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Comparing trunk/electrostaticMethodsPaper/electrostaticMethods.bib (file contents):
Revision 2575 by chrisfen, Sat Jan 28 22:42:46 2006 UTC vs.
Revision 2639 by chrisfen, Mon Mar 20 02:00:26 2006 UTC

#	Line 1 | Line 1
1	<	@string{jcp = "J. Chem. Phys."}
2	<	@string{cpl = "Chem. Phys. Lett."}
3	<	@string{jpc = "J. Phys. Chem."}
4	<	@string{jpcA = "J. Phys. Chem. A"}
5	<	@string{jpcB = "J. Phys. Chem. B"}
6	<	@string{cp  = "Chem. Phys."}
7	<	@string{acp = "Adv. Chem. Phys."}
8	<	@string{pra = "Phys. Rev. A"}
9	<	@string{prb = "Phys. Rev. B"}
10	<	@string{pre = "Phys. Rev. E"}
11	<	@string{prl = "Phys. Rev. Lett."}
12	<	@string{rmp = "Rev. Mod. Phys."}
13	<	@string{jml = "J. Mol. Liq."}
14	<	@string{mp = "Mol. Phys."}
15	<	@string{pnas = "Proc. Natl. Acad. Sci. USA"}
16	<	@string{jacs = "J. Am. Chem. Soc."}
17	<	@string{jcc = "J. Comput. Chem."}
18	<	@string{pccp = "Phys. Chem. Chem. Phys."}
1	>	%% This BibTeX bibliography file was created using BibDesk.
2	>	%% http://bibdesk.sourceforge.net/
3
20	–	@Book{Berne90,
21	–	author =       {B.~J. Berne and R. Pecora},
22	–	title =        {Dynamic Light Scattering},
23	–	publisher =    {Robert E. Krieger Publishing Company, Inc.},
24	–	year =         1990,
25	–	address =      {Malabar, Florida}
26	–	}
4
5	<	@Article{Evans77,
29	<	author =       {D.~J. Evans},
30	<	title =        {On the representation of orientation space},
31	<	journal =      {Mol. Phys.},
32	<	year =         1977,
33	<	volume =       34,
34	<	pages =        {317-325}
35	<	}
5	>	%% Created for Chris Fennell at 2006-03-19 20:12:21 -0500
6
37	–	@Article{Tuckerman92,
38	–	author =       {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
39	–	title =        {Reversible multiple time scale molecular dynamics},
40	–	journal =      jcp,
41	–	year =         1992,
42	–	volume =       97,
43	–	pages =        {1990-2001}
44	–	}
7
8	<	@Book{Hansen86,
47	<	author =       {J.~P. Hansen and I.~R. McDonald},
48	<	title =        {Theory of Simple Liquids},
49	<	chapter =      7,
50	<	publisher =    {Academic Press},
51	<	year =         1986,
52	<	address =      {London},
53	<	pages =        {199-206}
54	<	}
8	>	%% Saved with string encoding Western (ASCII)
9
56	–	@Article{Angelani98,
57	–	author =       {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
58	–	title =        {Connected Network of Minima as a Model Glass: Long
59	–	Time Dynamics},
60	–	journal =      prl,
61	–	year =         1998,
62	–	volume =       81,
63	–	number =       21,
64	–	pages =        {4648-4651}
65	–	}
10
11	<	@Article{Stillinger82,
68	<	author =       {F.~H. Stillinger and T.~A. Weber},
69	<	title =        {Hidden structure in liquids},
70	<	journal =      pra,
71	<	year =         1982,
72	<	volume =       25,
73	<	number =       2,
74	<	pages =        {978-989}
75	<	}
11	>	@STRING{acp = "Adv. Chem. Phys."}
12
13	<	@Article{Stillinger83,
78	<	author =       {F.~H. Stillinger and T.~A. Weber},
79	<	title =        {Dynamics of structural transitions in liquids},
80	<	journal =      pra,
81	<	year =         1983,
82	<	volume =       28,
83	<	number =       4,
84	<	pages =        {2408-2416}
85	<	}
13	>	@STRING{cp = "Chem. Phys."}
14
15	<	@Article{Weber84,
88	<	author =       {T.~A. Weber and F.~H. Stillinger},
89	<	title =        {The effect of density on the inherent structure in
90	<	liquids},
91	<	journal =      jcp,
92	<	year =         1984,
93	<	volume =       80,
