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root/group/trunk/electrostaticMethodsPaper/electrostaticMethods.bib
Revision: 2630
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more citations and some spell checking

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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 2630 %% Created for Chris Fennell at 2006-03-16 10:02:01 -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 2630 @article{Weber00,
49     Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
50     Date-Added = {2006-03-16 09:49:22 -0500},
51     Date-Modified = {2006-03-16 09:51:17 -0500},
52     Doi = {10.1021/jp9937757},
53     Journal = {J. Phys. Chem. B},
54     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
55     Number = {15},
56     Pages = {3668-3675},
57     Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
58     Volume = {104},
59     Year = {2000}}
60    
61     @article{Hunenberger99,
62     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
63     Date-Added = {2006-03-16 09:45:10 -0500},
64     Date-Modified = {2006-03-16 09:49:15 -0500},
65     Journal = {Biophys. Chem.},
66     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
67     Pages = {69-88},
68     Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
69     Volume = {78},
70     Year = {1999}}
71    
72     @article{Petersen95,
73     Author = {H.~G. Petersen},
74     Date-Added = {2006-03-16 08:43:02 -0500},
75     Date-Modified = {2006-03-16 08:44:32 -0500},
76     Journal = {J. Chem. Phys.},
77     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
78     Month = {September},
79     Number = {9},
80     Pages = {3668-3679},
81     Title = {Accuracy and efficiency of the particle mesh Ewald method},
82     Volume = {103},
83     Year = {1995}}
84    
85     @article{Luty95,
86     Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
87     Date-Added = {2006-03-16 08:39:13 -0500},
88     Date-Modified = {2006-03-16 08:41:15 -0500},
89     Journal = {J. Chem. Phys.},
90     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
91     Number = {8},
92     Pages = {3014-3021},
93     Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
94     Volume = {103},
95     Year = {1995}}
96    
97 chrisfen 2629 @article{Barker73,
98     Author = {J.~A. Barker and R.~O. Watts },
99     Date-Added = {2006-03-15 18:58:17 -0500},
100     Date-Modified = {2006-03-15 21:17:31 -0500},
101     Journal = {Mol. Phys.},
102     Pages = {789=792},
103     Title = {Monte Carlo studies of the dielectric properties of water-like models},
104     Volume = {26},
105     Year = {1973}}
106    
107     @article{Adams79,
108     Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
109     Date-Added = {2006-03-15 17:46:36 -0500},
110     Date-Modified = {2006-03-15 17:48:04 -0500},
111     Journal = {Mol. Phys.},
112     Number = {2},
113     Pages = {387-400},
114     Title = {The computer simulation of polar liquids},
115     Volume = {38},
116     Year = {1979}}
117    
118     @article{Rahman71,
119     Author = {A. Rahman and F.~H. Stillinger},
120     Date-Added = {2006-03-15 17:04:53 -0500},
121     Date-Modified = {2006-03-15 17:07:29 -0500},
122     Journal = {J. Chem. Phys.},
123     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
124     Month = {October},
125     Number = {7},
126     Pages = {3336-3359},
127     Title = {Molecular Dynamics Study of Liquid Water},
128     Volume = {55},
129     Year = {1971}}
130    
131     @article{Andrea83,
132     Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
133     Date-Added = {2006-03-15 15:16:12 -0500},
134     Date-Modified = {2006-03-15 15:18:10 -0500},
135     Journal = {J. Chem. Phys.},
136     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
137     Number = {9},
138     Pages = {4576-4584},
139     Title = {The role of long ranged forces in determining the structure and properties of liquid water},
140     Volume = {79},
141     Year = {1983}}
142    
143 chrisfen 2612 @article{Brush66,
144     Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
145     Date-Added = {2006-03-13 16:55:39 -0500},
