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root/group/trunk/electrostaticMethodsPaper/electrostaticMethods.bib
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# Content
1 %% This BibTeX bibliography file was created using BibDesk.
2 %% http://bibdesk.sourceforge.net/
3
4
5 %% Created for Chris Fennell at 2006-03-17 18:29:44 -0500
6
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 @STRING{jcc = "J. Comput. Chem."}
20
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 @article{Sagui99,
49 Author = {C. Sagui and T.~A. Darden},
50 Date-Added = {2006-03-17 18:27:01 -0500},
51 Date-Modified = {2006-03-17 18:29:36 -0500},
52 Journal = {Annu. Rev. Biophys. Biomol. Struct.},
53 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Darden_electrostaticInBiomolecules_99.pdf},
54 Pages = {155-179},
55 Title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic Effects},
56 Volume = {28},
57 Year = {1999}}
58
59 @article{Perram88,
60 Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
61 Date-Added = {2006-03-17 13:42:04 -0500},
62 Date-Modified = {2006-03-17 13:59:01 -0500},
63 Journal = {Mol. Phys.},
64 Pages = {875-893},
65 Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
66 Volume = {65},
67 Year = {1988}}
68
69 @article{Woodcock71,
70 Author = {L.~V. Woodcock and K. Singer},
71 Date-Added = {2006-03-17 11:14:17 -0500},
72 Date-Modified = {2006-03-17 11:16:52 -0500},
73 Journal = {Trans. Faraday Soc.},
74 Pages = {12-30},
75 Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by Monte Carlo Computation},
76 Volume = {67},
77 Year = {1971}}
78
79 @article{Smith81,
80 Author = {E.~R. Smith},
81 Date-Added = {2006-03-16 13:47:17 -0500},
82 Date-Modified = {2006-03-16 13:48:34 -0500},
83 Journal = {Proc. R. Soc. London Ser. A},
84 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
85 Pages = {475-505},
86 Title = {Electrostatic Energy in Ionic Crystals},
87 Volume = {375},
88 Year = {1981}}
89
90 @article{Weber00,
91 Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
92 Date-Added = {2006-03-16 09:49:22 -0500},
93 Date-Modified = {2006-03-16 09:51:17 -0500},
94 Doi = {10.1021/jp9937757},
95 Journal = {J. Phys. Chem. B},
96 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
97 Number = {15},
98 Pages = {3668-3675},
99 Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
100 Volume = {104},
101 Year = {2000}}
102
103 @article{Hunenberger99,
104 Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
105 Date-Added = {2006-03-16 09:45:10 -0500},
106 Date-Modified = {2006-03-16 09:49:15 -0500},
107 Journal = {Biophys. Chem.},
108 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
109 Pages = {69-88},
110 Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
111 Volume = {78},
112 Year = {1999}}
113
114 @article{Petersen95,
115 Author = {H.~G. Petersen},
116 Date-Added = {2006-03-16 08:43:02 -0500},
117 Date-Modified = {2006-03-16 08:44:32 -0500},
118 Journal = {J. Chem. Phys.},
119 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
120 Month = {September},
121 Number = {9},
122 Pages = {3668-3679},
123 Title = {Accuracy and efficiency of the particle mesh Ewald method},
124 Volume = {103},
125 Year = {1995}}
126
127 @article{Luty95,
128 Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
129 Date-Added = {2006-03-16 08:39:13 -0500},
130 Date-Modified = {2006-03-16 08:41:15 -0500},
131 Journal = {J. Chem. Phys.},
132 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
133 Number = {8},
134 Pages = {3014-3021},
135 Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
136 Volume = {103},
137 Year = {1995}}
138
139 @article{Barker73,
140 Author = {J.~A. Barker and R.~O. Watts },
141 Date-Added = {2006-03-15 18:58:17 -0500},
142 Date-Modified = {2006-03-15 21:17:31 -0500},
143 Journal = {Mol. Phys.},
144 Pages = {789=792},
145 Title = {Monte Carlo studies of the dielectric properties of water-like models},
146 Volume = {26},
147 Year = {1973}}
148
149 @article{Adams79,
150 Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
151 Date-Added = {2006-03-15 17:46:36 -0500},
152 Date-Modified = {2006-03-15 17:48:04 -0500},
153 Journal = {Mol. Phys.},
154 Number = {2},
155 Pages = {387-400},
156 Title = {The computer simulation of polar liquids},
157 Volume = {38},
158 Year = {1979}}
159
160 @article{Rahman71,
161 Author = {A. Rahman and F.~H. Stillinger},
162 Date-Added = {2006-03-15 17:04:53 -0500},
163 Date-Modified = {2006-03-15 17:07:29 -0500},
164 Journal = {J. Chem. Phys.},
165 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
166 Month = {October},
167 Number = {7},
168 Pages = {3336-3359},
169 Title = {Molecular Dynamics Study of Liquid Water},
170 Volume = {55},
171 Year = {1971}}
172
173 @article{Andrea83,
174 Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
175 Date-Added = {2006-03-15 15:16:12 -0500},
176 Date-Modified = {2006-03-15 15:18:10 -0500},
177 Journal = {J. Chem. Phys.},
178 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
179 Number = {9},
180 Pages = {4576-4584},
181 Title = {The role of long ranged forces in determining the structure and properties of liquid water},
182 Volume = {79},
183 Year = {1983}}
184
185 @article{Brush66,
