liquids},
1462 Volume = 104,
1463 Year = 1996}
1464
1465 @article{Sun97a,
1466 Author = {X. Sun and W.~H. Miller},
1467 Date-Modified = {2006-02-15 10:33:35 -0500},
1468 Journal = jcp,
1469 Pages = 6346,
1470 Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
1471 Volume = 106,
1472 Year = 1997}
1473
1474 @book{Warshel91,
1475 Address = {New York},
1476 Author = {Arieh Warshel},
1477 Publisher = {Wiley},
1478 Title = {Computer modeling of chemical reactions in enzymes and solutions},
1479 Year = 1991}
1480
1481 @article{Vuilleumier97,
1482 Author = {Rodolphe Vuilleumier and Daniel Borgis},
1483 Journal = jpc,
1484 Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
1485 Volume = {in press},
1486 Year = 1997}
1487
1488 @article{Kob95a,
1489 Author = {W. Kob and H.~C. Andersen},
1490 Date-Modified = {2006-07-18 15:04:56 -0400},
1491 Journal = pre,
1492 Pages = {4626-4641},
1493 Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones}$ mixtures: \uppercase{T}he van \uppercase{H}ove corraltion function},
1494 Volume = 51,
1495 Year = 1995}
1496
1497 @article{Kob95b,
1498 Author = {W. Kob and H.~C. Andersen},
1499 Date-Modified = {2006-07-18 14:50:19 -0400},
1500 Journal = pre,
1501 Pages = {4134-4153},
1502 Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones}$ mixtures. \uppercase{II. I}ntermediate scattering function and dynamic susceptibility},
1503 Volume = 52,
1504 Year = 1995}
1505
1506 @inproceedings{Gotze89,
1507 Address = {Amsterdam},
1508 Author = {W. G{\"{o}}tze},
1509 Booktitle = {Liquids, Freezing and Glass Transitions},
1510 Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
1511 Pages = {287-503},
1512 Publisher = {North-Holland},
1513 Title = {Aspects of Structural Glass Transitions},
1514 Volume = {I},
1515 Year = 1989}
1516
1517 @article{Sun97b,
1518 Author = {X. Sun and W.~H. Miller},
1519 Date-Modified = {2006-02-15 10:33:29 -0500},
1520 Journal = jcp,
1521 Pages = 916,
1522 Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
1523 Year = 1997}
1524
1525 @article{Chang90,
1526 Author = {Y.-T. Chang and W.~H. Miller},
1527 Journal = jpc,
1528 Pages = {5884-5888},
1529 Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
1530 Volume = 94,
1531 Year = 1990}
1532
1533 @article{Shor94,
1534 Author = {P.W. Shor},
1535 Date-Modified = {2006-07-18 15:13:14 -0400},
1536 Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
1537 Pages = {124-134},
1538 Title = {Algorithms for quantum computation: $\mbox{D}$iscrete logarithms and factoring},
1539 Year = 1994}
1540
1541 @article{Feynman82,
1542 Author = {R.~P. Feynman},
1543 Journal = {Int. J. Theor. Phys.},
1544 Pages = {467-488},
1545 Title = {Simulating physics with computers},
1546 Volume = 21,
1547 Year = 1982}
1548
1549 @article{Grover97,
1550 Author = {L.~K. Grover},
1551 Journal = prl,
1552 Pages = {4709-4712},
1553 Title = {Quantum computers can search arbitrarily large databases by a single query},
1554 Volume = 79,
1555 Year = 1997}
1556
1557 @article{Chuang98,
1558 Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
1559 Journal = prl,
1560 Pages = {3408-3411},
1561 Title = {Experimental Implementation of Fast Quantum Searching},
1562 Volume = 80,
1563 Year = 1998}
1564
1565 @article{Monroe95,
1566 Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
1567 Journal = prl,
1568 Pages = 4714,
1569 Title = {Demonstration of a fundamental quantum logic gate},
1570 Volume = 75,
1571 Year = 1995}
1572
1573 @article{Lent93,
1574 Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
1575 Journal = {Nanotechnology},
1576 Pages = {49-57},
1577 Title = {Quantum Cellular Automata},
1578 Volume = 4,
1579 Year = 1993}
1580
1581 @article{Barenco95,
1582 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},
1583 Journal = pra,
1584 Pages = {3457-3467},
1585 Title = {elementary gates for quantum computation},
1586 Volume = 52,
1587 Year = 1995}
1588
1589 @article{Reinot97,
1590 Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
1591 Date-Modified = {2006-02-15 10:31:21 -0500},
1592 Journal = jcp,
1593 Pages = {457-466},
1594 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},
1595 Volume = 106,
1596 Year = 1997}
1597
1598 @article{Laflamme96,
1599 Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
1600 Journal = prl,
1601 Pages = 77,
1602 Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
1603 Volume = 98,
1604 Year = 1996}
1605
1606 @article{Calderbank96,
1607 Author = {A.~R. Calderbank and P.~W. Shor},
1608 Journal = pra,
1609 Pages = {1098-1105},
1610 Title = {Good quantum error-correcting codes exist},
1611 Volume = 54,
1612 Year = 1996}
1613
1614 @article{Steane96,
1615 Author = {A.~M. Steane},
1616 Journal = prl,
1617 Pages = {793-797},
1618 Title = {Error correcting codes in quantum theory},
1619 Volume = 77,
1620 Year = 1996}
1621
1622 @article{Gezelter95,
1623 Author = {J.~D. Gezelter and W.~H. Miller},
1624 Journal = jcp,
1625 Pages = {7868-7876},
1626 Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
1627 Volume = 103,
1628 Year = 1995}
1629
1630 @article{Chakrabarti92,
1631 Author = {A.~C. Chakrabarti and D.~W. Deamer},
1632 Journal = {Biochimica et Biophysica Acta},
1633 Pages = {171-177},
1634 Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
1635 Volume = 1111,
1636 Year = 1992}
1637
1638 @article{Paula96,
1639 Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
1640 Journal = {Biophys. J.},
1641 Pages = {339-348},
1642 Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
1643 Volume = 70,
1644 Year = 1996}
1645
1646 @article{McKinnon92,
1647 Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
1648 Journal = jpc,
1649 Pages = {10497-10506},
1650 Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
1651 Volume = 96,
1652 Year = 1992}
1653
1654 @article{Venable93,
1655 Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
1656 Date-Modified = {2006-07-18 15:17:14 -0400},
1657 Journal = {Science},
1658 Pages = {223-226},
1659 Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: $\mbox{A}$n Investigation of Membrane Fluidity},
1660 Volume = 262,
1661 Year = 1993}
1662
1663 @article{Essmann99,
1664 Author = {U. Essmann and M.~L. Berkowitz},
1665 Journal = {Biophys. J.},
1666 Pages = {2081-2089},
1667 Title = {Dynamical properties of phospholipid bilayers from computer simulation},
1668 Volume = 76,
1669 Year = 1999}
1670
1671 @article{Tu98,
1672 Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
1673 Date-Modified = {2006-07-18 15:16:12 -0400},
1674 Journal = {Biophys. J.},
1675 Pages = {2123-2134},
1676 Title = {Effects of anesthetics on the structure of a phospholipid bilayer: $\mbox{M}$olecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
1677 Volume = 75,
1678 Year = 1998}
1679
1680 @article{Pomes96,
1681 Author = {R. Pomes and B. Roux},
1682 Date-Modified = {2006-07-18 15:10:47 -0400},
1683 Journal = {Biophys. J.},
1684 Pages = {19-39},
1685 Title = {Structure and dynamics of a proton wire: $\mbox{A}$ theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
1686 Volume = 71,
1687 Year = 1996}
1688
1689 @article{Duwez60,
1690 Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
1691 Journal = {J. Appl. Phys.},
1692 Pages = {1136-1137},
