ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/chrisDissertation/dissertation.bib
Revision: 3004
Committed: Mon Sep 18 20:32:11 2006 UTC (18 years, 7 months ago) by chrisfen
File size: 106318 byte(s)
Log Message:
updated plot and text on newer results

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