94	<	number =       6,
95	<	pages =        {2742-2746}
96	<	}
15	>	@STRING{cpl = "Chem. Phys. Lett."}
16
17	<	@Article{Stillinger85,
99	<	author =       {F.~H. Stillinger and T.~A. Weber},
100	<	title =        {Inherent structure theory of liquids in the
101	<	hard-sphere limit},
102	<	journal =      jcp,
103	<	year =         1985,
104	<	volume =       83,
105	<	number =       9,
106	<	pages =        {4767-4775}
107	<	}
17	>	@STRING{jacs = "J. Am. Chem. Soc."}
18
19	<	@Article{Stillinger98,
110	<	author =       {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
111	<	title =        {Signatures of distinct dynamical regimes in the
112	<	energy landscape of a glass-forming liquid},
113	<	journal =      {Nature},
114	<	year =         1998,
115	<	volume =       393,
116	<	pages =        {554-557}
117	<	}
19	>	@STRING{jcc = "J. Comput. Chem."}
20
21	+	@STRING{jcp = "J. Chem. Phys."}
22
23	<	@Article{Parkhurst75a,
121	<	author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
122	<	title =        {Dense liquids. I. The effect of density and
123	<	temperature on viscosity of tetramethylsilane and
124	<	benzene-$\mbox{D}_6$},
125	<	journal =      jcp,
126	<	year =         1975,
127	<	volume =       63,
128	<	number =       6,
129	<	pages =        {2698-2704}
130	<	}
23	>	@STRING{jml = "J. Mol. Liq."}
24
25	<	@Article{Parkhurst75b,
133	<	author =       {H.~J. {Parkhurst, Jr.} and J. Jonas},
134	<	title =        {Dense liquids. II. The effect of density and
135	<	temperature on viscosity of tetramethylsilane and
136	<	benzene },
137	<	journal =      jcp,
138	<	year =         1975,
139	<	volume =       63,
140	<	number =       6,
141	<	pages =        {2705-2709}
142	<	}
25	>	@STRING{jpc = "J. Phys. Chem."}
26
27	<	@Article{Forester97,
145	<	author =       {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
146	<	title =        {Antibiotic activity of valinomycin - Molecular
147	<	dynamics simulations involving the water/membrane
148	<	interface},
149	<	journal =      {J. Chem. Soc. - Faraday Transactions},
150	<	year =         1997,
151	<	volume =       93,
152	<	pages =        {613-619}
153	<	}
27	>	@STRING{jpca = "J. Phys. Chem. A"}
28
29	<	@Article{Tieleman98,
156	<	author =       {D.~P. Tieleman and H.~J.~C. Berendsen},
157	<	title =        {A molecular dynamics study of the pores formed by
158	<	Escherichia coli OmpF porin in a fully hydrated
159	<	palmitoyloleoylphosphatidylcholine bilayer},
160	<	journal =      {Biophys. J.},
161	<	year =         1998,
162	<	volume =       74,
163	<	pages =        {2786-2801}
164	<	}
29	>	@STRING{jpcb = "J. Phys. Chem. B"}
30
31	<	@Article{Cascales98,
167	<	author =       {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
168	<	title =        {Anaesthetic mechanism on a model biological
169	<	membrane: A molecular dynamics simulation study},
170	<	journal =      {J. Phys. Chem. B},
171	<	year =         1998,
172	<	volume =       102,
173	<	pages =        {625-631}
174	<	}
31	>	@STRING{mp = "Mol. Phys."}
32
33	<	@Article{Bassolino95,
177	<	author =       {D. Bassolino and H.~E. Alper and T.~R. Stouch},
178	<	title =        {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID
179	<	BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
180	<	journal =      {J. Am. Chem. Soc.},
181	<	year =         1995,
182	<	volume =       117,
183	<	pages =        {4118-4129}
184	<	}
33	>	@STRING{pccp = "Phys. Chem. Chem. Phys."}
34
35	<	@Article{Alper95,