1693 Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
1694 Volume = 31,
1695 Year = 1960}
1696
1697 @article{Peker93,
1698 Author = {A. Peker and W.~L. Johnson},
1699 Journal = {Appl. Phys. Lett.},
1700 Pages = {2342-2344},
1701 Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
1702 Volume = 63,
1703 Year = 1993}
1704
1705 @article{ChoiYim97,
1706 Author = {H. Choi-Yim and W.~L. Johnson},
1707 Journal = {Appl. Phys. Lett.},
1708 Pages = {3808-3810},
1709 Title = {Bulk metallic glass matrix composites},
1710 Volume = 71,
1711 Year = 1997}
1712
1713 @article{Sun96,
1714 Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
1715 Journal = {J. Mater. Res.},
1716 Pages = {2738-2743},
1717 Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
1718 Volume = 11,
1719 Year = 1996}
1720
1721 @article{Heller93,
1722 Author = {H. Heller and M. Schaefer and K. Schulten},
1723 Journal = jpc,
1724 Pages = {8343-8360},
1725 Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
1726 Volume = 97,
1727 Year = 1993}
1728
1729 @article{Kushick76,
1730 Author = {J. Kushick and B.~J. Berne},
1731 Journal = jcp,
1732 Pages = {1362-1367},
1733 Title = {Computer Simulation of anisotropic molecular fluids},
1734 Volume = 64,
1735 Year = 1976}
1736
1737 @article{Berardi96,
1738 Author = {R. Berardi and S. Orlandi and C Zannoni},
1739 Journal = cpl,
1740 Pages = {357-362},
1741 Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
1742 Volume = 261,
1743 Year = 1996}
1744
1745 @article{Berardi99,
1746 Author = {R. Berardi and S. Orlandi and C. Zannoni},
1747 Date-Modified = {2006-07-18 14:44:37 -0400},
1748 Journal = {Int. J. Mod. Phys. C},
1749 Pages = {477-484},
1750 Title = {$\mbox{Monte Carlo}$ simulations of rod-like $\mbox{Gay-Berne}$ mesogens with transverse dipoles},
1751 Volume = 10,
1752 Year = 1999}
1753
1754 @article{Pasterny00,
1755 Author = {K. Pasterny and E. Gwozdz and A. Brodka},
1756 Date-Modified = {2006-07-18 15:10:06 -0400},
1757 Journal = {J. Mol. Liq.},
1758 Pages = {173-184},
1759 Title = {Properties of a model liquid crystal: $\mbox{Polar Gay-Berne}$ particles},
1760 Volume = 85,
1761 Year = 2000}
1762
1763 @article{Jorgensen83,
1764 Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
1765 Journal = jcp,
1766 Pages = {926-935},
1767 Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
1768 Volume = 79,
1769 Year = 1983}
1770
1771 @article{Berardi98,
1772 Author = {R. Berardi and C. Fava and C. Zannoni},
1773 Journal = cpl,
1774 Pages = {8-14},
1775 Title = {A Gay-Berne potential for dissimilar biaxial particles},
1776 Volume = 297,
1777 Year = 1998}
1778
1779 @article{Luckhurst90,
1780 Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
1781 Date-Modified = {2006-07-18 14:54:27 -0400},
1782 Journal = {Liquid Crystals},
1783 Pages = {451-464},
1784 Title = {Computer simulation studies of anisotropic systems {XIX}. \uppercase{M}esophases formed by the $\mbox{Gay-Berne}$ model mesogen},
1785 Volume = 8,
1786 Year = 1990}
1787
1788 @article{Gay81,
1789 Author = {J.~G. Gay and B.~J. Berne},
1790 Journal = jcp,
1791 Pages = {3316-3319},
1792 Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
1793 Volume = 74,
1794 Year = 1981}
1795
1796 @article{Berne72,
1797 Author = {B.~J. Berne and P. Pechukas},
1798 Journal = jcp,
1799 Pages = {4213-4216},
1800 Title = {Gaussian Model Potentials for Molecular Interactions},
1801 Volume = 56,
1802 Year = 1972}
1803
1804 @article{Perram96,
1805 Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
1806 Date-Modified = {2006-07-18 15:10:36 -0400},
1807 Journal = pre,
1808 Pages = {6565-6572},
1809 Title = {Ellipsoid contact potential: $\mbox{T}$heory and relation to overlap potentials},
1810 Volume = 54,
1811 Year = 1996}
1812
1813 @article{Cornell95,
1814 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},
1815 Journal = jacs,
1816 Pages = {5179-5197},
1817 Title = {A second generation force field for the simulation of proteins and nucleic acids},
1818 Volume = 117,
1819 Year = 1995}
1820
1821 @article{Brooks83,
1822 Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
1823 Date-Modified = {2006-07-18 15:00:32 -0400},
1824 Journal = jcc,
1825 Pages = {187-217},
1826 Title = {\uppercase{CHARMM: A} Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
1827 Volume = 4,
1828 Year = 1983}
1829
1830 @incollection{MacKerell98,
1831 Address = {New York},
1832 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},
1833 Booktitle = {The Encyclopedia of Computational Chemistry},
1834 Date-Modified = {2006-07-18 15:06:36 -0400},
1835 Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1836 Pages = {271-277},
1837 Publisher = {John Wiley \& Sons},
1838 Title = {$\mbox{CHARMM: T}$he Energy Function and Its Parameterization with an Overview of the Program},
1839 Volume = 1,
1840 Year = 1998}
1841
1842 @incollection{Jorgensen98a,
1843 Address = {New York},
1844 Author = {W.~L. Jorgensen},
1845 Booktitle = {The Encyclopedia of Computational Chemistry},
1846 Date-Modified = {2006-02-15 10:21:45 -0500},
1847 Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1848 Pages = {1986-1989},
1849 Publisher = {John Wiley \& Sons},
1850 Title = {OPLS Force Fields},
1851 Volume = 3,
1852 Year = 1998}
1853
1854 @article{Rabani00,
1855 Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1856 Date-Modified = {2006-02-15 10:30:55 -0500},
1857 Journal = prl,
1858 Pages = 467,
1859 Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
1860 Volume = 85,
1861 Year = 2000}
1862
1863 @book{Cevc87,
1864 Address = {New York},
1865 Author = {G. Cevc and D. Marsh},
1866 Publisher = {John Wiley \& Sons},
1867 Title = {Phospholipid Bilayers},
1868 Year = 1987}
1869
1870 @article{Janiak79,
1871 Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
1872 Journal = {J. Biol. Chem.},
1873 Pages = {6068-6078},
1874 Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
1875 Volume = 254,
1876 Year = 1979}
1877
1878 @article{Mazur92,
1879 Author = {E. Mazur},
1880 Date-Modified = {2006-07-18 14:55:07 -0400},
1881 Journal = {Optics and Photonics News},
1882 Pages = 38,
1883 Title = {Qualitative vs. Quantititative Thinking: \uppercase{A}re we teaching the right thing?},
1884 Volume = 3,
1885 Year = 1992}
1886
1887 @article{Wigner55,
1888 Author = {E.~P. Wigner},
1889 Journal = {Annals of Mathematics},
1890 Pages = {548-564},
1891 Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
1892 Volume = 62,
1893 Year = 1955}
1894
1895 @article{Gaukel98,
1896 Author = {C. Gaukel and H.~R. Schober},
1897 Journal = {Solid State Comm.},
1898 Pages = {1-5},
1899 Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
1900 Volume = 107,
1901 Year = 1998}
1902
1903 @article{Qi99,
1904 Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
1905 Journal = prb,
1906 Number = 5,
1907 Pages = {3527-3533},
1908 Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
1909 Volume = 59,
1910 Year = 1999}
1911
1912 @article{Khorunzhy97,
1913 Author = {A. Khorunzhy and G.~J. Rodgers},
1914 Journal = {J. Math. Phys.},
1915 Pages = {3300-3320},
1916 Title = {Eigenvalue distribution of large dilute random matrices},
1917 Volume = 38,
1918 Year = 1997}
1919
1920 @article{Rodgers88,
1921 Author = {G.~J. Rodgers and A. Bray},
