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root/group/trunk/chrisDissertation/dissertation.bib
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# Content
1 %% This BibTeX bibliography file was created using BibDesk.
2 %% http://bibdesk.sourceforge.net/
3
4
5 %% Created for Chris Fennell at 2006-09-21 15:41:30 -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 @book{Tolman38,
49 Address = {New York},
50 Author = {R.~C. Tolman},
51 Date-Added = {2006-09-21 15:37:16 -0400},
52 Date-Modified = {2006-09-21 15:41:28 -0400},
53 Publisher = {Oxford University Press, Inc.},
54 Title = {The Principles of Statistical Mechanics},
55 Year = {1938}}
56
57 @article{Beeman76,
58 Author = {D. Beeman},
59 Date-Added = {2006-09-20 14:44:19 -0400},
60 Date-Modified = {2006-09-20 14:45:33 -0400},
61 Journal = {J. Comp. Phys.},
62 Pages = {130-139},
63 Title = {Some Multistep Methods for Use in Molecular Dynamics Calculations},
64 Volume = {20},
65 Year = {1976}}
66
67 @inproceedings{Berendsen86,
68 Address = {North Holland, Amsterdam},
69 Author = {H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
70 Booktitle = {Molecular Dynamics Simulations of Statistical Mechanics Systems},
71 Date-Added = {2006-09-20 14:11:30 -0400},
72 Date-Modified = {2006-09-20 14:19:19 -0400},
73 Editor = {G. Ciccotti and W.~G. Hoover},
74 Pages = {43-65},
75 Series = {Proceedings of the 97th Int. ``Enrico Fermi" School of Physics},
76 Title = {Practical algorithms for dynamics simulations},
77 Year = {1986}}
78
79 @techreport{Gear66,
80 Address = {Argonne, IL},
81 Author = {C.~W. Gear},
82 Date-Added = {2006-09-20 14:00:35 -0400},
83 Date-Modified = {2006-09-20 14:05:03 -0400},
84 Institution = {Argonne National Laboratory},
85 Number = {ANL-7126},
86 Title = {The Numerical Integration of Ordinary Differential Equations of Various Orders},
87 Year = {1966}}
88
89 @article{Abascal05,
90 Author = {J.~L.~F. Abascal and E. Sanz and R. {Garc\'{i}a Fern\'{a}ndez} and C. Vega},
91 Date-Added = {2006-09-18 14:20:06 -0400},
92 Date-Modified = {2006-09-18 14:27:13 -0400},
93 Doi = {10.1063/1.1931662},
94 Journal = {J. Chem. Phys.},
95 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Abascal_Tip4p-Ice_05.pdf},
96 Number = {23},
97 Pages = {234511},
98 Title = {A potential model for the study of ices and amorphous water: \uppercase{TIP4P/I}ce},
99 Volume = {122},
100 Year = {2005}}
101
102 @article{Vega05,
103 Author = {C. Vega and E. Sanz and J.~L.~F. Abascal},
104 Date-Added = {2006-09-18 09:40:15 -0400},
105 Date-Modified = {2006-09-18 09:41:55 -0400},
106 Doi = {10.1063/1.1862245},
107 Journal = {J. Chem. Phys.},
108 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Vega_MeltTempModels_05.pdf},
109 Number = {11},
110 Pages = {114507},
111 Title = {The melting temperature of the most common models of water},
112 Volume = {122},
113 Year = {2005}}
114
115 @article{Harvey98,
116 Author = {S.~C. Harvey and R.~K.-Z. Tan and T.~E. {Cheatham III}},
117 Date-Added = {2006-09-07 00:53:34 -0400},
118 Date-Modified = {2006-09-07 00:55:37 -0400},
119 Journal = {J. Comp. Chem.},
120 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Harvey_FlyingIceCube_98.pdf},
121 Number = {7},
122 Pages = {726-740},
123 Title = {The Flying Ice Cube: \uppercase{V}elocity Rescaling in Molecular Dynamics Leads to Violation of Energy Equipartition},
124 Volume = {19},
125 Year = {1998}}
126
127 @article{Verlet68,
128 Author = {L. Verlet},
129 Date-Added = {2006-09-06 12:19:09 -0400},
130 Date-Modified = {2006-09-20 14:22:53 -0400},
131 Journal = {Phys. Rev.},
132 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_EqCorrFunc_67.pdf},
133 Number = {1},
134 Pages = {201-214},
135 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{II. E}quilibrium Correlation Functions},
136 Volume = {165},
137 Year = {1968}}
138
139 @article{Verlet67,
140 Author = {L. Verlet},
141 Date-Added = {2006-09-06 12:16:19 -0400},
