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# User Rev Content
1 chrisfen 2594 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3 chrisfen 2575
4    
5 chrisfen 2629 %% Created for Chris Fennell at 2006-03-15 21:43:19 -0500
6 chrisfen 2575
7    
8 chrisfen 2594 %% Saved with string encoding Western (ASCII)
9 chrisfen 2575
10    
11 chrisfen 2594 @STRING{acp = "Adv. Chem. Phys."}
12 chrisfen 2575
13 chrisfen 2594 @STRING{cp = "Chem. Phys."}
14 chrisfen 2575
15 chrisfen 2594 @STRING{cpl = "Chem. Phys. Lett."}
16 chrisfen 2575
17 chrisfen 2594 @STRING{jacs = "J. Am. Chem. Soc."}
18 chrisfen 2575
19 chrisfen 2594 @STRING{jcc = "J. Comput. Chem."}
20 chrisfen 2575
21 chrisfen 2594 @STRING{jcp = "J. Chem. Phys."}
22 chrisfen 2575
23 chrisfen 2594 @STRING{jml = "J. Mol. Liq."}
24 chrisfen 2575
25 chrisfen 2594 @STRING{jpc = "J. Phys. Chem."}
26 chrisfen 2575
27 chrisfen 2594 @STRING{jpca = "J. Phys. Chem. A"}
28 chrisfen 2575
29 chrisfen 2594 @STRING{jpcb = "J. Phys. Chem. B"}
30 chrisfen 2575
31 chrisfen 2594 @STRING{mp = "Mol. Phys."}
32 chrisfen 2575
33 chrisfen 2594 @STRING{pccp = "Phys. Chem. Chem. Phys."}
34 chrisfen 2575
35 chrisfen 2594 @STRING{pnas = "Proc. Natl. Acad. Sci. USA"}
36 chrisfen 2575
37 chrisfen 2594 @STRING{pra = "Phys. Rev. A"}
38 chrisfen 2575
39 chrisfen 2594 @STRING{prb = "Phys. Rev. B"}
40 chrisfen 2575
41 chrisfen 2594 @STRING{pre = "Phys. Rev. E"}
42 chrisfen 2575
43 chrisfen 2594 @STRING{prl = "Phys. Rev. Lett."}
44 chrisfen 2575
45 chrisfen 2594 @STRING{rmp = "Rev. Mod. Phys."}
46 chrisfen 2575
47    
48 chrisfen 2629 @article{Barker73,
49     Author = {J.~A. Barker and R.~O. Watts },
50     Date-Added = {2006-03-15 18:58:17 -0500},
51     Date-Modified = {2006-03-15 21:17:31 -0500},
52     Journal = {Mol. Phys.},
53     Pages = {789=792},
54     Title = {Monte Carlo studies of the dielectric properties of water-like models},
55     Volume = {26},
56     Year = {1973}}
57    
58     @article{Adams79,
59     Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
60     Date-Added = {2006-03-15 17:46:36 -0500},
61     Date-Modified = {2006-03-15 17:48:04 -0500},
62     Journal = {Mol. Phys.},
63     Number = {2},
64     Pages = {387-400},
65     Title = {The computer simulation of polar liquids},
66     Volume = {38},
67     Year = {1979}}
68    
69     @article{Rahman71,
70     Author = {A. Rahman and F.~H. Stillinger},
71     Date-Added = {2006-03-15 17:04:53 -0500},
72     Date-Modified = {2006-03-15 17:07:29 -0500},
73     Journal = {J. Chem. Phys.},
74     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
75     Month = {October},
76     Number = {7},
77     Pages = {3336-3359},
78     Title = {Molecular Dynamics Study of Liquid Water},
79     Volume = {55},
80     Year = {1971}}
81    
82     @article{Andrea83,
83     Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
84     Date-Added = {2006-03-15 15:16:12 -0500},
85     Date-Modified = {2006-03-15 15:18:10 -0500},
86     Journal = {J. Chem. Phys.},
87     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
88     Number = {9},
89     Pages = {4576-4584},
90     Title = {The role of long ranged forces in determining the structure and properties of liquid water},
91     Volume = {79},
92     Year = {1983}}
93    
94 chrisfen 2612 @article{Brush66,
95     Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
96     Date-Added = {2006-03-13 16:55:39 -0500},
97     Date-Modified = {2006-03-13 17:01:15 -0500},
98     Journal = {J. Chem. Phys.},
99     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
100     Month = {September},
101     Number = {6},
102     Pages = {2102-2118},
103     Title = {Monte Carlo Study of a One-Component Plasma. I},
104     Volume = {45},
105     Year = {1966}}
106    
107     @article{Ewald21,
108     Author = {P.~P. Ewald},
109     Date-Added = {2006-03-13 13:32:04 -0500},
110     Date-Modified = {2006-03-13 13:32:55 -0500},
111     Journal = {Ann. Physik},
112     Pages = {253},
113     Volume = {64},
114     Year = {1921}}
115    
116     @article{Jones56,
117     Author = {R.~E. Jones and D.~H. Templeton},
118     Date-Added = {2006-03-13 13:25:58 -0500},
119     Date-Modified = {2006-03-13 13:27:15 -0500},
120     Journal = {J. Chem. Phys.},
121     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
122     Number = {5},
123     Pages = {1062-1063},
124     Title = {Optimum Atomic Shape for Bertaut Series},
125     Volume = {25},
126     Year = {1956}}
127    
128     @article{Heyes81,
129     Author = {D.~M. Heyes},
