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root/group/trunk/chrisDissertation/dissertation.bib
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Proofed appendix. Final form unless there are later catches.

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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 2006-09-27 10:13:35 -0400
6
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8 %% Saved with string encoding Western (ASCII)
9
10
11 @string{acp = {Adv. Chem. Phys.}}
12
13 @string{ccp5 = {CCP5 Quarterly}}
14
15 @string{cp = {Chem. Phys.}}
16
17 @string{cpl = {Chem. Phys. Lett.}}
18
19 @string{jacs = {J. Am. Chem. Soc.}}
20
21 @string{jcc = {J. Comp. Chem.}}
22
23 @string{jcp = {J. Chem. Phys.}}
24
25 @string{jcop = {J. Comp. Phys.}}
26
27 @string{jml = {J. Mol. Liq.}}
28
29 @string{jpc = {J. Phys. Chem.}}
30
31 @string{jpca = {J. Phys. Chem. A}}
32
33 @string{jpcb = {J. Phys. Chem. B}}
34
35 @string{mp = {Mol. Phys.}}
36
37 @string{pams = {Proc. Am. Math Soc.}}
38
39 @string{pccp = {Phys. Chem. Chem. Phys.}}
40
41 @string{pnas = {Proc. Natl. Acad. Sci. USA}}
42
43 @string{pr = {Phys. Rev.}}
44
45 @string{pra = {Phys. Rev. A}}
46
47 @string{prb = {Phys. Rev. B}}
48
49 @string{pre = {Phys. Rev. E}}
50
51 @string{prl = {Phys. Rev. Lett.}}
52
53 @string{rmp = {Rev. Mod. Phys.}}
54
55
56 @book{Tolman38,
57 Address = {New York},
58 Author = {R.~C. Tolman},
59 Date-Added = {2006-09-21 15:37:16 -0400},
60 Date-Modified = {2006-09-21 15:41:28 -0400},
61 Publisher = {Oxford University Press, Inc.},
62 Title = {The Principles of Statistical Mechanics},
63 Year = {1938}}
64
65 @article{Beeman76,
66 Author = {D. Beeman},
67 Date-Added = {2006-09-20 14:44:19 -0400},
68 Date-Modified = {2006-09-20 14:45:33 -0400},
69 Journal = jcop,
70 Pages = {130-139},
71 Title = {Some Multistep Methods for Use in Molecular Dynamics Calculations},
72 Volume = {20},
73 Year = {1976}}
74
75 @inproceedings{Berendsen86,
76 Address = {North Holland, Amsterdam},
77 Author = {H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
78 Booktitle = {Molecular Dynamics Simulations of Statistical Mechanics Systems},
79 Date-Added = {2006-09-20 14:11:30 -0400},
80 Date-Modified = {2006-09-20 14:19:19 -0400},
81 Editor = {G. Ciccotti and W.~G. Hoover},
82 Pages = {43-65},
83 Series = {Proceedings of the 97th Int. ``Enrico Fermi" School of Physics},
84 Title = {Practical algorithms for dynamics simulations},
85 Year = {1986}}
86
87 @techreport{Gear66,
88 Address = {Argonne, IL},
89 Author = {C.~W. Gear},
90 Date-Added = {2006-09-20 14:00:35 -0400},
91 Date-Modified = {2006-09-20 14:05:03 -0400},
92 Institution = {Argonne National Laboratory},
93 Number = {ANL-7126},
94 Title = {The Numerical Integration of Ordinary Differential Equations of Various Orders},
95 Year = {1966}}
96
97 @article{Abascal05,
98 Author = {J.~L.~F. Abascal and E. Sanz and R. {Garc\'{i}a Fern\'{a}ndez} and C. Vega},
99 Date-Added = {2006-09-18 14:20:06 -0400},
100 Date-Modified = {2006-09-18 14:27:13 -0400},
101 Doi = {10.1063/1.1931662},
102 Journal = jcp,
103 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Abascal_Tip4p-Ice_05.pdf},
104 Number = {23},
105 Pages = {234511},
106 Title = {A potential model for the study of ices and amorphous water: \uppercase{TIP4P/I}ce},
107 Volume = {122},
108 Year = {2005}}
109
110 @article{Vega05,
111 Author = {C. Vega and E. Sanz and J.~L.~F. Abascal},
112 Date-Added = {2006-09-18 09:40:15 -0400},
113 Date-Modified = {2006-09-18 09:41:55 -0400},
114 Doi = {10.1063/1.1862245},
115 Journal = jcp,
116 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Vega_MeltTempModels_05.pdf},
117 Number = {11},
118 Pages = {114507},
119 Title = {The melting temperature of the most common models of water},
120 Volume = {122},
121 Year = {2005}}
122
123 @article{Harvey98,
124 Author = {S.~C. Harvey and R.~K.-Z. Tan and T.~E. {Cheatham III}},
125 Date-Added = {2006-09-07 00:53:34 -0400},
126 Date-Modified = {2006-09-07 00:55:37 -0400},
127 Journal = jcc,
128 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Harvey_FlyingIceCube_98.pdf},