1922 Journal = {Phys. Rev. B},
1923 Pages = 355703562,
1924 Title = {Density of States of a Sparse Random Matrix},
1925 Volume = 37,
1926 Year = 1988}
1927
1928 @article{Rodgers90,
1929 Author = {G.~J. Rodgers and C. {De Dominicis}},
1930 Journal = {J. Phys. A: Math. Gen.},
1931 Pages = {1567-1573},
1932 Title = {Density of states of sparse random matrices},
1933 Volume = 23,
1934 Year = 1990}
1935
1936 @inproceedings{Barker80,
1937 Author = {J.~A. Barker},
1938 Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
1939 Editor = {D. Ceperley},
1940 Pages = {45-6},
1941 Series = {NRCC Workshop Proceedings},
1942 Title = {Reaction field method for polar fluids},
1943 Volume = 9,
1944 Year = 1980}
1945
1946 @article{Smith82,
1947 Author = {W. Smith},
1948 Date-Modified = {2006-10-23 23:35:51 -0400},
1949 Journal = ccp5,
1950 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Smith_PointMultipoleEwald_82.pdf},
1951 Pages = {13-25},
1952 Title = {Point multipoles in the \uppercase{E}wald summation},
1953 Volume = 4,
1954 Year = 1982}
1955
1956 @article{Daw84,
1957 Author = {M.~S. Daw and M.~I. Baskes},
1958 Date-Modified = {2006-07-18 15:01:56 -0400},
1959 Journal = prb,
1960 Number = 12,
1961 Pages = {6443-6453},
1962 Title = {Embedded-atom method: \uppercase{D}erivation and application to impurities, surfaces, and other defects in metals},
1963 Volume = 29,
1964 Year = 1984}
1965
1966 @article{Sutton90,
1967 Author = {A.~P. Sutton and J. Chen},
1968 Date-Modified = {2006-02-15 10:33:48 -0500},
1969 Journal = {Phil. Mag. Lett.},
1970 Pages = {139-146},
1971 Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
1972 Volume = 61,
1973 Year = 1990}
1974
1975 @article{Lu97,
1976 Author = {J. Lu and J.~A. Szpunar},
1977 Journal = {Phil. Mag. A},
1978 Pages = {1057-1066},
1979 Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
1980 Volume = {75},
1981 Year = {1997}}
1982
1983 @article{Shlesinger99,
1984 Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
1985 Journal = {Am. J. Phys.},
1986 Pages = {1253-1259},
1987 Title = {Above, below, and beyond Brownian motion},
1988 Volume = 67,
1989 Year = 1999}
1990
1991 @article{Klafter96,
1992 Author = {J. Klafter and M. Shlesinger and G. Zumofen},
1993 Journal = {Physics Today},
1994 Pages = {33-39},
1995 Title = {Beyond Brownian Motion},
1996 Volume = 49,
1997 Year = 1996}
1998
1999 @article{Blumen83,
2000 Author = {A. Blumen and J. Klafter and G. Zumofen},
2001 Journal = {Phys. Rev. B},
2002 Pages = {3429-3435},
2003 Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
2004 Volume = 27,
2005 Year = 1983}
2006
2007 @article{Klafter94,
2008 Author = {J. Klafter and G. Zumofen},
2009 Journal = jpc,
2010 Pages = {7366-7370},
2011 Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
2012 Volume = 98,
2013 Year = 1994}
2014
2015 @article{Dzugutov92,
2016 Author = {M. Dzugutov},
2017 Journal = pra,
2018 Pages = {R2984-R2987},
2019 Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
2020 Volume = 46,
2021 Year = 1992}
2022
2023 @article{Moore94,
2024 Author = {P. Moore and T. Keyes},
2025 Date-Modified = {2006-07-18 15:07:46 -0400},
2026 Journal = jcp,
2027 Pages = 6709,
2028 Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: $\mbox{V}$elocity Correlation Functions and Self-Diffusion Constants},
2029 Volume = 100,
2030 Year = 1994}
2031
2032 @article{Seeley89,
2033 Author = {G. Seeley and T. Keyes},
2034 Journal = jcp,
2035 Pages = {5581-5586},
2036 Title = {Normal-mode analysis of liquid-state dynamics},
2037 Volume = 91,
2038 Year = 1989}
2039
2040 @article{Madan90,
2041 Author = {B. Madan and T. Keyes and G. Seeley},
2042 Journal = jcp,
2043 Pages = {7565-7569},
2044 Title = {Diffusion in supercooled liquids via normal mode analysis},
2045 Volume = 92,
2046 Year = 1990}
2047
2048 @article{Madan91,
2049 Author = {B. Madan and T. Keyes and G. Seeley},
2050 Journal = jcp,
2051 Pages = {6762-6769},
2052 Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
2053 Volume = 94,
2054 Year = 1991}
2055
2056 @article{Buchner92,
2057 Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
2058 Date-Modified = {2006-07-18 14:49:51 -0400},
2059 Journal = jcp,
2060 Pages = {8522-8535},
2061 Title = {The short-time dynamics of molecular liquids. \uppercase{I}nstantaneous-normal-mode theory},
2062 Volume = 97,
2063 Year = 1992}
2064
2065 @article{Wan94,
2066 Author = {Yi. Wan and R.~M. Stratt},
2067 Journal = jcp,
2068 Pages = {5123-5138},
2069 Title = {Liquid theory for the instantaneous normal modes of a liquid},
2070 Volume = 100,
2071 Year = 1994}
2072
2073 @article{Stratt95,
2074 Author = {R.~M. Stratt},
2075 Journal = {Acc. Chem. Res.},
2076 Pages = {201-207},
2077 Title = {The instantaneous normal modes of liquids},
2078 Volume = 28,
2079 Year = 1995}
2080
2081 @article{Nitzan95,
2082 Author = {G.~V. Vijayadamodar and A. Nitzan},
2083 Journal = jcp,
2084 Pages = {2169-2177},
2085 Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
2086 Volume = 103,
2087 Year = 1995}
2088
2089 @article{Ribeiro98,
2090 Author = {M.~C.~C. Ribeiro and P.~A. Madden},
2091 Journal = jcp,
2092 Pages = {3256-3263},
2093 Title = {Unstable Modes in Ionic Melts},
2094 Volume = 108,
2095 Year = 1998}
2096
2097 @article{Keyes98,
2098 Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
2099 Date-Modified = {2006-07-18 14:53:08 -0400},
2100 Journal = jcp,
2101 Pages = {4693-4694},
2102 Title = {Comment on a critique of the instantaneous normal mode (\uppercase{INM}) approach to diffusion},
2103 Volume = 109,
2104 Year = 1998}
2105
2106 @article{Alemany98,
2107 Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
2108 Date-Modified = {2006-07-18 14:58:53 -0400},
2109 Journal = jcp,
2110 Pages = {5175-5176},
2111 Title = {Transport coefficients of liquid transition metals: \uppercase{A} computer simulation study using the embedded atom model},
2112 Volume = 109,
2113 Year = 1998}
2114
2115 @article{Belonoshko00,
2116 Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
2117 Journal = prb,
2118 Pages = {3838-3844},
2119 Title = {Quasi ab initio molecular dynamic study of Cu melting},
2120 Volume = 61,
2121 Year = 2000}
2122
2123 @article{Banhart92,
2124 Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
2125 Journal = prb,
2126 Pages = {9968-9975},
2127 Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
2128 Volume = 46,
2129 Year = 1992}
2130
2131 @article{Lewis91,
2132 Author = {L.~J. Lewis},
2133 Journal = prb,
2134 Pages = {4245-4254},
2135 Title = {Atomic dynamics through the glass transition},
2136 Volume = 44,
2137 Year = 1991}
2138
2139 @article{Liu92,
2140 Author = {R.~S. Liu and D.~W. Qi and S. Wang},
2141 Journal = prb,
2142 Pages = {451-453},
2143 Title = {Subpeaks of structure factors for rapidly quenched metals},
2144 Volume = 45,
2145 Year = 1992}
2146
2147 @article{Pense92,
2148 Author = {A. W. Pense},
2149 Journal = {Mat. Char.},
2150 Pages = 213,
2151 Title = {The Decline and Fall of the Roman Denarius},
2152 Volume = 29,
2153 Year = 1992}
2154
2155 @article{Ngai81,
2156 Author = {K.~L. Ngai and F.-S. Liu},
2157 Journal = prb,
2158 Pages = {1049-1065},
2159 Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