146     Date-Modified = {2006-03-13 17:01:15 -0500},
147     Journal = {J. Chem. Phys.},
148     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
149     Month = {September},
150     Number = {6},
151     Pages = {2102-2118},
152     Title = {Monte Carlo Study of a One-Component Plasma. I},
153     Volume = {45},
154     Year = {1966}}
155    
156     @article{Ewald21,
157     Author = {P.~P. Ewald},
158     Date-Added = {2006-03-13 13:32:04 -0500},
159     Date-Modified = {2006-03-13 13:32:55 -0500},
160     Journal = {Ann. Physik},
161     Pages = {253},
162     Volume = {64},
163     Year = {1921}}
164    
165     @article{Jones56,
166     Author = {R.~E. Jones and D.~H. Templeton},
167     Date-Added = {2006-03-13 13:25:58 -0500},
168     Date-Modified = {2006-03-13 13:27:15 -0500},
169     Journal = {J. Chem. Phys.},
170     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
171     Number = {5},
172     Pages = {1062-1063},
173     Title = {Optimum Atomic Shape for Bertaut Series},
174     Volume = {25},
175     Year = {1956}}
176    
177     @article{Heyes81,
178     Author = {D.~M. Heyes},
179     Date-Added = {2006-03-13 13:12:45 -0500},
180     Date-Modified = {2006-03-13 13:14:27 -0500},
181     Journal = {J. Chem. Phys.},
182     Keywords = {Empty Keywords},
183     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
184     Number = {3},
185     Pages = {1924-1929},
186     Title = {Electrostatic potentials and fields in infinite point charge lattices},
187     Volume = {74},
188     Year = {1981}}
189    
190 chrisfen 2610 @article{Steinbach94,
191     Author = {P.~J. Steinbach and B.~R. Brooks},
192     Date-Added = {2006-03-12 19:26:45 -0500},
193     Date-Modified = {2006-03-12 19:29:43 -0500},
194     Doi = {10.1002/jcc.540150702},
195     Journal = {J. Comput. Chem.},
196     Number = {7},
197     Pages = {667-683},
198     Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
199     Volume = {15},
200     Year = {1994}}
201    
202 chrisfen 2609 @article{deLeeuw80,
203     Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
204     Date-Added = {2006-03-07 10:26:31 -0500},
205     Date-Modified = {2006-03-07 10:30:11 -0500},
206     Journal = {Proc. R. Soc. London Ser. A},
207     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
208     Number = {1752},
209     Pages = {27-56},
210     Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
211     Volume = {373},
212     Year = {1980}}
213    
214 chrisfen 2601 @article{Essmann95,
215     Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
216     Date-Added = {2006-03-05 12:25:25 -0500},
217     Date-Modified = {2006-03-05 12:29:07 -0500},
218     Journal = {J. Chem. Phys.},
219     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
220     Number = {19},
221     Pages = {8577-8593},
222 chrisfen 2610 Title = {A smooth particle mesh Ewald method},
223 chrisfen 2601 Volume = {103},
224     Year = {1995}}
225    
226 chrisfen 2595 @article{Kast03,
227     Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
228     Date-Added = {2006-02-18 16:47:26 -0500},
229     Date-Modified = {2006-02-18 16:51:25 -0500},
230     Journal = {Chem. Phys. Lett.},
231     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
232     Pages = {398-404},
233     Title = {Integral equation theory for correcting truncation errors in molecular simulations},
234     Volume = {367},
235     Year = {2003}}
236    
237 chrisfen 2594 @article{Tobias01,
238     Author = {D.~J. Tobias},
239     Date-Added = {2006-02-15 11:28:58 -0500},
240     Date-Modified = {2006-02-15 11:32:16 -0500},
241     Journal = {Curr. Opin. Struct. Biol.},
242     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
243     Pages = {253-261},
244     Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
245     Volume = {11},
246     Year = {2001}}
247 chrisfen 2575
248 chrisfen 2594 @article{Zahn02,
249     Author = {D. Zahn and B. Schilling and S.~M. Kast},
250     Date-Added = {2006-02-15 09:21:27 -0500},
251     Date-Modified = {2006-02-15 09:24:07 -0500},
252     Journal = {J. Phys. Chem. B},
253     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
254     Number = {41},