187	<	author =       {H.~E. Alper and T.~R. Stouch},
188	<	title =        {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN
189	<	BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
190	<	journal =      {J. Phys. Chem.},
191	<	year =         1995,
192	<	volume =       99,
193	<	pages =        {5724-5731}
194	<	}
35	>	@STRING{pnas = "Proc. Natl. Acad. Sci. USA"}
36
37	<	@Article{Sok92,
197	<	author =       {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
198	<	title =        {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF
199	<	SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
200	<	journal =      {J. Chem. Phys.},
201	<	year =         1992,
202	<	volume =       96,
203	<	pages =        {4699-4704}
204	<	}
37	>	@STRING{pra = "Phys. Rev. A"}
38
39	<	@Article{Rabani99,
207	<	author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
208	<	title =        {Direct Observation of Stretched-Exponential
209	<	Relaxation in Low-Temperature Lennard-Jones Systems
210	<	Using the Cage Correlation Function},
211	<	journal =      prl,
212	<	year =         {1999},
213	<	volume =       82,
214	<	pages =        {3649}
215	<	}
39	>	@STRING{prb = "Phys. Rev. B"}
40
41	<	@Article{Rabani97,
218	<	author =       {E. Rabani and J.~D. Gezelter and B.~J. Berne},
219	<	title =        {Calculating the hopping rate for self-diffusion on
220	<	rough potential energy surfaces: Cage correlations},
221	<	journal =      {J. Chem. Phys.},
222	<	year =         1997,
223	<	volume =       107,
224	<	pages =        {6867-6876}
225	<	}
41	>	@STRING{pre = "Phys. Rev. E"}
42
43	<	@Article{Gezelter99,
228	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
229	<	title =        {Methods for calculating the hopping rate for
230	<	orientational and spatial diffusion in a molecular
231	<	liquid: $\mbox{CS}_{2}$},
232	<	journal =      jcp,
233	<	year =         1999,
234	<	volume =       110,
235	<	pages =        3444
236	<	}
43	>	@STRING{prl = "Phys. Rev. Lett."}
44
45	<	@Article{Gezelter98a,
239	<	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
240	<	title =        {Response to 'Comment on a Critique of the
241	<	Instantaneous Normal Mode (INM) Approach to
242	<	Diffusion'},
243	<	journal =      jcp,
244	<	year =         1998,
245	<	volume =       109,
246	<	pages =        4695
247	<	}
45	>	@STRING{rmp = "Rev. Mod. Phys."}
46
249	–	@Article{Gezelter97,
250	–	author =       {J.~D. Gezelter and E. Rabani and B.~J. Berne},
251	–	title =        {Can imaginary instantaneous normal mode frequencies
252	–	predict barriers to self-diffusion?},
253	–	journal =      jcp,
254	–	year =         1997,
255	–	volume =       107,
256	–	pages =        4618
257	–	}
47
48	<	@Article{Zwanzig83,
49	<	author =       {R. Zwanzig},
50	<	title =        {On the relation between self-diffusion and viscosity
51	<	of liquids},
52	<	journal =      jcp,
53	<	year =         1983,
54	<	volume =       79,
55	<	pages =        {4507-4508}
56	<	}
57	<
269	<	@Article{Zwanzig88,
270	<	author =       {R. Zwanzig},
271	<	title =        {Diffusion in rough potential},
272	<	journal =      {Proc. Natl. Acad. Sci. USA},
273	<	year =         1988,
274	<	volume =       85,
275	<	pages =        2029
276	<	}
48	>	@article{Roux99,
49	>	Author = {B. Roux and T. Simonson},
50	>	Date-Added = {2006-03-19 20:10:18 -0500},
51	>	Date-Modified = {2006-03-19 20:12:10 -0500},
52	>	Journal = {Biophys. Chem.},
53	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
54	>	Pages = {1-20},