2160 Volume = 24,
2161 Year = 1981}
2162
2163 @article{Truhlar78,
2164 Author = {Donald G. Truhlar},
2165 Journal = {J. Chem. Ed.},
2166 Pages = 309,
2167 Title = {Interpretation of the Activation Energy},
2168 Volume = 55,
2169 Year = 1978}
2170
2171 @book{Tolman27,
2172 Address = {New York},
2173 Author = {R. C. Tolman},
2174 Pages = {260-270},
2175 Publisher = {Chemical Catalog Co.},
2176 Title = {Statistical Mechanics with Applications to Physics and Chemistry},
2177 Year = 1927}
2178
2179 @article{Tolman20,
2180 Author = {R. C. Tolman},
2181 Journal = jacs,
2182 Pages = 2506,
2183 Title = {Statistical Mechanics Applied to Chemical Kinetics},
2184 Volume = 42,
2185 Year = 1920}
2186
2187 @article{Ediger96,
2188 Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
2189 Date-Modified = {2006-02-15 10:16:35 -0500},
2190 Journal = jpc,
2191 Pages = 13200,
2192 Title = {Supercooled Liquids and Glasses},
2193 Volume = 100,
2194 Year = 1996}
2195
2196 @inbook{Blumen86,
2197 Address = {Amsterdam},
2198 Author = {A. Blumen and J. Klafter and G. Zumofen},
2199 Chapter = {Reactions in Disordered Media Modelled by Fractals},
2200 Editor = {Luciano Peitronero and E. Tosatti},
2201 Pages = 399,
2202 Publisher = {North-Holland},
2203 Series = {International Symposium on Fractals in Physics},
2204 Title = {Fractals in Physics},
2205 Year = 1986}
2206
2207 @article{Shlesinger84,
2208 Author = {M.~F. Shlesinger and E.~W. Montroll},
2209 Journal = pnas,
2210 Pages = {1280-1283},
2211 Title = {On the Williams-Watts function of dielectric relaxation},
2212 Volume = 81,
2213 Year = 1984}
2214
2215 @article{Klafter86,
2216 Author = {J. Klafter and M.~F. Shlesinger},
2217 Journal = pnas,
2218 Pages = {848-851},
2219 Title = {On the relationship among three theories of relaxation in disordered systems},
2220 Volume = 83,
2221 Year = 1986}
2222
2223 @article{Li01,
2224 Author = {Z. Li and M. Lieberman and W. Hill},
2225 Date-Modified = {2006-07-18 15:05:41 -0400},
2226 Journal = {Langmuir},
2227 Pages = {4887-4894},
2228 Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: \uppercase{U}mbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
2229 Volume = 17,
2230 Year = 2001}
2231
2232 @article{Evans93,
2233 Author = {J.~W. Evans},
2234 Date-Modified = {2006-02-15 10:17:03 -0500},
2235 Journal = rmp,
2236 Pages = {1281-1329},
2237 Title = {Random and Cooperative Sequential Adsorption},
2238 Volume = 65,
2239 Year = 1993}
2240
2241 @article{Viot92,
2242 Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2243 Date-Modified = {2006-08-24 10:33:17 -0400},
2244 Journal = jpc,
2245 Pages = {5212-5218},
2246 Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. \uppercase{J}AMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
2247 Volume = 97,
2248 Year = 1992}
2249
2250 @article{Viot92b,
2251 Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2252 Date-Modified = {2006-02-15 10:12:57 -0500},
2253 Journal = {Physica A},
2254 Pages = {248-252},
2255 Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
2256 Volume = 191,
2257 Year = 1992}
2258
2259 @article{Boyer95,
2260 Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
2261 Date-Modified = {2006-02-15 10:15:52 -0500},
2262 Journal = jcp,
2263 Pages = 1607,
2264 Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
2265 Volume = 103,
2266 Year = 1995}
2267
2268 @article{Viot92c,
2269 Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2270 Date-Modified = {2006-02-15 10:13:03 -0500},
2271 Journal = {Physica A},
2272 Pages = {248-252},
2273 Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
2274 Volume = 191,
2275 Year = 1992}
2276
2277 @article{Ricci94,
2278 Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
2279 Date-Modified = {2006-02-15 10:31:32 -0500},
2280 Journal = jcp,
2281 Pages = 9164,
2282 Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
2283 Volume = 101,
2284 Year = 1994}
2285
2286 @article{Semmler98,
2287 Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
2288 Date-Modified = {2006-02-15 10:14:46 -0500},
2289 Journal = {Langmuir},
2290 Pages = {5127-5132},
2291 Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
2292 Volume = 14,
2293 Year = 1998}
2294
2295 @article{Bonnier93,
2296 Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
2297 Date-Modified = {2006-02-15 10:08:35 -0500},
2298 Journal = {Physica A},
2299 Pages = {1-10},
2300 Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
2301 Volume = 198,
2302 Year = 1993}
2303
2304 @book{Frenkel02,
2305 Address = {New York},
2306 Author = {D. Frenkel and B. Smit},
2307 Date-Modified = {2006-09-05 18:18:32 -0400},
2308 Edition = {2nd},
2309 Publisher = {Academic Press},
2310 Title = {Understanding Molecular Simulation: \uppercase{F}rom Algorithms to Applications},
2311 Year = 2002}
2312
2313 @article{Dullweber97,
2314 Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
2315 Date-Modified = {2006-08-24 09:55:06 -0400},
2316 Journal = jcp,
2317 Number = 15,
2318 Pages = {5840-5851},
2319 Title = {Symplectic splitting methods for rigid body molecular dynamics},
2320 Volume = 107,
2321 Year = 1997}
2322
2323 @article{Martin98,
2324 Author = {M. Martin and J.~I. Siepmann},
2325 Date-Modified = {2006-07-18 14:54:51 -0400},
2326 Journal = jpcB,
2327 Pages = {2569-2577},
2328 Title = {Transferable Potentials for Phase Equilibria. 1. \uppercase{U}nited-Atom Description of n-Alkanes},
2329 Volume = 102,
2330 Year = 1998}
2331
2332 @article{Marrink01a,
2333 Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
2334 Date-Modified = {2006-02-15 10:28:09 -0500},
2335 Journal = jacs,
2336 Pages = {8638-8639},
2337 Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
2338 Volume = 123,
2339 Year = 2001}
2340
2341 @article{Liu96b,
2342 Author = {Y. Liu and T. Ichiye},
2343 Date-Modified = {2006-08-22 14:42:05 -0400},
2344 Journal = jpc,
2345 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/SSDStuff/Ichiye_SSD_96.pdf},
2346 Pages = {2723-2730},
2347 Title = {Soft sticky dipole potential for liquid water: \uppercase{a} new model},
2348 Volume = 100,
2349 Year = 1996}
2350
2351 @article{Liu96,
2352 Author = {Y. Liu and T. Ichiye},
2353 Date-Modified = {2006-08-22 14:39:40 -0400},
2354 Journal = cpl,
2355 Pages = {334-340},
2356 Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
2357 Volume = 256,
2358 Year = 1996}
2359
2360 @article{Chandra99,
2361 Author = {A. Chandra and T. Ichiye},
2362 Date-Modified = {2006-08-22 14:41:50 -0400},
2363 Journal = jcp,
2364 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/SSDStuff/Chandra_SSDdynamics_99.pdf},
2365 Number = 6,
2366 Pages = {2701-2709},
2367 Title = {Dynamical properties of the soft sticky dipole model of water: \uppercase{M}olecular dynamics simulation},
2368 Volume = 111,
2369 Year = 1999}
2370
2371 @book{Allen87,
2372 Address = {New York},
2373 Author = {M.~P. Allen and D.~J. Tildesley},
2374 Date-Modified = {2006-02-15 10:08:08 -0500},
2375 Publisher = {Oxford University Press},
2376 Title = {Computer Simulations of Liquids},
2377 Year = 1987}
2378
2379 @book{Leach01,
2380 Address = {Harlow, England},
2381 Author = {A.~R. Leach},
2382 Date-Modified = {2006-07-18 15:19:59 -0400},
2383 Edition = {2nd},