129 Number = {7},
130 Pages = {726-740},
131 Title = {The Flying Ice Cube: \uppercase{V}elocity Rescaling in Molecular Dynamics Leads to Violation of Energy Equipartition},
132 Volume = {19},
133 Year = {1998}}
134
135 @article{Verlet68,
136 Author = {L. Verlet},
137 Date-Added = {2006-09-06 12:19:09 -0400},
138 Date-Modified = {2006-09-20 14:22:53 -0400},
139 Journal = pr,
140 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_EqCorrFunc_67.pdf},
141 Number = {1},
142 Pages = {201-214},
143 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{II. E}quilibrium Correlation Functions},
144 Volume = {165},
145 Year = {1968}}
146
147 @article{Verlet67,
148 Author = {L. Verlet},
149 Date-Added = {2006-09-06 12:16:19 -0400},
150 Date-Modified = {2006-09-20 14:22:43 -0400},
151 Journal = pr,
152 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_ClassicalFluids_67.pdf},
153 Number = {1},
154 Pages = {98-103},
155 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{I. T}hermodynamic Properties of \uppercase{L}ennard-\uppercase{J}ones Molecules},
156 Volume = {159},
157 Year = {1967}}
158
159 @article{Thompson83,
160 Author = {C.~J. Thompson},
161 Date-Added = {2006-09-06 11:59:49 -0400},
162 Date-Modified = {2006-09-06 12:02:07 -0400},
163 Journal = ccp5,
164 Pages = {20-28},
165 Title = {Use of neighbor lists in molecular dynamics},
166 Volume = {8},
167 Year = {1983}}
168
169 @article{Krautler01,
170 Author = {V. Kr\"{a}utler and W.~F. {van Gunsteren} and P.~H. H\"{u}nenberger},
171 Date-Added = {2006-09-04 00:17:15 -0400},
172 Date-Modified = {2006-09-04 00:29:36 -0400},
173 Journal = jcc,
174 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Krautler_FastSHAKE_01.pdf},
175 Number = {5},
176 Pages = {501-508},
177 Title = {A Fast \uppercase{SHAKE} Algorithm to Solve Distance Constraint Equations for Small Molecules in Molecular Dynamics Simulations},
178 Volume = {22},
179 Year = {2001}}
180
181 @article{Swope82,
182 Author = {W.~C. Swope and H.~C. Andersen and P.~H. Berens and K.~R. Wilson},
183 Date-Added = {2006-09-03 21:47:42 -0400},
184 Date-Modified = {2006-09-03 21:50:26 -0400},
185 Journal = jcp,
186 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Swope_VelocityVerlet_82.pdf},
187 Number = {1},
188 Pages = {637-649},
189 Title = {A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: \uppercase{A}pplication to small water clusters},
190 Volume = {76},
191 Year = {1982}}
192
193 @article{Trotter59,
194 Author = {H.~F. Trotter},
195 Date-Added = {2006-09-03 18:05:35 -0400},
196 Date-Modified = {2006-09-03 18:07:32 -0400},
197 Journal = pams,
198 Pages = {545-551},
199 Title = {On the product of Semi-Groups of Operators},
200 Volume = {10},
201 Year = {1959}}
202
203 @article{Barojas73,
204 Author = {J. Barojas and D. Levesque and B. Quentrec},
205 Date-Added = {2006-09-03 14:32:02 -0400},
206 Date-Modified = {2006-09-03 14:34:00 -0400},
207 Journal = pra,
208 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Barojas_EulerSwitch_73.pdf},
209 Number = {3},
210 Pages = {1092-1105},
211 Title = {Simulation of Diatomic Homonuclear Liquids},
212 Volume = {7},
213 Year = {1973}}
214
215 @article{Mezei92,
216 Author = {M. Mezei},
217 Date-Added = {2006-08-28 07:48:49 -0400},
218 Date-Modified = {2006-08-28 07:50:59 -0400},
219 Doi = {10.1002/jcc.540130515},
220 Journal = jcc,
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224 Volume = {13},
225 Year = {1992}}
226
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228 Author = {L. Pauling},
229 Date-Added = {2006-08-27 22:01:49 -0400},
230 Date-Modified = {2006-08-27 22:03:59 -0400},
231 Journal = jacs,
232 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ResidualEntropy/Pauling_ResidEntropy_33.pdf},
233 Pages = {2680-2684},
234 Title = {The Structure and Entropy of Ice and of Other Crystals with Some Randomness of Atomic Arrangement},
235 Volume = {57},
236 Year = {1935}}
237
238 @article{Nada03,
239 Author = {H. Nada and J.~P.~J.~M. {van der Eerden}},