255     Pages = {10725-10732},
256 chrisfen 2595 Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
257 chrisfen 2594 Volume = {106},
258     Year = {2002}}
259 chrisfen 2575
260 chrisfen 2594 @article{Wolf99,
261     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
262     Date-Added = {2006-02-15 09:09:39 -0500},
263     Date-Modified = {2006-02-15 09:25:30 -0500},
264     Journal = {J. Chem. Phys.},
265     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
266     Number = {17},
267     Pages = {8255-8282},
268     Rating = {0},
269     Read = {No},
270 chrisfen 2595 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
271 chrisfen 2594 Volume = {110},
272     Year = {1999}}
273 chrisfen 2575
274 chrisfen 2594 @book{Berne90,
275     Address = {Malabar, Florida},
276     Author = {B.~J. Berne and R. Pecora},
277     Publisher = {Robert E. Krieger Publishing Company, Inc.},
278     Title = {Dynamic Light Scattering},
279     Year = 1990}
280 chrisfen 2575
281 chrisfen 2594 @article{Evans77,
282     Author = {D.~J. Evans},
283     Journal = {Mol. Phys.},
284     Pages = {317-325},
285     Title = {On the representation of orientation space},
286     Volume = 34,
287     Year = 1977}
288 chrisfen 2575
289 chrisfen 2594 @article{Tuckerman92,
290     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
291     Journal = jcp,
292     Pages = {1990-2001},
293     Title = {Reversible multiple time scale molecular dynamics},
294     Volume = 97,
295     Year = 1992}
296 chrisfen 2575
297 chrisfen 2594 @book{Hansen86,
298     Address = {London},
299     Author = {J.~P. Hansen and I.~R. McDonald},
300     Chapter = 7,
301     Pages = {199-206},
302     Publisher = {Academic Press},
303     Title = {Theory of Simple Liquids},
304     Year = 1986}
305 chrisfen 2575
306 chrisfen 2594 @article{Angelani98,
307     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
308     Journal = prl,
309     Number = 21,
310     Pages = {4648-4651},
311     Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
312     Volume = 81,
313     Year = 1998}
314 chrisfen 2575
315 chrisfen 2594 @article{Stillinger82,
316     Author = {F.~H. Stillinger and T.~A. Weber},
317     Journal = pra,
318     Number = 2,
319     Pages = {978-989},
320     Title = {Hidden structure in liquids},
321     Volume = 25,
322     Year = 1982}
323 chrisfen 2575
324 chrisfen 2594 @article{Stillinger83,
325     Author = {F.~H. Stillinger and T.~A. Weber},
326     Journal = pra,
327     Number = 4,
328     Pages = {2408-2416},
329     Title = {Dynamics of structural transitions in liquids},
330     Volume = 28,
331     Year = 1983}
332 chrisfen 2575
333 chrisfen 2594 @article{Weber84,
334     Author = {T.~A. Weber and F.~H. Stillinger},
335     Journal = jcp,
336     Number = 6,
337     Pages = {2742-2746},
338     Title = {The effect of density on the inherent structure in liquids},
339     Volume = 80,
340     Year = 1984}
341 chrisfen 2575
342 chrisfen 2594 @article{Stillinger85,
343     Author = {F.~H. Stillinger and T.~A. Weber},
344     Journal = jcp,
345     Number = 9,
346     Pages = {4767-4775},
347     Title = {Inherent structure theory of liquids in the hard-sphere limit},
348     Volume = 83,
349     Year = 1985}
350 chrisfen 2575
351 chrisfen 2594 @article{Stillinger98,
352     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
353     Journal = {Nature},
354     Pages = {554-557},
355     Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
356     Volume = 393,
357     Year = 1998}
358 chrisfen 2575
359 chrisfen 2594 @article{Parkhurst75a,
360     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
361     Journal = jcp,
362     Number = 6,
363     Pages = {2698-2704},
364     Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
365     Volume = 63,
366     Year = 1975}
367 chrisfen 2575
368 chrisfen 2594 @article{Parkhurst75b,
369     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
370     Journal = jcp,
371     Number = 6,
372     Pages = {2705-2709},
373     Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
374     Volume = 63,
375     Year = 1975}
376 chrisfen 2575
377 chrisfen 2594 @article{Forester97,