142 Date-Modified = {2006-09-20 14:22:43 -0400},
143 Journal = {Phys. Rev.},
144 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_ClassicalFluids_67.pdf},
145 Number = {1},
146 Pages = {98-103},
147 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{I. T}hermodynamic Properties of \uppercase{L}ennard-\uppercase{J}ones Molecules},
148 Volume = {159},
149 Year = {1967}}
150
151 @article{Thompson83,
152 Author = {C.~J. Thompson},
153 Date-Added = {2006-09-06 11:59:49 -0400},
154 Date-Modified = {2006-09-06 12:02:07 -0400},
155 Journal = {CCP5 Quarterly},
156 Pages = {20-28},
157 Title = {Use of neighbor lists in molecular dynamics},
158 Volume = {8},
159 Year = {1983}}
160
161 @article{Krautler01,
162 Author = {V. Kr\"{a}utler and W.~F. {van Gunsteren} and P.~H. H\"{u}nenberger},
163 Date-Added = {2006-09-04 00:17:15 -0400},
164 Date-Modified = {2006-09-04 00:29:36 -0400},
165 Journal = {J. Comp. Chem.},
166 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Krautler_FastSHAKE_01.pdf},
167 Number = {5},
168 Pages = {501-508},
169 Title = {A Fast \uppercase{SHAKE} Algorithm to Solve Distance Constraint Equations for Small Molecules in Molecular Dynamics Simulations},
170 Volume = {22},
171 Year = {2001}}
172
173 @article{Swope82,
174 Author = {W.~C. Swope and H.~C. Andersen and P.~H. Berens and K.~R. Wilson},
175 Date-Added = {2006-09-03 21:47:42 -0400},
176 Date-Modified = {2006-09-03 21:50:26 -0400},
177 Journal = {J. Chem. Phys.},
178 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Swope_VelocityVerlet_82.pdf},
179 Number = {1},
180 Pages = {637-649},
181 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},
182 Volume = {76},
183 Year = {1982}}
184
185 @article{Trotter59,
186 Author = {H.~F. Trotter},
187 Date-Added = {2006-09-03 18:05:35 -0400},
188 Date-Modified = {2006-09-03 18:07:32 -0400},
189 Journal = {Proc. Am. Math Soc.},
190 Pages = {545-551},
191 Title = {On the product of Semi-Groups of Operators},
192 Volume = {10},
193 Year = {1959}}
194
195 @article{Barojas73,
196 Author = {J. Barojas and D. Levesque and B. Quentrec},
197 Date-Added = {2006-09-03 14:32:02 -0400},
198 Date-Modified = {2006-09-03 14:34:00 -0400},
199 Journal = {Phys. Rev. A},
200 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Barojas_EulerSwitch_73.pdf},
201 Number = {3},
202 Pages = {1092-1105},
203 Title = {Simulation of Diatomic Homonuclear Liquids},
204 Volume = {7},
205 Year = {1973}}
206
207 @article{Mezei92,
208 Author = {M. Mezei},
209 Date-Added = {2006-08-28 07:48:49 -0400},
210 Date-Modified = {2006-08-28 07:50:59 -0400},
211 Doi = {10.1002/jcc.540130515},
212 Journal = {J. Comp. Chem.},
213 Number = {5},
214 Pages = {651-656},
215 Title = {Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water},
216 Volume = {13},
217 Year = {1992}}
218
219 @article{Pauling35,
220 Author = {L. Pauling},
221 Date-Added = {2006-08-27 22:01:49 -0400},
222 Date-Modified = {2006-08-27 22:03:59 -0400},
223 Journal = {J. Am. Chem. Soc.},
224 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ResidualEntropy/Pauling_ResidEntropy_33.pdf},
225 Pages = {2680-2684},
226 Title = {The Structure and Entropy of Ice and of Other Crystals with Some Randomness of Atomic Arrangement},
227 Volume = {57},
228 Year = {1935}}
229
230 @article{Nada03,
231 Author = {H. Nada and J.~P.~J.~M. {van der Eerden}},
232 Date-Added = {2006-08-27 21:44:08 -0400},
233 Date-Modified = {2006-08-27 21:47:37 -0400},
234 Doi = {10.1063/1.1562610},
235 Journal = {J. Chem. Phys.},
236 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Nada_6siteH2O_03.pdf},
237 Number = {16},
238 Pages = {7401-7413},
239 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}},
240 Volume = {118},
241 Year = {2003}}
242
243 @article{Kindt96,
244 Author = {J.~T. Kindt and C.~A. Schmuttenmaer},
245 Date-Added = {2006-08-27 13:55:26 -0400},
246 Date-Modified = {2006-08-27 13:56:35 -0400},
247 Journal = {J. Phys. Chem.},