130     Date-Added = {2006-03-13 13:12:45 -0500},
131     Date-Modified = {2006-03-13 13:14:27 -0500},
132     Journal = {J. Chem. Phys.},
133     Keywords = {Empty Keywords},
134     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
135     Number = {3},
136     Pages = {1924-1929},
137     Title = {Electrostatic potentials and fields in infinite point charge lattices},
138     Volume = {74},
139     Year = {1981}}
140    
141 chrisfen 2610 @article{Steinbach94,
142     Author = {P.~J. Steinbach and B.~R. Brooks},
143     Date-Added = {2006-03-12 19:26:45 -0500},
144     Date-Modified = {2006-03-12 19:29:43 -0500},
145     Doi = {10.1002/jcc.540150702},
146     Journal = {J. Comput. Chem.},
147     Number = {7},
148     Pages = {667-683},
149     Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
150     Volume = {15},
151     Year = {1994}}
152    
153 chrisfen 2609 @article{deLeeuw80,
154     Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
155     Date-Added = {2006-03-07 10:26:31 -0500},
156     Date-Modified = {2006-03-07 10:30:11 -0500},
157     Journal = {Proc. R. Soc. London Ser. A},
158     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
159     Number = {1752},
160     Pages = {27-56},
161     Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
162     Volume = {373},
163     Year = {1980}}
164    
165 chrisfen 2601 @article{Essmann95,
166     Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
167     Date-Added = {2006-03-05 12:25:25 -0500},
168     Date-Modified = {2006-03-05 12:29:07 -0500},
169     Journal = {J. Chem. Phys.},
170     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
171     Number = {19},
172     Pages = {8577-8593},
173 chrisfen 2610 Title = {A smooth particle mesh Ewald method},
174 chrisfen 2601 Volume = {103},
175     Year = {1995}}
176    
177 chrisfen 2595 @article{Kast03,
178     Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
179     Date-Added = {2006-02-18 16:47:26 -0500},
180     Date-Modified = {2006-02-18 16:51:25 -0500},
181     Journal = {Chem. Phys. Lett.},
182     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
183     Pages = {398-404},
184     Title = {Integral equation theory for correcting truncation errors in molecular simulations},
185     Volume = {367},
186     Year = {2003}}
187    
188 chrisfen 2594 @article{Tobias01,
189     Author = {D.~J. Tobias},
190     Date-Added = {2006-02-15 11:28:58 -0500},
191     Date-Modified = {2006-02-15 11:32:16 -0500},
192     Journal = {Curr. Opin. Struct. Biol.},
193     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
194     Pages = {253-261},
195     Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
196     Volume = {11},
197     Year = {2001}}
198 chrisfen 2575
199 chrisfen 2594 @article{Zahn02,
200     Author = {D. Zahn and B. Schilling and S.~M. Kast},
201     Date-Added = {2006-02-15 09:21:27 -0500},
202     Date-Modified = {2006-02-15 09:24:07 -0500},
203     Journal = {J. Phys. Chem. B},
204     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
205     Number = {41},
206     Pages = {10725-10732},
207 chrisfen 2595 Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
208 chrisfen 2594 Volume = {106},
209     Year = {2002}}
210 chrisfen 2575
211 chrisfen 2594 @article{Wolf99,
212     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
213     Date-Added = {2006-02-15 09:09:39 -0500},
214     Date-Modified = {2006-02-15 09:25:30 -0500},
215     Journal = {J. Chem. Phys.},
216     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
217     Number = {17},
218     Pages = {8255-8282},
219     Rating = {0},
220     Read = {No},
221 chrisfen 2595 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
222 chrisfen 2594 Volume = {110},
223     Year = {1999}}
224 chrisfen 2575
225 chrisfen 2594 @book{Berne90,
226     Address = {Malabar, Florida},
227     Author = {B.~J. Berne and R. Pecora},
228     Publisher = {Robert E. Krieger Publishing Company, Inc.},
229     Title = {Dynamic Light Scattering},
230     Year = 1990}
231 chrisfen 2575
232 chrisfen 2594 @article{Evans77,
233     Author = {D.~J. Evans},
234     Journal = {Mol. Phys.},
235     Pages = {317-325},
236     Title = {On the representation of orientation space},
237     Volume = 34,
238     Year = 1977}
239 chrisfen 2575
240 chrisfen 2594 @article{Tuckerman92,
241     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
242     Journal = jcp,
243     Pages = {1990-2001},
244     Title = {Reversible multiple time scale molecular dynamics},
245     Volume = 97,