378     Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
379     Journal = {J. Chem. Soc. - Faraday Transactions},
380     Pages = {613-619},
381     Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
382     Volume = 93,
383     Year = 1997}
384 chrisfen 2575
385 chrisfen 2594 @article{Tieleman98,
386     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
387     Journal = {Biophys. J.},
388     Pages = {2786-2801},
389     Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
390     Volume = 74,
391     Year = 1998}
392 chrisfen 2575
393 chrisfen 2594 @article{Cascales98,
394     Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
395     Journal = {J. Phys. Chem. B},
396     Pages = {625-631},
397     Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
398     Volume = 102,
399     Year = 1998}
400 chrisfen 2575
401 chrisfen 2594 @article{Bassolino95,
402     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
403     Journal = {J. Am. Chem. Soc.},
404     Pages = {4118-4129},
405     Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
406     Volume = 117,
407     Year = 1995}
408 chrisfen 2575
409 chrisfen 2594 @article{Alper95,
410     Author = {H.~E. Alper and T.~R. Stouch},
411     Journal = {J. Phys. Chem.},
412     Pages = {5724-5731},
413     Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
414     Volume = 99,
415     Year = 1995}
416 chrisfen 2575
417 chrisfen 2594 @article{Sok92,
418     Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
419     Journal = {J. Chem. Phys.},
420     Pages = {4699-4704},
421     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
422     Volume = 96,
423     Year = 1992}
424 chrisfen 2575
425 chrisfen 2594 @article{Rabani99,
426     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
427     Journal = prl,
428     Pages = {3649},
429     Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
430     Volume = 82,
431     Year = {1999}}
432 chrisfen 2575
433 chrisfen 2594 @article{Rabani97,
434     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
435     Journal = {J. Chem. Phys.},
436     Pages = {6867-6876},
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438     Volume = 107,
439     Year = 1997}
440 chrisfen 2575
441 chrisfen 2594 @article{Gezelter99,
442     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
443     Journal = jcp,
444     Pages = 3444,
445     Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
446     Volume = 110,
447     Year = 1999}
448 chrisfen 2575
449 chrisfen 2594 @article{Gezelter98,
450     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
451     Date-Modified = {2006-02-15 10:18:42 -0500},
452     Journal = jcp,
453     Pages = 4695,
454     Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
455     Volume = 109,
456     Year = 1998}
457 chrisfen 2575
458 chrisfen 2594 @article{Gezelter97,
459     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
460     Journal = jcp,
461     Pages = 4618,
462     Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
463     Volume = 107,
464     Year = 1997}
465 chrisfen 2575
466 chrisfen 2594 @article{Zwanzig83,
467     Author = {R. Zwanzig},
468     Journal = jcp,
469     Pages = {4507-4508},
470     Title = {On the relation between self-diffusion and viscosity of liquids},
471     Volume = 79,
472     Year = 1983}
473 chrisfen 2575
474 chrisfen 2594 @article{Zwanzig88,
475     Author = {R. Zwanzig},
476     Journal = {Proc. Natl. Acad. Sci. USA},
477     Pages = 2029,
478     Title = {Diffusion in rough potential},
479     Volume = 85,
480     Year = 1988}
481 chrisfen 2575
482 chrisfen 2594 @article{Stillinger95,
483     Author = {F.~H. Stillinger},
484     Journal = {Science},
485     Pages = {1935-1939},
486     Title = {A Topographic View of Supercooled Liquids and Glass Formation},
487     Volume = 267,
488     Year = 1995}
489 chrisfen 2575
490 chrisfen 2594 @incollection{Angell85,
491     Address = {Springfield, VA},
492     Author = {C.~A. Angell},
493     Booktitle = {Relaxations in Complex Systems},
494     Editor = {K.~Ngai and G.~B. Wright},
495     Pages = 1,
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