248 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kindt_FarIRDielectricOfPolarLiquids_96.pdf},
249 Number = {24},
250 Pages = {10373-10379},
251 Title = {Far-Infrared Dielectric Properties of Polar Liquids Probed by Femtosecond Terahertz Pulse Spectroscopy},
252 Volume = {100},
253 Year = {1996}}
254
255 @article{Freddolino06,
256 Author = {P.~L. Freddolino and A.~S. Arkhipov and S.~B. Larson and A. McPherson and K. Schulten},
257 Date-Added = {2006-08-24 16:11:43 -0400},
258 Date-Modified = {2006-08-24 16:14:03 -0400},
259 Doi = {10.1016/j.str.2005.11.014},
260 Journal = {Structure},
261 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Freddolino_VirusSimulation_06.pdf},
262 Pages = {437-449},
263 Title = {Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus},
264 Volume = {14},
265 Year = {2006}}
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268 Author = {K.~T. Gillen and D.~C. Douglas and M.~J.~R. Hoch},
269 Date-Added = {2006-08-24 10:40:48 -0400},
270 Date-Modified = {2006-08-24 10:41:10 -0400},
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280 Date-Added = {2006-08-24 10:35:25 -0400},
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284 Year = 1984}
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290 Journal = {Physica},
291 Pages = {167-178},
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294 Year = 1966}
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297 Address = {Oxford},
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299 Date-Added = {2006-08-24 10:33:59 -0400},
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303 Year = 1969}
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306 Author = {R. Mills},
307 Date-Added = {2006-08-24 10:24:33 -0400},
308 Date-Modified = {2006-08-24 10:25:04 -0400},
309 Journal = jpc,
310 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Mills_Diffuse_73.pdf},
311 Number = 5,
312 Pages = {685-688},
313 Title = {Self-Diffusion in Normal and Heavy Water in the Range 1-45$^\circ$},
314 Volume = 77,
315 Year = 1973}
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322 Pages = {4643-4645},
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325 Year = 1964}
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329 Date-Added = {2006-08-24 10:21:10 -0400},
330 Date-Modified = {2006-08-24 10:22:49 -0400},
331 Journal = jcp,
332 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Badyal_ElectronDistributionInH2O_00.pdf},
333 Number = 21,
334 Pages = {9206-9208},
335 Title = {Electron distribution in water},
336 Volume = 112,
337 Year = 2000}
338
339 @article{Gubskaya02,
340 Author = {A.~V. Gubskaya and P.~G. Kusalik},
341 Date-Added = {2006-08-24 10:17:41 -0400},
342 Date-Modified = {2006-08-24 10:18:37 -0400},
343 Journal = jcp,
344 Number = 11,
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347 Volume = 117,
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351 Author = {M. Sprik},
352 Date-Added = {2006-08-24 10:10:41 -0400},
353 Date-Modified = {2006-08-24 10:17:06 -0400},
354 Journal = jcp,
355 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Sprik_HBondingAndStaticDielectricInH2O_91.pdf},
356 Number = 9,
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358 Title = {Hydrogen bonding and the static dielectric constant in liquid water},
359 Volume = 95,
360 Year = 1991}
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364 Date-Added = {2006-08-24 10:08:19 -0400},
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366 Journal = jcp,
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370 Volume = 117,
371 Year = 2002}
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375 Date-Added = {2006-08-24 10:03:48 -0400},
376 Date-Modified = {2006-08-24 10:09:05 -0400},
377 Journal = jcp,
378 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Ice_Simulations/Rahman_ProtonDistributionInIce_72.pdf},
379 Number = 9,
380 Pages = {4009-4017},
381 Title = {Proton Distribution in Ice and the \uppercase{K}irkwood Correlation Factor},