240 Date-Added = {2006-08-27 21:44:08 -0400},
241 Date-Modified = {2006-08-27 21:47:37 -0400},
242 Doi = {10.1063/1.1562610},
243 Journal = jcp,
244 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Nada_6siteH2O_03.pdf},
245 Number = {16},
246 Pages = {7401-7413},
247 Title = {An intermolecular potential model for the simulation of ice and water near the melting point: \uppercase{A} six-site model of \uppercase{H}$_2$\uppercase{O}},
248 Volume = {118},
249 Year = {2003}}
250
251 @article{Kindt96,
252 Author = {J.~T. Kindt and C.~A. Schmuttenmaer},
253 Date-Added = {2006-08-27 13:55:26 -0400},
254 Date-Modified = {2006-08-27 13:56:35 -0400},
255 Journal = jpc,
256 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kindt_FarIRDielectricOfPolarLiquids_96.pdf},
257 Number = {24},
258 Pages = {10373-10379},
259 Title = {Far-Infrared Dielectric Properties of Polar Liquids Probed by Femtosecond Terahertz Pulse Spectroscopy},
260 Volume = {100},
261 Year = {1996}}
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266 Date-Modified = {2006-08-24 16:14:03 -0400},
267 Doi = {10.1016/j.str.2005.11.014},
268 Journal = {Structure},
269 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Freddolino_VirusSimulation_06.pdf},
270 Pages = {437-449},
271 Title = {Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus},
272 Volume = {14},
273 Year = {2006}}
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278 Date-Modified = {2006-08-24 10:41:10 -0400},
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292 Year = 1984}
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299 Pages = {167-178},
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311 Year = 1969}
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316 Date-Modified = {2006-08-24 10:25:04 -0400},
317 Journal = jpc,
318 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Mills_Diffuse_73.pdf},
319 Number = 5,
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322 Volume = 77,
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337 Date-Added = {2006-08-24 10:21:10 -0400},
338 Date-Modified = {2006-08-24 10:22:49 -0400},
339 Journal = jcp,
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344 Volume = 112,
345 Year = 2000}
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355 Volume = 117,
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359 Author = {M. Sprik},
360 Date-Added = {2006-08-24 10:10:41 -0400},
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362 Journal = jcp,
363 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Sprik_HBondingAndStaticDielectricInH2O_91.pdf},
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368 Year = 1991}
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383 Date-Added = {2006-08-24 10:03:48 -0400},
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397 Journal = jcp,
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479 Year = {1967}}
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507 Date-Added = {2006-08-02 08:23:46 -0400},
508 Date-Modified = {2006-08-02 13:09:18 -0400},
509 Journal = jcp,
510 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Laasonen_AbInitioLiquidWater_93.pdf},
511 Number = {11},
512 Pages = {9080-9089},
513 Title = {``{\it \uppercase{A}b initio}" liquid water},
514 Volume = {99},
515 Year = {1993}}
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519 Date-Added = {2006-08-02 08:15:11 -0400},
520 Date-Modified = {2006-08-02 08:16:16 -0400},
521 Doi = {www.pnas.org/cgi/doi/10.1073/pnas.0602982103},
522 Journal = pnas,
523 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Donchev_QuantumWater_06.pdf},
524 Number = {23},
525 Pages = {8613-8617},
526 Title = {Water properties from first principles: \uppercase{S}imulations by a general-purpose quantum mechanical polarizable force field},
527 Volume = {103},
528 Year = {2006}}
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531 Author = {G.~G. Malmberg and A.~A. Maryott},
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539 Year = {1956}}