55	>	Title = {Implicit solvent models},
56	>	Volume = {78},
57	>	Year = {1999}}
58
59	<	@Article{Stillinger95,
60	<	author =       {F.~H. Stillinger},
61	<	title =        {A Topographic View of Supercooled Liquids and Glass
62	<	Formation},
63	<	journal =      {Science},
64	<	year =         1995,
65	<	volume =       267,
66	<	pages =        {1935-1939}
67	<	}
59	>	@article{Rokhlin85,
60	>	Author = {V. Rokhlin},
61	>	Date-Added = {2006-03-19 20:02:25 -0500},
62	>	Date-Modified = {2006-03-19 20:04:19 -0500},
63	>	Doi = {10.1016/0021-9991(85)90002-6},
64	>	Journal = {J. Comput. Phys.},
65	>	Month = {September},
66	>	Number = {2},
67	>	Pages = {187-207},
68	>	Title = {Rapid solution of integral equations of classical potential theory},
69	>	Volume = {60},
70	>	Year = {1985}}
71
72	<	@InCollection{Angell85,
73	<	author =       {C.~A. Angell},
74	<	title =        {unknown},
75	<	booktitle =    {Relaxations in Complex Systems},
76	<	publisher =    {National Technical Information Service,
77	<	U.S. Department of Commerce},
78	<	year =         1985,
79	<	editor =       {K.~Ngai and G.~B. Wright},
80	<	address =      {Springfield, VA},
81	<	pages =        1
298	<	}
72	>	@article{Grossfield00,
73	>	Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
74	>	Date-Added = {2006-03-19 19:52:19 -0500},
75	>	Date-Modified = {2006-03-19 19:54:14 -0500},
76	>	Journal = {Proteins},
77	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
78	>	Pages = {211-223},
79	>	Title = {Dipole Lattice Membrane Model for Protein Calculations},
80	>	Volume = {41},
81	>	Year = {2000}}
82
83	<	@Article{Bembenek96,
84	<	author =       {S.~D. Bembenek and B.~B. Laird},
85	<	title =        {The role of localization in glasses and supercooled liquids},
86	<	journal =      jcp,
87	<	year =         1996,
88	<	volume =       104,
89	<	pages =        5199
90	<	}
83	>	@article{Born20,
84	>	Author = {M. Born},
85	>	Date-Added = {2006-03-19 18:05:01 -0500},
86	>	Date-Modified = {2006-03-19 18:07:42 -0500},
87	>	Journal = {Z. Physik},
88	>	Pages = {45-48},
89	>	Title = {Volumen und hydratationswame der ionen},
90	>	Volume = {1},
91	>	Year = {1920}}
92
93	<	@Article{Sun97,
94	<	author =       {X. Sun and W.~H. Miller},
95	<	title =        {Semiclassical initial value representation for
96	<	electronically nonadiabatic molecular dynamics},
97	<	journal =      jcp,
98	<	year =         1997,
99	<	volume =       106,
100	<	pages =        6346
101	<	}
93	>	@article{Luty96,
94	>	Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
95	>	Date-Added = {2006-03-18 20:59:19 -0500},
96	>	Date-Modified = {2006-03-18 21:00:33 -0500},
97	>	Journal = {J. Phys. Chem.},
98	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
99	>	Number = {7},
100	>	Pages = {2581-2587},
101	>	Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
102	>	Volume = {100},
103	>	Year = {1996}}
104
105	<	@Article{Spath96,
106	<	author =       {B.~W. Spath and W.~H. Miller},
107	<	title =        {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
108	<	PROBABILITIES},
109	<	journal =      jcp,
110	<	year =         1996,
111	<	volume =       104,
112	<	pages =        95
113	<	}
105	>	@article{Rhee89,
106	>	Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
107	>	Date-Added = {2006-03-18 20:48:07 -0500},
108	>	Date-Modified = {2006-03-18 20:51:09 -0500},
109	>	Journal = {Phys. Rev. B},
110	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
111	>	Number = {1},
112	>	Pages = {36-42},