2384 Publisher = {Pearson Educated Limited},
2385 Title = {Molecular Modeling: Principles and Applications},
2386 Year = 2001}
2387
2388 @article{Katsaras00,
2389 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},
2390 Date-Modified = {2006-02-15 10:21:52 -0500},
2391 Journal = {Physical Review E},
2392 Number = 5,
2393 Pages = {5668-5677},
2394 Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
2395 Volume = 61,
2396 Year = 2000}
2397
2398 @article{Sengupta00,
2399 Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
2400 Date-Modified = {2006-02-15 10:32:00 -0500},
2401 Journal = {Europhysics Letters},
2402 Number = 6,
2403 Pages = {722-728},
2404 Title = {Novel structural Features of the ripple phase of phospholipids},
2405 Volume = 49,
2406 Year = 2000}
2407
2408 @article{Venable00,
2409 Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
2410 Date-Modified = {2006-02-15 10:11:19 -0500},
2411 Journal = jcp,
2412 Number = 10,
2413 Pages = {4822-4832},
2414 Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
2415 Volume = 112,
2416 Year = 2000}
2417
2418 @article{Lindahl00,
2419 Author = {E. Lindahl and O. Edholm},
2420 Date-Modified = {2006-02-15 10:26:05 -0500},
2421 Journal = {Biophysical Journal},
2422 Month = {July},
2423 Pages = {426-433},
2424 Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
2425 Volume = 79,
2426 Year = 2000}
2427
2428 @article{Saiz02,
2429 Author = {L. Saiz and M. Klein},
2430 Date-Modified = {2006-02-15 10:31:50 -0500},
2431 Journal = jcp,
2432 Number = 7,
2433 Pages = {3052-3057},
2434 Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
2435 Volume = 116,
2436 Year = 2002}
2437
2438 @article{Stevens95,
2439 Author = {M.~J. Stevens and G.~S. Grest},
2440 Date-Modified = {2006-02-15 10:10:47 -0500},
2441 Journal = {Physical Review E},
2442 Number = 6,
2443 Pages = {5976-5983},
2444 Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
2445 Volume = 51,
2446 Year = 1995}
2447
2448 @article{Darden93,
2449 Author = {T. Darden and D. York and L. Pedersen},
2450 Date-Modified = {2006-07-18 15:01:45 -0400},
2451 Journal = jcp,
2452 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
2453 Number = 12,
2454 Pages = {10089-10092},
2455 Title = {Particle mesh \uppercase{E}wald: \uppercase{A}n $\uppercase{N} \log \uppercase{N}$ method for \uppercase{E}wald sums in large systems},
2456 Volume = 98,
2457 Year = 1993}
2458
2459 @article{Goetz98,
2460 Author = {R. Goetz and R. Lipowsky},
2461 Date-Modified = {2006-07-18 15:03:05 -0400},
2462 Journal = jcp,
2463 Number = 17,
2464 Pages = 7397,
2465 Title = {Computer simulations of bilayer membranes: \uppercase{S}elf-assembly and interfacial tension},
2466 Volume = 108,
2467 Year = 1998}
2468
2469 @article{Marrink01b,
2470 Author = {S.~J. Marrink and A.~E. Mark},
2471 Date-Modified = {2006-02-15 10:28:01 -0500},
2472 Journal = {Journal of Physical Chemistry B},
2473 Pages = {6122-6127},
2474 Title = {Effect of undulations on surface tension in simulated bilayers},
2475 Volume = 105,
2476 Year = 2001}
2477
2478 @article{Metropolis49,
2479 Author = {N. Metropolis and S. Ulam},
2480 Date-Modified = {2006-02-15 10:29:03 -0500},
2481 Journal = {J. Am. Stat. Ass.},
2482 Pages = {335-341},
2483 Title = {The $\mbox{Monte Carlo}$ Method},
2484 Volume = 44,
2485 Year = 1949}
2486
2487 @article{Metropolis53,
2488 Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
2489 Date-Modified = {2006-03-09 10:44:24 -0500},
2490 Journal = jcp,
2491 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
2492 Pages = {1087-1092},
2493 Title = {Equation of State Calculations by Fast Computing Machines},
2494 Volume = 21,
2495 Year = 1953}
2496
2497 @article{Born12,
2498 Author = {M. Born and Th. Von~Karman},
2499 Date-Modified = {2006-02-15 10:08:50 -0500},
2500 Journal = {Physik Z.},
2501 Number = {297-309},
2502 Title = {Uber Schwingungen in Raumgittern},
2503 Volume = 13,
2504 Year = 1912}
2505
2506 @book{Chandler87,
2507 Author = {David Chandler},
2508 Date-Modified = {2006-02-15 10:09:20 -0500},
2509 Publisher = {Oxford University Press},
2510 Title = {Introduction to Modern Statistical Mechanics},
2511 Year = 1987}
2512
2513 @article{Pearlman95,
2514 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},
2515 Date-Modified = {2006-09-27 10:00:28 -0400},
2516 Journal = {Computer Physics Communications},
2517 Pages = {1-41},
2518 Title = {\uppercase{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},
2519 Volume = 91,
2520 Year = 1995}
2521
2522 @book{Goldstein01,
2523 Address = {San Francisco},
2524 Author = {H. Goldstein and C. Poole and J. Safko},
2525 Edition = {3rd},
2526 Publisher = {Addison Wesley},
2527 Title = {Classical Mechanics},
2528 Year = 2001}
2529
2530 @article{Bratko85,
2531 Author = {D. Bratko and L. Blum and A. Luzar},
2532 Journal = jcp,
2533 Number = 12,
2534 Pages = {6367-6370},
2535 Title = {A simple model for the intermolecular potential of water},
2536 Volume = 83,
2537 Year = 1985}
2538
2539 @article{Bratko95,
2540 Author = {L. Blum and F. Vericat and D. Bratko},
2541 Date-Modified = {2006-07-18 15:00:02 -0400},
2542 Journal = jcp,
2543 Number = 3,
2544 Pages = {1461-1462},
2545 Title = {Towards an analytical model of water: \uppercase{T}he octupolar model},
2546 Volume = 102,
2547 Year = 1995}
2548
2549 @article{Tan03,
2550 Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
2551 Journal = cpl,
2552 Pages = {646-652},
2553 Title = {A temperature of maximum density in soft sticky dipole water},
2554 Volume = 376,
2555 Year = 2003}
2556
2557 @article{Soper86,
2558 Author = {A.~K. Soper and M.~G. Phillips},
2559 Date-Modified = {2006-09-27 10:08:19 -0400},
2560 Journal = cp,
2561 Number = 1,
2562 Pages = {47-60},
2563 Title = {A new determination of the structure of water at 298\uppercase{K}},
2564 Volume = 107,
2565 Year = 1986}
2566
2567 @article{Plimpton95,
2568 Author = {S. Plimpton},
2569 Date-Modified = {2006-02-15 10:30:31 -0500},
2570 Journal = jcop,
2571 Pages = {1-19},
2572 Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
2573 Volume = 117,
2574 Year = 1995}
2575
2576 @article{Tartaglino02,
2577 Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
2578 Date-Modified = {2006-07-18 15:14:01 -0400},
2579 Journal = prb,
2580 Pages = 241406,
2581 Title = {Bending strain-driven modification of surface resconstructions: $\mbox{Au}$(111)},
2582 Volume = 65,
2583 Year = 2002}
2584
2585 @article{Ercolessi88,
2586 Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
2587 Date-Modified = {2006-07-18 14:52:08 -0400},
2588 Journal = {Philosophical Magazine A},
2589 Pages = {213-226},
2590 Title = {Simulation of Gold in the Glue Model},
2591 Volume = 58,
2592 Year = 1988}
2593
2594 @article{Finnis84,
2595 Author = {M.~W Finnis and J.~E. Sinclair},
2596 Journal = {Phil. Mag. A},
2597 Pages = {45-55},
2598 Title = {A Simple Empirical N-Body Potential for Transition-Metals},
2599 Volume = 50,
2600 Year = 1984}
2601
2602 @article{Foiles86,
2603 Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
2604 Date-Modified = {2006-02-15 10:17:44 -0500},
2605 Journal = prb,
2606 Number = 12,
2607 Pages = 7983,
2608 Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2609 Volume = 33,