246     Year = 1992}
247 chrisfen 2575
248 chrisfen 2594 @book{Hansen86,
249     Address = {London},
250     Author = {J.~P. Hansen and I.~R. McDonald},
251     Chapter = 7,
252     Pages = {199-206},
253     Publisher = {Academic Press},
254     Title = {Theory of Simple Liquids},
255     Year = 1986}
256 chrisfen 2575
257 chrisfen 2594 @article{Angelani98,
258     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
259     Journal = prl,
260     Number = 21,
261     Pages = {4648-4651},
262     Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
263     Volume = 81,
264     Year = 1998}
265 chrisfen 2575
266 chrisfen 2594 @article{Stillinger82,
267     Author = {F.~H. Stillinger and T.~A. Weber},
268     Journal = pra,
269     Number = 2,
270     Pages = {978-989},
271     Title = {Hidden structure in liquids},
272     Volume = 25,
273     Year = 1982}
274 chrisfen 2575
275 chrisfen 2594 @article{Stillinger83,
276     Author = {F.~H. Stillinger and T.~A. Weber},
277     Journal = pra,
278     Number = 4,
279     Pages = {2408-2416},
280     Title = {Dynamics of structural transitions in liquids},
281     Volume = 28,
282     Year = 1983}
283 chrisfen 2575
284 chrisfen 2594 @article{Weber84,
285     Author = {T.~A. Weber and F.~H. Stillinger},
286     Journal = jcp,
287     Number = 6,
288     Pages = {2742-2746},
289     Title = {The effect of density on the inherent structure in liquids},
290     Volume = 80,
291     Year = 1984}
292 chrisfen 2575
293 chrisfen 2594 @article{Stillinger85,
294     Author = {F.~H. Stillinger and T.~A. Weber},
295     Journal = jcp,
296     Number = 9,
297     Pages = {4767-4775},
298     Title = {Inherent structure theory of liquids in the hard-sphere limit},
299     Volume = 83,
300     Year = 1985}
301 chrisfen 2575
302 chrisfen 2594 @article{Stillinger98,
303     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
304     Journal = {Nature},
305     Pages = {554-557},
306     Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
307     Volume = 393,
308     Year = 1998}
309 chrisfen 2575
310 chrisfen 2594 @article{Parkhurst75a,
311     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
312     Journal = jcp,
313     Number = 6,
314     Pages = {2698-2704},
315     Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
316     Volume = 63,
317     Year = 1975}
318 chrisfen 2575
319 chrisfen 2594 @article{Parkhurst75b,
320     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
321     Journal = jcp,
322     Number = 6,
323     Pages = {2705-2709},
324     Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
325     Volume = 63,
326     Year = 1975}
327 chrisfen 2575
328 chrisfen 2594 @article{Forester97,
329     Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
330     Journal = {J. Chem. Soc. - Faraday Transactions},
331     Pages = {613-619},
332     Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
333     Volume = 93,
334     Year = 1997}
335 chrisfen 2575
336 chrisfen 2594 @article{Tieleman98,
337     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
338     Journal = {Biophys. J.},
339     Pages = {2786-2801},
340     Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
341     Volume = 74,
342     Year = 1998}
343 chrisfen 2575
344 chrisfen 2594 @article{Cascales98,
345     Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
346     Journal = {J. Phys. Chem. B},
347     Pages = {625-631},
348     Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
349     Volume = 102,
350     Year = 1998}
351 chrisfen 2575
352 chrisfen 2594 @article{Bassolino95,
353     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
354     Journal = {J. Am. Chem. Soc.},
355     Pages = {4118-4129},
356     Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
357     Volume = 117,
358     Year = 1995}
359 chrisfen 2575
360 chrisfen 2594 @article{Alper95,
361     Author = {H.~E. Alper and T.~R. Stouch},
362     Journal = {J. Phys. Chem.},
363     Pages = {5724-5731},
364     Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
365     Volume = 99,
366     Year = 1995}
367 chrisfen 2575
368 chrisfen 2594 @article{Sok92,
369     Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
370     Journal = {J. Chem. Phys.},
371     Pages = {4699-4704},
372     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
373     Volume = 96,
374     Year = 1992}
375 chrisfen 2575
376 chrisfen 2594 @article{Rabani99,
377     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
378     Journal = prl,
379     Pages = {3649},