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541 @article{Neumann80,
542 Author = {M. Neumann and O. Steinhauser},
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554 Date-Added = {2006-08-01 17:16:51 -0400},
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567 Journal = {J. Chem. Eng. Data},
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569 Number = {1},
570 Pages = {91-105},
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578 Date-Modified = {2006-08-02 13:16:50 -0400},
579 Journal = {J. Phys. Chem. Ref. Data},
580 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Wagner_ThermodynamicPropertiesOfH2O_03.pdf},
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585 Year = {2002}}
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600 Date-Added = {2006-07-31 10:19:17 -0400},
601 Date-Modified = {2006-08-02 13:17:58 -0400},
602 Journal = jcp,
603 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/DielectricConst./Neumann_H2ODielConst_85.pdf},
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614 Date-Modified = {2006-07-30 14:53:08 -0400},
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620 Year = {2000}}
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625 Date-Modified = {2006-07-21 11:44:44 -0400},
626 Journal = jcp,
627 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayRadial_2000.pdf},
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634 @book{CRC80,
635 Address = {Boca Raton, FL},
636 Date-Added = {2006-07-21 09:20:17 -0400},
637 Date-Modified = {2006-07-21 09:20:17 -0400},
638 Edition = 60,
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646 Date-Added = {2006-07-20 15:28:29 -0400},
647 Date-Modified = {2006-07-20 15:29:45 -0400},
648 Doi = {10.1021/jp062700h},
649 Journal = jpcb,
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652 Year = {2006}}
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654 @article{Weis06,
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656 Date-Added = {2006-07-20 15:22:45 -0400},
657 Date-Modified = {2006-07-20 15:24:22 -0400},
658 Doi = {10.1063/1.2215614},
659 Journal = jcp,
660 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Weis_OrientationalOrderHardSphereDipole_06.pdf},
661 Number = {3},
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667 @article{Rick04,
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669 Date-Added = {2006-07-18 10:49:48 -0400},
670 Date-Modified = {2006-08-19 19:34:36 -0400},
671 Doi = {10.1063/1.1652434},
672 Journal = jcp,
673 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Rick_TIP5P-E_04.pdf},
674 Number = {13},
675 Pages = {6085-6093},
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678 Year = {2004}}
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680 @article{Horn04,
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682 Date-Added = {2006-07-18 10:18:42 -0400},
683 Date-Modified = {2006-07-18 14:21:48 -0400},
684 Doi = {10.1063/1.1683075},
685 Journal = jcp,
686 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Horn_TIP4P-Ew_04.pdf},
687 Number = {20},
688 Pages = {9665-9678},
689 Title = {Development of an improved four-site water model for biomolecular simulations: \uppercase{TIP4P-E}w},
690 Volume = {120},
691 Year = {2004}}
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693 @article{Brodka04,
694 Author = {A. Br\'{o}dka},
695 Date-Added = {2006-04-26 09:41:52 -0400},
696 Date-Modified = {2006-07-18 14:29:43 -0400},
697 Doi = {10.1016/j.cplett.2004.10.086},
698 Journal = cpl,
699 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
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710 Journal = jcp,
711 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
712 Number = {6},
713 Pages = {2503-2512},
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830 Year = {1989}}
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871 Journal = jcp,
872 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
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877 Year = {1999}}
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