186 Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
187 Date-Added = {2006-03-13 16:55:39 -0500},
188 Date-Modified = {2006-03-13 17:01:15 -0500},
189 Journal = {J. Chem. Phys.},
190 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
191 Month = {September},
192 Number = {6},
193 Pages = {2102-2118},
194 Title = {Monte Carlo Study of a One-Component Plasma. I},
195 Volume = {45},
196 Year = {1966}}
197
198 @article{Ewald21,
199 Author = {P.~P. Ewald},
200 Date-Added = {2006-03-13 13:32:04 -0500},
201 Date-Modified = {2006-03-16 22:39:27 -0500},
202 Journal = {Ann. Physik},
203 Pages = {253-287},
204 Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
205 Volume = {64},
206 Year = {1921}}
207
208 @article{Jones56,
209 Author = {R.~E. Jones and D.~H. Templeton},
210 Date-Added = {2006-03-13 13:25:58 -0500},
211 Date-Modified = {2006-03-13 13:27:15 -0500},
212 Journal = {J. Chem. Phys.},
213 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
214 Number = {5},
215 Pages = {1062-1063},
216 Title = {Optimum Atomic Shape for Bertaut Series},
217 Volume = {25},
218 Year = {1956}}
219
220 @article{Heyes81,
221 Author = {D.~M. Heyes},
222 Date-Added = {2006-03-13 13:12:45 -0500},
223 Date-Modified = {2006-03-13 13:14:27 -0500},
224 Journal = {J. Chem. Phys.},
225 Keywords = {Empty Keywords},
226 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
227 Number = {3},
228 Pages = {1924-1929},
229 Title = {Electrostatic potentials and fields in infinite point charge lattices},
230 Volume = {74},
231 Year = {1981}}
232
233 @article{Steinbach94,
234 Author = {P.~J. Steinbach and B.~R. Brooks},
235 Date-Added = {2006-03-12 19:26:45 -0500},
236 Date-Modified = {2006-03-12 19:29:43 -0500},
237 Doi = {10.1002/jcc.540150702},
238 Journal = {J. Comput. Chem.},
239 Number = {7},
240 Pages = {667-683},
241 Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
242 Volume = {15},
243 Year = {1994}}
244
245 @article{deLeeuw80,
246 Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
247 Date-Added = {2006-03-07 10:26:31 -0500},
248 Date-Modified = {2006-03-07 10:30:11 -0500},
249 Journal = {Proc. R. Soc. London Ser. A},
250 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
251 Number = {1752},
252 Pages = {27-56},
253 Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
254 Volume = {373},
255 Year = {1980}}
256
257 @article{Essmann95,
258 Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
259 Date-Added = {2006-03-05 12:25:25 -0500},
260 Date-Modified = {2006-03-05 12:29:07 -0500},
261 Journal = {J. Chem. Phys.},
262 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
263 Number = {19},
264 Pages = {8577-8593},
265 Title = {A smooth particle mesh Ewald method},
266 Volume = {103},
267 Year = {1995}}
268
269 @article{Kast03,
270 Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
271 Date-Added = {2006-02-18 16:47:26 -0500},
272 Date-Modified = {2006-02-18 16:51:25 -0500},
273 Journal = {Chem. Phys. Lett.},
274 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
275 Pages = {398-404},
276 Title = {Integral equation theory for correcting truncation errors in molecular simulations},
277 Volume = {367},
278 Year = {2003}}
279
280 @article{Tobias01,
281 Author = {D.~J. Tobias},
282 Date-Added = {2006-02-15 11:28:58 -0500},
283 Date-Modified = {2006-02-15 11:32:16 -0500},
284 Journal = {Curr. Opin. Struct. Biol.},
285 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
286 Pages = {253-261},
287 Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
288 Volume = {11},
289 Year = {2001}}
290
291 @article{Zahn02,
292 Author = {D. Zahn and B. Schilling and S.~M. Kast},
293 Date-Added = {2006-02-15 09:21:27 -0500},
294 Date-Modified = {2006-02-15 09:24:07 -0500},
295 Journal = {J. Phys. Chem. B},
296 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
297 Number = {41},
298 Pages = {10725-10732},
299 Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
300 Volume = {106},
301 Year = {2002}}
302
303 @article{Wolf99,
304 Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
305 Date-Added = {2006-02-15 09:09:39 -0500},
306 Date-Modified = {2006-02-15 09:25:30 -0500},
307 Journal = {J. Chem. Phys.},
308 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
309 Number = {17},
310 Pages = {8255-8282},
311 Rating = {0},
312 Read = {No},
313 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
314 Volume = {110},
315 Year = {1999}}
316
317 @book{Berne90,
318 Address = {Malabar, Florida},
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320 Publisher = {Robert E. Krieger Publishing Company, Inc.},
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322 Year = 1990}
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330 Year = 1977}
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338 Year = 1992}
339
340 @book{Hansen86,
341 Address = {London},
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347 Year = 1986}
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356 Year = 1998}
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360 Journal = pra,
361 Number = 2,
362 Pages = {978-989},
363 Title = {Hidden structure in liquids},
364 Volume = 25,
365 Year = 1982}
366
367 @article{Stillinger83,