2610 Year = 1986}
2611
2612 @article{Daw93,
2613 Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
2614 Date-Modified = {2006-02-15 10:16:13 -0500},
2615 Journal = {Mat. Sci. Rep.},
2616 Pages = {251-310},
2617 Title = {The embededd-atom method},
2618 Volume = 9,
2619 Year = 1993}
2620
2621 @article{Johnson89,
2622 Author = {R.~A. Johnson},
2623 Date-Modified = {2006-02-15 10:21:36 -0500},
2624 Journal = prb,
2625 Number = 17,
2626 Pages = 12554,
2627 Title = {Alloy models with the embedded-atom method},
2628 Volume = 39,
2629 Year = 1989}
2630
2631 @article{Kol97,
2632 Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
2633 Date-Modified = {2006-02-15 10:24:53 -0500},
2634 Journal = jcp,
2635 Number = 7,
2636 Pages = {2580-2588},
2637 Title = {A symplectic method for rigid-body molecular simulation},
2638 Volume = 107,
2639 Year = 1997}
2640
2641 @article{Hoover85,
2642 Author = {W.~G. Hoover},
2643 Date-Modified = {2006-07-18 15:03:15 -0400},
2644 Journal = pra,
2645 Pages = 1695,
2646 Title = {Canonical dynamics: \uppercase{E}quilibrium phase-space distributions},
2647 Volume = 31,
2648 Year = 1985}
2649
2650 @article{Roux91,
2651 Author = {B. Roux and M. Karplus},
2652 Date-Modified = {2006-07-18 15:12:04 -0400},
2653 Journal = jpc,
2654 Number = 15,
2655 Pages = {4856-4868},
2656 Title = {Ion transport in a Gramicidin-like channel: $\mbox{D}$ynamics and mobility},
2657 Volume = 95,
2658 Year = 1991}
2659
2660 @article{Marrink94,
2661 Author = {S.~J Marrink and H.~J.~C. Berendsen},
2662 Journal = jpc,
2663 Number = 15,
2664 Pages = {4155-4168},
2665 Title = {Simulation of water transport through a lipid membrane},
2666 Volume = 98,
2667 Year = 1994}
2668
2669 @article{Daw89,
2670 Author = {Murray~S. Daw},
2671 Date-Modified = {2006-07-18 15:02:06 -0400},
2672 Journal = {Physical Review B},
2673 Pages = {7441-7452},
2674 Title = {Model of metallic cohesion: \uppercase{T}he embedded-atom method},
2675 Volume = 39,
2676 Year = 1989}
2677
2678 @inbook{Voter95b,
2679 Author = {A.~F. Voter},
2680 Chapter = 4,
2681 Date-Modified = {2006-02-15 10:35:07 -0500},
2682 Editor = {J.~H. Westbrook and R.~L. Fleischer},
2683 Pages = 77,
2684 Publisher = {John Wiley and Sons Ltd},
2685 Title = {Intermetallic Compounds: Principles and Practice},
2686 Volume = 1,
2687 Year = 1995}
2688
2689 @article{Marrink02,
2690 Author = {S.~J. Marrink and D.~P. Teileman},
2691 Date-Modified = {2006-02-15 10:28:20 -0500},
2692 Journal = {Biophysical Journal},
2693 Pages = {2386-2392},
2694 Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
2695 Volume = 83,
2696 Year = 2002}
2697
2698 @article{Sum03,
2699 Author = {A.~K. Sum and J.~J. de~Pablo},
2700 Date-Modified = {2006-02-15 10:11:01 -0500},
2701 Journal = {Biophysical Journal},
2702 Pages = {3636-3645},
2703 Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2704 Volume = 85,
2705 Year = 2003}
2706
2707 @article{Gomez03,
2708 Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
2709 Date-Modified = {2006-02-15 10:17:14 -0500},
2710 Journal = {Eur. Biophys. J.},
2711 Pages = {217-227},
2712 Title = {Setting up and optimization of membrane protein simulations},
2713 Volume = 31,
2714 Year = 2002}
2715
2716 @article{Smondyrev99,
2717 Author = {A.~M. Smondyrev and M.~L. Berkowitz},
2718 Date-Modified = {2006-02-15 10:10:29 -0500},
2719 Journal = {Biophysical Journal},
2720 Pages = {2472-2478},
2721 Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
2722 Volume = 76,
2723 Year = 1999}
2724
2725 @article{Nina02,
2726 Author = {M. Nina and T. Simonson},
2727 Date-Modified = {2006-07-18 15:08:00 -0400},
2728 Journal = jpcb,
2729 Pages = {3696-3705},
2730 Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: $\mbox{C}$omparison between Continuum Reaction Field and Particle-Mesh \uppercase{E}wald Electrostatic Treatments},
2731 Volume = 106,
2732 Year = 2002}
2733
2734 @article{Norberg00,
2735 Author = {J. Norberg and L. Nilsson},
2736 Date-Modified = {2006-02-15 10:29:36 -0500},
2737 Journal = {Biophysical Journal},
2738 Pages = {1537-1553},
2739 Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2740 Volume = 79,
2741 Year = 2000}
2742
2743 @article{Patra03,
2744 Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2745 Date-Modified = {2006-07-18 15:10:24 -0400},
2746 Journal = {Biophysical Journal},
2747 Pages = {3636-3645},
2748 Title = {Molecular Dynamics Simulations of Lipid Bilayers: $\mbox{M}$ajor Artifacts Due to Truncating Electrostatic Interactions},
2749 Volume = 84,
2750 Year = 2003}
2751
2752 @article{Marrink04,
2753 Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
2754 Date-Modified = {2006-02-15 10:28:28 -0500},
2755 Journal = jpcb,
2756 Pages = {750-760},
2757 Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
2758 Volume = 108,
2759 Year = 2004}
2760
2761 @article{Andersen83,
2762 Author = {H.~C. Andersen},
2763 Date-Modified = {2006-09-05 22:28:45 -0400},
2764 Journal = jcop,
2765 Pages = {24-34},
2766 Title = {\uppercase{RATTLE: A} Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
2767 Volume = 52,
2768 Year = 1983}
2769
2770 @article{Hura00,
2771 Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
2772 Date-Modified = {2006-07-21 11:45:15 -0400},
2773 Journal = jcp,
2774 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayH2O_2000.pdf},
2775 Pages = {9140-9148},
2776 Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
2777 Volume = 113,
2778 Year = 2000}
2779
2780 @inbook{Fowles99,
2781 Author = {G.~R. Fowles and G.~L. Cassiday},
2782 Chapter = 10,
2783 Date-Modified = {2006-02-15 10:18:00 -0500},
2784 Edition = {6th},
2785 Publisher = {Saunders College Publishing},
2786 Title = {Analytical Mechanics},
2787 Year = 1999}
2788
2789 @article{Petrache00,
2790 Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2791 Date-Modified = {2006-02-15 10:30:24 -0500},
2792 Journal = {Biophysical Journal},
2793 Pages = {3172-3192},
2794 Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2795 Volume = 79,
2796 Year = 2000}
2797
2798 @article{Egberts88,
2799 Author = {E. Egberts and H.~J.~C. Berendsen},
2800 Date-Modified = {2006-02-15 10:16:43 -0500},
2801 Journal = jcp,
2802 Pages = {3718-3732},
2803 Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
2804 Volume = 89,
2805 Year = 1988}
2806
2807 @article{Holz00,
2808 Author = {M. Holz and S.~R. Heil and A. Sacco},
2809 Date-Modified = {2006-08-06 14:07:16 -0400},
2810 Journal = pccp,
2811 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Holz_SelfDiffusionOfWaterFromNMR_00.pdf},
2812 Pages = {4740-4742},
2813 Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1$\uppercase{h nmr pfg} measurements},
2814 Volume = 2,
2815 Year = 2000}
2816
2817 @incollection{Zannoni94,
2818 Author = {C. Zannoni},
2819 Booktitle = {The Molecular Dynamics of Liquid Crstals},
2820 Chapter = 6,
2821 Date-Modified = {2006-02-15 10:12:36 -0500},
2822 Editor = {G.~R. Luckhurst and C.~A. Veracini},
2823 Pages = {139-169},
2824 Publisher = {Kluwer Academic Publishers},
2825 Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
2826 Year = 1994}
2827
2828 @article{Melchionna93,
2829 Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
2830 Date-Modified = {2006-07-20 08:41:04 -0400},
