ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/chrisDissertation/dissertation.bib
Revision: 3004
Committed: Mon Sep 18 20:32:11 2006 UTC (17 years, 11 months ago) by chrisfen
File size: 106318 byte(s)
Log Message:
updated plot and text on newer results

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