ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/chrisDissertation/dissertation.bib
Revision: 3029
Committed: Wed Sep 27 14:43:49 2006 UTC (17 years, 9 months ago) by chrisfen
File size: 106794 byte(s)
Log Message:
Proofed appendix. Final form unless there are later catches.

File Contents

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