382 Volume = 57,
383 Year = 1972}
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385 @article{Bernal33,
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388 Date-Modified = {2006-08-24 09:59:43 -0400},
389 Journal = {J. Chem. Phys.},
390 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Bernal_TheoryOfWater_33.pdf},
391 Number = {8},
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394 Volume = {1},
395 Year = {1933}}
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397 @article{Hoover86,
398 Author = {W.~G. Hoover},
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406 Year = 1986}
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412 Doi = {10.1063/1.2206581},
413 Journal = {J. Chem. Phys.},
414 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_PairwiseSummationMethods_06.pdf},
415 Number = {23},
416 Pages = {234104(12)},
417 Rating = {5},
418 Read = {Yes},
419 Title = {Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics},
420 Volume = {124},
421 Year = {2006}}
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424 Author = {D.~J. Evans and S. Murad},
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430 Volume = 34,
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437 Doi = {10.1063/1.1605941},
438 Journal = {J. Chem. Phys.},
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452 Title = {Point multipoles in the \uppercase{E}wald summation (Revisited)},
453 Year = {1998}}
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456 Author = {A.~J. Stone},
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462 Year = {2002}}
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466 Date-Added = {2006-08-14 10:15:21 -0400},
467 Date-Modified = {2006-08-14 22:45:43 -0400},
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471 Year = {1967}}
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473 @article{Ryckaert77,
474 Author = {J.-P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
475 Date-Added = {2006-08-06 17:05:44 -0400},
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484 Year = {1977}}
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490 Journal = {Mol. Phys.},
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495 Year = {1982}}
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498 Author = {K. Laasonen and M. Sprik and M. Parrinello and R. Car},
499 Date-Added = {2006-08-02 08:23:46 -0400},
500 Date-Modified = {2006-08-02 13:09:18 -0400},
501 Journal = {J. Chem. Phys.},
502 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Laasonen_AbInitioLiquidWater_93.pdf},
503 Number = {11},
504 Pages = {9080-9089},
505 Title = {``{\it \uppercase{A}b initio}" liquid water},
506 Volume = {99},
507 Year = {1993}}
508
509 @article{Donchev06,
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511 Date-Added = {2006-08-02 08:15:11 -0400},
512 Date-Modified = {2006-08-02 08:16:16 -0400},
513 Doi = {www.pnas.org/cgi/doi/10.1073/pnas.0602982103},
514 Journal = {Proc. Natl. Acad. Sci. USA},
515 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Donchev_QuantumWater_06.pdf},
516 Number = {23},
517 Pages = {8613-8617},
518 Title = {Water properties from first principles: \uppercase{S}imulations by a general-purpose quantum mechanical polarizable force field},
519 Volume = {103},
520 Year = {2006}}
521
522 @article{Malmberg56,
523 Author = {G.~G. Malmberg and A.~A. Maryott},
524 Date-Added = {2006-08-01 17:19:00 -0400},
525 Date-Modified = {2006-08-02 13:16:04 -0400},
526 Journal = {J. Res. Natl. Bur. Stand.},
527 Number = {1},
528 Pages = {1-8},
529 Title = {Dielectric constant of Water from 0$^\circ$ to 100$^\circ$\uppercase{C}},
530 Volume = {56},
531 Year = {1956}}
532
533 @article{Neumann80,
534 Author = {M. Neumann and O. Steinhauser},
535 Date-Added = {2006-08-01 17:17:52 -0400},
536 Date-Modified = {2006-08-01 17:18:51 -0400},
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