368 Author = {F.~H. Stillinger and T.~A. Weber},
369 Journal = pra,
370 Number = 4,
371 Pages = {2408-2416},
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373 Volume = 28,
374 Year = 1983}
375
376 @article{Weber84,
377 Author = {T.~A. Weber and F.~H. Stillinger},
378 Journal = jcp,
379 Number = 6,
380 Pages = {2742-2746},
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382 Volume = 80,
383 Year = 1984}
384
385 @article{Stillinger85,
386 Author = {F.~H. Stillinger and T.~A. Weber},
387 Journal = jcp,
388 Number = 9,
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390 Title = {Inherent structure theory of liquids in the hard-sphere limit},
391 Volume = 83,
392 Year = 1985}
393
394 @article{Stillinger98,
395 Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
396 Journal = {Nature},
397 Pages = {554-557},
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400 Year = 1998}
401
402 @article{Parkhurst75a,
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409 Year = 1975}
410
411 @article{Parkhurst75b,
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413 Journal = jcp,
414 Number = 6,
415 Pages = {2705-2709},
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417 Volume = 63,
418 Year = 1975}
419
420 @article{Forester97,
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426 Year = 1997}
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428 @article{Tieleman98,
429 Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
430 Journal = {Biophys. J.},
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433 Volume = 74,
434 Year = 1998}
435
436 @article{Cascales98,
437 Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
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439 Pages = {625-631},
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441 Volume = 102,
442 Year = 1998}
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449 Volume = 117,
450 Year = 1995}
451
452 @article{Alper95,
453 Author = {H.~E. Alper and T.~R. Stouch},
454 Journal = {J. Phys. Chem.},
455 Pages = {5724-5731},
456 Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
457 Volume = 99,
458 Year = 1995}
459
460 @article{Sok92,
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466 Year = 1992}
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468 @article{Rabani99,
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473 Volume = 82,
474 Year = {1999}}
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489 Volume = 110,
490 Year = 1999}
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492 @article{Gezelter98,
493 Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
494 Date-Modified = {2006-02-15 10:18:42 -0500},
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506 Volume = 107,
507 Year = 1997}
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510 Author = {R. Zwanzig},
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514 Volume = 79,
515 Year = 1983}
516
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518 Author = {R. Zwanzig},
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523 Year = 1988}
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526 Author = {F.~H. Stillinger},
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533 @incollection{Angell85,
534 Address = {Springfield, VA},
535 Author = {C.~A. Angell},
536 Booktitle = {Relaxations in Complex Systems},
537 Editor = {K.~Ngai and G.~B. Wright},
538 Pages = 1,
539 Publisher = {National Technical Information Service, U.S. Department of Commerce},
540 Title = {unknown},
541 Year = 1985}
542
543 @article{Bembenek96,
544 Author = {S.~D. Bembenek and B.~B. Laird},
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550
551 @article{Sun97a,
552 Author = {X. Sun and W.~H. Miller},
553 Date-Modified = {2006-02-15 10:33:35 -0500},
554 Journal = jcp,
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557 Volume = 106,
558 Year = 1997}
559
560 @article{Spath96,
561 Author = {B.~W. Spath and W.~H. Miller},
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564 Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
565 Volume = 104,
566 Year = 1996}
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568 @book{Warshel91,
569 Address = {New York},
570 Author = {Arieh Warshel},
571 Publisher = {Wiley},
572 Title = {Computer modeling of chemical reactions in enzymes and solutions},
573 Year = 1991}
574
575 @article{Vuilleumier97,
576 Author = {Rodolphe Vuilleumier and Daniel Borgis},
577 Journal = jpc,
578 Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
579 Volume = {in press},
580 Year = 1997}
581
582 @article{Kob95a,
583 Author = {W. Kob and H.~C. Andersen},
584 Journal = pre,
585 Pages = {4626-4641},
586 Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
587 Volume = 51,
588 Year = 1995}
589
590 @article{Kob95b,
591 Author = {W. Kob and H.~C. Andersen},
592 Journal = pre,
593 Pages = {4134-4153},
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2448
2449 @article{Yang04,
2450 Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2451 Journal = prl,
2452 Number = 14,
2453 Pages = 146102,
2454 Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2455 Volume = 92,
2456 Year = 2004}