2831 Journal = {Molecular Physics},
2832 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Melchionna_HooverNVTandNPT_93.pdf},
2833 Pages = {533-544},
2834 Title = {Hoover \uppercase{$NPT$} dynamics for systems varying in shape and size},
2835 Volume = 78,
2836 Year = 1993}
2837
2838 @article{Fennell04,
2839 Author = {C.~J. Fennell and J.~D. Gezelter},
2840 Date-Modified = {2006-07-18 14:20:59 -0400},
2841 Journal = jcp,
2842 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
2843 Number = 19,
2844 Pages = {9175-9184},
2845 Title = {On the structural and transport properties of the soft sticky dipole (\uppercase{SSD}) and related single point water models},
2846 Volume = 120,
2847 Year = 2004}
2848
2849 @article{Klein01,
2850 Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
2851 Date-Modified = {2006-02-15 10:27:22 -0500},
2852 Journal = jpcb,
2853 Pages = {4464-4470},
2854 Title = {A Coarse Grain Model for Phospholipid Simulations},
2855 Volume = 105,
2856 Year = 2001}
2857
2858 @article{Marrink03,
2859 Author = {S.~J. Marrink and A.~E. Mark},
2860 Date-Modified = {2006-03-16 09:54:52 -0500},
2861 Journal = jacs,
2862 Pages = {15233-15242},
2863 Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2864 Volume = 125,
2865 Year = 2003}
2866
2867 @article{Fletcher64,
2868 Author = {R. Fletcher and C.~M. Reeves},
2869 Date-Modified = {2006-02-15 10:17:34 -0500},
2870 Journal = {Comput. J.},
2871 Number = 2,
2872 Pages = {149-154},
2873 Title = {Function minimization by conjugate gradients},
2874 Volume = 7,
2875 Year = 1964}
2876
2877 @article{Polak69,
2878 Author = {E. Polak and G. Ribiere},
2879 Date-Modified = {2006-02-15 10:14:00 -0500},
2880 Journal = {Rev. Fr. Inform. Rech. Oper.},
2881 Pages = {35-43},
2882 Title = {Note sur la convergence de methodes de directions conjugees},
2883 Volume = {16-R1},
2884 Year = 1969}
2885
2886 @article{Voter87,
2887 Author = {A.~F. Voter and S.~P. Chen},
2888 Date-Modified = {2006-02-15 10:35:19 -0500},
2889 Journal = {Mat. Res. Soc. Symp. Proc.},
2890 Pages = {175},
2891 Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
2892 Volume = {82},
2893 Year = {1987}}
2894
2895 @article{Hendrickson95,
2896 Author = {Bruce Hendrickson and Steve Plimpton},
2897 Date-Modified = {2006-02-15 10:19:11 -0500},
2898 Journal = {Journal of Parallel and Distributed Computing},
2899 Pages = {15-25},
2900 Title = {Parallel Many-body Simulations without All-to-All Communication},
2901 Volume = {27},
2902 Year = {1995}}
2903
2904 @inproceedings{Paradyn93,
2905 Address = {Pittsburgh, PA},
2906 Author = {S.~J. Plimpton and B.~A. Hendrickson},
2907 Booktitle = {Materials Theory and Modelling},
2908 Date-Modified = {2006-02-15 10:30:42 -0500},
2909 Editor = {J. Broughton and P. Bristowe and J. Newsam},
2910 Pages = 37,
2911 Publisher = {Materials Research Society},
2912 Series = {MRS Proceedings},
2913 Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
2914 Volume = 291,
2915 Year = 1993}
2916
2917 @article{Voter95a,
2918 Author = {A.~F. Voter},
2919 Date-Modified = {2006-02-15 10:35:27 -0500},
2920 Journal = {Intermetallic Compounds: Principles and Practice},
2921 Pages = {77},
2922 Title = {The Embedded-Atom Method},
2923 Volume = {1},
2924 Year = {1995}}
2925
2926 @article{Heller90,
2927 Author = {H. Heller and H. Grubmuller and K. Schulten},
2928 Date-Modified = {2006-02-15 10:19:02 -0500},
2929 Journal = {Molecular Simulation},
2930 Pages = {133},
2931 Title = {Molecular dynamics simulation on a parallel computer},
2932 Volume = {5},
2933 Year = {1990}}
2934
2935 @book{Fox88,
2936 Address = {Englewood Cliffs, NJ},
2937 Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
2938 Publisher = {Prentice-Hall},
2939 Title = {Solving Promblems on Concurrent Processors},
2940 Volume = {I},
2941 Year = 1988}
2942
2943 @article{Berendsen95,
2944 Author = {H.~J.~C. Berendsen and D. van~der~Spoel and R. van~Drunen},
2945 Date-Modified = {2006-07-18 14:59:51 -0400},
2946 Journal = {Comp. Phys. Comm.},
2947 Pages = {43-56},
2948 Title = {\uppercase{GROMACS: A} message-passing parallel molecular dynamics implementation},
2949 Volume = 91,
2950 Year = 1995}
2951
2952 @article{Lindahl01,
2953 Author = {E. Lindahl and B. Hess and D. van~der~Spoel},
2954 Date-Modified = {2006-07-18 14:53:59 -0400},
2955 Journal = {J. Mol. Mod.},
2956 Pages = {306-317},
2957 Title = {\uppercase{GROMACS 3.0: A} package for molecular simulation and trajectory analysis},
2958 Volume = 7,
2959 Year = 2001}
2960
2961 @article{Smith96,
2962 Author = {W. Smith and T. Forester},
2963 Date-Modified = {2006-09-07 14:48:19 -0400},
2964 Journal = {J. Molec. Graphics.},
2965 Number = 3,
2966 Pages = {136-141},
2967 Title = {\uppercase{DL\_POLY\_2.0: A} general-purpose parallel molecular dynamics simulation package},
2968 Volume = 14,
2969 Year = 1996}
2970
2971 @article{Ponder87,
2972 Author = {J.~W. Ponder and F.~M. Richards},
2973 Date-Modified = {2006-02-15 10:13:45 -0500},
2974 Journal = jcc,
2975 Number = 7,
2976 Pages = {1016-1024},
2977 Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
2978 Volume = 8,
2979 Year = 1987}
2980
2981 @article{Berendsen87,
2982 Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
2983 Journal = jpc,
2984 Pages = {6269-6271},
2985 Title = {The Missing Term in Effective Pair Potentials},
2986 Volume = 91,
2987 Year = 1987}
2988
2989 @incollection{Berendsen81,
2990 Address = {Dordrecht},
2991 Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
2992 Booktitle = {Intermolecular Forces},
2993 Date-Modified = {2006-08-02 13:23:53 -0400},
2994 Editor = {B. Pullman},
2995 Pages = {331-342},
2996 Publisher = {Reidel},
2997 Title = {Simple Point Charge Water},
2998 Year = 1981}
2999
3000 @article{Mahoney00,
3001 Author = {M.~W. Mahoney and W.~L. Jorgensen},
3002 Journal = jcp,
3003 Number = 20,
3004 Pages = {8910-8922},
3005 Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
3006 Volume = 112,
3007 Year = 2000}
3008
3009 @article{Meineke05,
3010 Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
3011 Date-Modified = {2006-07-18 15:22:51 -0400},
3012 Journal = jcc,
3013 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
3014 Pages = {252-271},
3015 Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
3016 Volume = 26,
3017 Year = 2005}
3018
3019 @article{Baez95a,
3020 Author = {L.~A. B\'{a}ez and P. Clancy},
3021 Date-Modified = {2006-08-28 10:20:00 -0400},
3022 Journal = mp,
3023 Number = 3,
3024 Pages = {385-396},
3025 Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
3026 Volume = 86,
3027 Year = 1995}
3028
3029 @article{Baez95b,
3030 Author = {L.~A. B\'{a}ez and P. Clancy},
3031 Date-Modified = {2006-08-28 10:20:16 -0400},
3032 Journal = jcp,
3033 Number = 22,
3034 Pages = {9744-9755},
3035 Title = {Phase equilibria in extended simple point charge ice-water systems},
3036 Volume = 103,
3037 Year = 1995}
3038
3039 @article{Davidson84,
3040 Author = {E.~R. Davidson and K. Morokuma},
3041 Journal = jcp,
3042 Number = 8,
3043 Pages = {3741-3742},
3044 Title = {A proposed antiferroelectric structure for proton ordered ice Ih},
3045 Volume = 81,
3046 Year = 1984}
3047
3048 @article{Sanz04,
