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root/group/trunk/electrostaticMethodsPaper/electrostaticMethods.bib
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1 chrisfen 2594 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3 chrisfen 2575
4    
5 chrisfen 2636 %% Created for Chris Fennell at 2006-03-17 18:29:44 -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 2636 @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 chrisfen 2630 @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 chrisfen 2629 @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 chrisfen 2612 @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 chrisfen 2636 Date-Modified = {2006-03-16 22:39:27 -0500},
202 chrisfen 2612 Journal = {Ann. Physik},
203 chrisfen 2636 Pages = {253-287},
204     Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
205 chrisfen 2612 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 chrisfen 2610 @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 chrisfen 2609 @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 chrisfen 2601 @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 chrisfen 2610 Title = {A smooth particle mesh Ewald method},
266 chrisfen 2601 Volume = {103},
267     Year = {1995}}
268    
269 chrisfen 2595 @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},
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277     Volume = {367},
278     Year = {2003}}
279    
280 chrisfen 2594 @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},
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288     Volume = {11},
289     Year = {2001}}
290 chrisfen 2575
291 chrisfen 2594 @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 chrisfen 2595 Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
300 chrisfen 2594 Volume = {106},
301     Year = {2002}}
302 chrisfen 2575
303 chrisfen 2594 @article{Wolf99,
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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},
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311     Rating = {0},
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314 chrisfen 2594 Volume = {110},
315     Year = {1999}}
316 chrisfen 2575
317 chrisfen 2594 @book{Berne90,
318     Address = {Malabar, Florida},
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322     Year = 1990}
323 chrisfen 2575
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339 chrisfen 2575
340 chrisfen 2594 @book{Hansen86,
341     Address = {London},
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343     Chapter = 7,
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345     Publisher = {Academic Press},
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347     Year = 1986}
348 chrisfen 2575
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351     Journal = prl,
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358 chrisfen 2594 @article{Stillinger82,
359     Author = {F.~H. Stillinger and T.~A. Weber},
360     Journal = pra,
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364     Volume = 25,
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366 chrisfen 2575
367 chrisfen 2594 @article{Stillinger83,
368     Author = {F.~H. Stillinger and T.~A. Weber},
369     Journal = pra,
370     Number = 4,
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373     Volume = 28,
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375 chrisfen 2575
376 chrisfen 2594 @article{Weber84,
377     Author = {T.~A. Weber and F.~H. Stillinger},
378     Journal = jcp,
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384 chrisfen 2575
385 chrisfen 2594 @article{Stillinger85,
386     Author = {F.~H. Stillinger and T.~A. Weber},
387     Journal = jcp,
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393 chrisfen 2575
394 chrisfen 2594 @article{Stillinger98,
395     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
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410 chrisfen 2575
411 chrisfen 2594 @article{Parkhurst75b,
412     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
413     Journal = jcp,
414     Number = 6,
415     Pages = {2705-2709},
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418     Year = 1975}
419 chrisfen 2575
420 chrisfen 2594 @article{Forester97,
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434     Year = 1998}
435 chrisfen 2575
436 chrisfen 2594 @article{Cascales98,
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438     Journal = {J. Phys. Chem. B},
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441     Volume = 102,
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443 chrisfen 2575
444 chrisfen 2594 @article{Bassolino95,
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449     Volume = 117,
450     Year = 1995}
451 chrisfen 2575
452 chrisfen 2594 @article{Alper95,
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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 chrisfen 2575
460 chrisfen 2594 @article{Sok92,
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462     Journal = {J. Chem. Phys.},
463     Pages = {4699-4704},
464     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
465     Volume = 96,
466     Year = 1992}
467 chrisfen 2575
468 chrisfen 2594 @article{Rabani99,
469     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
470     Journal = prl,
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473     Volume = 82,
474     Year = {1999}}
475 chrisfen 2575
476 chrisfen 2594 @article{Rabani97,
477     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
478     Journal = {J. Chem. Phys.},
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