380     Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
381     Volume = 82,
382     Year = {1999}}
383 chrisfen 2575
384 chrisfen 2594 @article{Rabani97,
385     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
386     Journal = {J. Chem. Phys.},
387     Pages = {6867-6876},
388     Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
389     Volume = 107,
390     Year = 1997}
391 chrisfen 2575
392 chrisfen 2594 @article{Gezelter99,
393     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
394     Journal = jcp,
395     Pages = 3444,
396     Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
397     Volume = 110,
398     Year = 1999}
399 chrisfen 2575
400 chrisfen 2594 @article{Gezelter98,
401     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
402     Date-Modified = {2006-02-15 10:18:42 -0500},
403     Journal = jcp,
404     Pages = 4695,
405     Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
406     Volume = 109,
407     Year = 1998}
408 chrisfen 2575
409 chrisfen 2594 @article{Gezelter97,
410     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
411     Journal = jcp,
412     Pages = 4618,
413     Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
414     Volume = 107,
415     Year = 1997}
416 chrisfen 2575
417 chrisfen 2594 @article{Zwanzig83,
418     Author = {R. Zwanzig},
419     Journal = jcp,
420     Pages = {4507-4508},
421     Title = {On the relation between self-diffusion and viscosity of liquids},
422     Volume = 79,
423     Year = 1983}
424 chrisfen 2575
425 chrisfen 2594 @article{Zwanzig88,
426     Author = {R. Zwanzig},
427     Journal = {Proc. Natl. Acad. Sci. USA},
428     Pages = 2029,
429     Title = {Diffusion in rough potential},
430     Volume = 85,
431     Year = 1988}
432 chrisfen 2575
433 chrisfen 2594 @article{Stillinger95,
434     Author = {F.~H. Stillinger},
435     Journal = {Science},
436     Pages = {1935-1939},
437     Title = {A Topographic View of Supercooled Liquids and Glass Formation},
438     Volume = 267,
439     Year = 1995}
440 chrisfen 2575
441 chrisfen 2594 @incollection{Angell85,
442     Address = {Springfield, VA},
443     Author = {C.~A. Angell},
444     Booktitle = {Relaxations in Complex Systems},
445     Editor = {K.~Ngai and G.~B. Wright},
446     Pages = 1,
447     Publisher = {National Technical Information Service, U.S. Department of Commerce},
448     Title = {unknown},
449     Year = 1985}
450 chrisfen 2575
451 chrisfen 2594 @article{Bembenek96,
452     Author = {S.~D. Bembenek and B.~B. Laird},
453     Journal = jcp,
454     Pages = 5199,
455     Title = {The role of localization in glasses and supercooled liquids},
456     Volume = 104,
457     Year = 1996}
458 chrisfen 2575
459 chrisfen 2594 @article{Sun97a,
460     Author = {X. Sun and W.~H. Miller},
461     Date-Modified = {2006-02-15 10:33:35 -0500},
462     Journal = jcp,
463     Pages = 6346,
464     Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
465     Volume = 106,
466     Year = 1997}
467 chrisfen 2575
468 chrisfen 2594 @article{Spath96,
469     Author = {B.~W. Spath and W.~H. Miller},
470     Journal = jcp,
471     Pages = 95,
472     Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
473     Volume = 104,
474     Year = 1996}
475 chrisfen 2575
476 chrisfen 2594 @book{Warshel91,
477     Address = {New York},
478     Author = {Arieh Warshel},
479     Publisher = {Wiley},
480     Title = {Computer modeling of chemical reactions in enzymes and solutions},
481     Year = 1991}
482 chrisfen 2575
483 chrisfen 2594 @article{Vuilleumier97,
484     Author = {Rodolphe Vuilleumier and Daniel Borgis},
485     Journal = jpc,
486     Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
487     Volume = {in press},
488     Year = 1997}
489 chrisfen 2575
490 chrisfen 2594 @article{Kob95a,
491     Author = {W. Kob and H.~C. Andersen},
492     Journal = pre,
493     Pages = {4626-4641},
494     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
495     Volume = 51,
496     Year = 1995}
497 chrisfen 2575
498 chrisfen 2594 @article{Kob95b,
499     Author = {W. Kob and H.~C. Andersen},
500     Journal = pre,
501     Pages = {4134-4153},
502     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
503     Volume = 52,
504     Year = 1995}
505 chrisfen 2575
506 chrisfen 2594 @inproceedings{Gotze89,
507     Address = {Amsterdam},
508     Author = {W. G{\"{o}}tze},
509     Booktitle = {Liquids, Freezing and Glass Transitions},
510     Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
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