3049 Author = {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
3050 Journal = prl,
3051 Number = 25,
3052 Pages = 255701,
3053 Title = {Phase Diagram of Water from Computer Simulation},
3054 Volume = 92,
3055 Year = 2004}
3056
3057 @article{Onsager36,
3058 Author = {L. Onsager},
3059 Date-Modified = {2006-08-02 10:49:57 -0400},
3060 Journal = jacs,
3061 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Onsager_electMoments_36.pdf},
3062 Pages = {1486-1493},
3063 Title = {Electric Moments of Molecules in Liquids},
3064 Volume = 58,
3065 Year = 1936}
3066
3067 @article{Matsumoto02,
3068 Author = {M. Matsumoto and S. Saito and I. Ohimine},
3069 Journal = {Nature (London)},
3070 Pages = {409-413},
3071 Title = {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
3072 Volume = 416,
3073 Year = 2002}
3074
3075 @article{Yamada02,
3076 Author = {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
3077 Journal = prl,
3078 Number = 19,
3079 Pages = 195701,
3080 Title = {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
3081 Volume = 88,
3082 Year = 2002}
3083
3084 @article{Wallqvist95,
3085 Author = {A. Wallqvist and B.~J. Berne},
3086 Journal = jpc,
3087 Pages = {2885-2892},
3088 Title = {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
3089 Volume = 99,
3090 Year = 1995}
3091
3092 @article{Vlot99,
3093 Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
3094 Date-Modified = {2006-08-26 23:57:49 -0400},
3095 Journal = jcp,
3096 Number = 1,
3097 Pages = {55-61},
3098 Title = {Free energy calculations on systems of rigid molecules: \uppercase{A}n application to the \uppercase{TIP4P} model of \uppercase{H}$_2$\uppercase{O}},
3099 Volume = 110,
3100 Year = 1999}
3101
3102 @article{Gao00,
3103 Author = {G.~T. Gao and X.~C. Zeng and H. Tanaka},
3104 Date-Modified = {2006-07-18 15:02:44 -0400},
3105 Journal = jcp,
3106 Number = 19,
3107 Pages = {8534-8538},
3108 Title = {The melting temperature of proton-disordered hexagonal ice: \uppercase{A} computer simulation of 4-site transferable intermolecular potential model of water},
3109 Volume = 112,
3110 Year = 2000}
3111
3112 @article{Bizid87,
3113 Author = {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
3114 Date-Modified = {2006-07-18 14:51:30 -0400},
3115 Journal = jcp,
3116 Number = 4,
3117 Pages = {2225-2230},
3118 Title = {Structure of high-density amorphous water. \uppercase{I. X}-ray diffraction study},
3119 Volume = 87,
3120 Year = 1987}
3121
3122 @article{Quintana92,
3123 Author = {J. Quintana and A.~D.~J. Haymet},
3124 Date-Modified = {2006-07-18 15:11:19 -0400},
3125 Journal = cpl,
3126 Number = 3,
3127 Pages = {273-277},
3128 Title = {The chemical potential of water: $\mbox{m}$olecular dynamics computer simulation of the $\mbox{CF and SPC}$ models},
3129 Volume = 189,
3130 Year = 1992}
3131
3132 @article{Baez94,
3133 Author = {L.~A. B\'{a}ez and P. Clancy},
3134 Date-Modified = {2006-08-28 08:04:23 -0400},
3135 Journal = jcp,
3136 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Baez_DensityMaxSPCE_94.pdf},
3137 Number = 11,
3138 Pages = {9837-9840},
3139 Title = {Existence of a density maximum in extended simple point charge water},
3140 Volume = 101,
3141 Year = 1994}
3142
3143 @article{Jorgensen98b,
3144 Author = {W.~L. Jorgensen and C. Jenson},
3145 Date-Modified = {2006-07-18 15:04:13 -0400},
3146 Journal = jcc,
3147 Number = 10,
3148 Pages = {1179-1186},
3149 Title = {Temperature Dependence of $\mbox{TIP3P, SPC, and TIP4P}$ Water from $\mbox{NPT Monte Carlo}$ Simulations: \uppercase{S}eeking Temperatures of Maximum Density},
3150 Volume = 19,
3151 Year = 1998}
3152
3153 @article{Mahoney01,
3154 Author = {M.~W. Mahoney and W.~L. Jorgensen},
3155 Journal = jcp,
3156 Number = 1,
3157 Pages = {363-366},
3158 Title = {Diffusion constant of the TIP5P model of liquid water},
3159 Volume = 114,
3160 Year = 2001}
3161
3162 @article{Rahman75,
3163 Author = {A. Rahman and F.~H. Stillinger and H.~L. Lemberg},
3164 Journal = jcp,
3165 Number = 12,
3166 Pages = {5223-5230},
3167 Title = {Study of a central force model for liquid water by molecular dynamics},
3168 Volume = 63,
3169 Year = 1975}
3170
3171 @article{vanderSpoel98,
3172 Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
3173 Date-Modified = {2006-07-18 15:14:10 -0400},
3174 Journal = jcp,
3175 Number = 24,
3176 Pages = {10220-10230},
3177 Title = {A systematic study of water models for molecular simulation: $\mbox{D}$erivation of water models optimized for use with a reaction field},
3178 Volume = 108,
3179 Year = 1998}
3180
3181 @article{Gallagher03,
3182 Author = {K.~R. Gallagher and K.~A. Sharp},
3183 Date-Modified = {2006-09-27 10:13:16 -0400},
3184 Journal = jacs,
3185 Pages = {9853-9860},
3186 Title = {A New Angle on Heat Capacity Changes in Hydrophobic Solvation},
3187 Volume = 125,
3188 Year = 2003}
3189
3190 @article{Frenkel84,
3191 Author = {D. Frenkel and A.~J.~C. Ladd},
3192 Date-Modified = {2006-07-18 14:52:23 -0400},
3193 Journal = jcp,
3194 Number = 7,
3195 Pages = {3188-3193},
3196 Title = {New $\mbox{Monte Carlo}$ method to compute the free energy of arbitrary solids. \uppercase{A}pplication to the fcc and hcp phases of hard spheres},
3197 Volume = 81,
3198 Year = 1984}
3199
3200 @article{Hermens88,
3201 Author = {J. Hermans and A. Pathiaseril and A. Anderson},
3202 Date-Modified = {2006-07-18 14:52:38 -0400},
3203 Journal = jacs,
3204 Pages = {5982-5986},
3205 Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. \uppercase{A}pplication to Water Models},
3206 Volume = 110,
3207 Year = 1988}
3208
3209 @article{Meijer90,
3210 Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
3211 Date-Modified = {2006-07-18 14:46:17 -0400},
3212 Journal = jcp,
3213 Number = 12,
3214 Pages = {7570-7575},
3215 Title = {Location of melting point at 300 \uppercase{K} of nitrogen by $\mbox{Monte Carlo}$ simulation},
3216 Volume = 92,
3217 Year = 1990}
3218
3219 @article{Li96,
3220 Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
3221 Journal = {Science},
3222 Pages = {666-669},
3223 Title = {Emergence of Preferred Structures in a Simple Model of Protein Folding},
3224 Volume = 273,
3225 Year = 1996}
3226
3227 @article{Stillinger74,
3228 Author = {F.~H. Stillinger and A. Rahman},
3229 Journal = jcp,
3230 Number = 4,
3231 Pages = {1545-1557},
3232 Title = {Improved simulation of liquid water by molecular dynamics},
3233 Volume = 60,
3234 Year = 1974}
3235
3236 @article{Caldwell95,
3237 Author = {J.~W. Caldwell and P.~A. Kollman},
3238 Journal = jpc,
3239 Number = 16,
3240 Pages = {6208-6219},
3241 Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
3242 Volume = 99,
3243 Year = 1995}
3244
3245 @article{Urbic00,
3246 Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
3247 Date-Modified = {2006-07-18 15:16:53 -0400},
3248 Journal = jcp,
3249 Number = 6,
3250 Pages = {2843-2848},
3251 Title = {A two-dimensional model of water: $\mbox{T}$heory and computer simulations},
3252 Volume = 112,
3253 Year = 2000}
3254
3255 @article{Yang04,
3256 Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
3257 Journal = prl,
3258 Number = 14,
3259 Pages = 146102,
3260 Title = {Ice Tessellation on a Hydroxylated Silica Surface},
3261 Volume = 92,
3262 Year = 2004}