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root/group/trunk/chrisDissertation/dissertation.bib
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# User Rev Content
1 chrisfen 2987 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3    
4    
5 chrisfen 3016 %% Created for Chris Fennell at 2006-09-21 15:41:30 -0400
6 chrisfen 2987
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 chrisfen 3001 @string{jcc = {J. Comp. Chem.}}
20 chrisfen 2987
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 chrisfen 3016 @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 chrisfen 3004 @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 chrisfen 3001 @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 chrisfen 3016 Date-Modified = {2006-09-20 14:22:53 -0400},
131 chrisfen 3001 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 chrisfen 3016 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{II. E}quilibrium Correlation Functions},
136 chrisfen 3001 Volume = {165},
137     Year = {1968}}
138    
139     @article{Verlet67,
140     Author = {L. Verlet},
141     Date-Added = {2006-09-06 12:16:19 -0400},
142 chrisfen 3016 Date-Modified = {2006-09-20 14:22:43 -0400},
143 chrisfen 3001 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 chrisfen 3016 Title = {Computer ``Experiments" on Classical Fluids. \uppercase{I. T}hermodynamic Properties of \uppercase{L}ennard-\uppercase{J}ones Molecules},
148 chrisfen 3001 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 chrisfen 2987 @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},
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253     Year = {1996}}
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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},
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266    
267     @article{Gillen72,
268     Author = {K.~T. Gillen and D.~C. Douglas and M.~J.~R. Hoch},
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280     Date-Added = {2006-08-24 10:35:25 -0400},
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299     Date-Added = {2006-08-24 10:33:59 -0400},
300     Date-Modified = {2006-08-24 10:33:59 -0400},
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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},
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315     Year = 1973}
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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},
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355     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Sprik_HBondingAndStaticDielectricInH2O_91.pdf},
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438     Journal = {J. Chem. Phys.},
439     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Aguado_MultipoleEwald_03.pdf},
440     Number = {14},
441     Pages = {7471-7483},
442     Title = {Ewald summation of electrostatic multipole interactions up to the quadrupolar level},
443     Volume = {119},
444     Year = {2003}}
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453     Year = {1998}}
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462     Year = {2002}}
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474     Author = {J.-P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
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