113	>	Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
114	>	Volume = {40},
115	>	Year = {1989}}
116
117	<	@Book{Warshel91,
118	<	author =       {Arieh Warshel},
119	<	title =        {Computer modeling of chemical reactions in enzymes
120	<	and solutions},
121	<	publisher =    {Wiley},
122	<	year =         1991,
123	<	address =      {New York}
124	<	}
117	>	@article{Hunenberger99a,
118	>	Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
119	>	Date-Added = {2006-03-18 20:14:24 -0500},
120	>	Date-Modified = {2006-03-18 20:16:01 -0500},
121	>	Journal = {J. Chem. Phys.},
122	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
123	>	Number = {4},
124	>	Pages = {1856-1872},
125	>	Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
126	>	Volume = {110},
127	>	Year = {1999}}
128
129	<	@Article{Vuilleumier97,
130	<	author =       {Rodolphe Vuilleumier and Daniel Borgis},
131	<	title =        {Molecular Dynamics of an excess proton in water
132	<	using a non-additive valence bond force field},
133	<	journal =      jpc,
134	<	year =         1997,
135	<	volume =       {in press}
136	<	}
129	>	@article{Roberts95,
130	>	Author = {J.~E. Roberts and J. Schnitker},
131	>	Date-Added = {2006-03-18 20:12:23 -0500},
132	>	Date-Modified = {2006-03-18 20:13:36 -0500},
133	>	Journal = {J. Phys. Chem.},
134	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
135	>	Pages = {1322-1331},
136	>	Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
137	>	Volume = {99},
138	>	Year = {1995}}
139
140	<	@Article{Kob95a,
141	<	author =       {W. Kob and H.~C. Andersen},
142	<	title =        {Testing mode-coupling theory for a supercooled
143	<	binary Lennard-Jones mixtures: The van Hove
144	<	corraltion function},
145	<	journal =      pre,
146	<	year =         1995,
147	<	volume =       51,
148	<	pages =        {4626-4641}
149	<	}
140	>	@article{Roberts94,
141	>	Author = {J.~E. Roberts and J. Schnitker},
142	>	Date-Added = {2006-03-18 20:10:37 -0500},
143	>	Date-Modified = {2006-03-18 20:12:19 -0500},
144	>	Journal = {J. Chem. Phys.},
145	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
146	>	Number = {6},
147	>	Pages = {5024-5031},
148	>	Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
149	>	Volume = {101},
150	>	Year = {1994}}
151
152	<	@Article{Kob95b,
153	<	author =       {W. Kob and H.~C. Andersen},
154	<	title =        {Testing mode-coupling theory for a supercooled
155	<	binary Lennard-Jones mixtures. II. Intermediate
156	<	scattering function and dynamic susceptibility},
157	<	journal =      pre,
158	<	year =         1995,
159	<	volume =       52,
160	<	pages =        {4134-4153}
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1159	<	ADSORPTION},
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1161	<	year =         1995,
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1163	<	pages =        1607
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1156	>	@incollection{MacKerell98,
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1159	>	Booktitle = {The Encyclopedia of Computational Chemistry},
1160	>	Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1161	>	Pages = {271-277},
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2401	<	address =      {Dordrecht}
2217	<	}
2393	>	@incollection{Berendsen81,
2394	>	Address = {Dordrecht},
2395	>	Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
2396	>	Booktitle = {Intermolecular Forces},
2397	>	Editor = {B. Pullman},
2398	>	Pages = 331,
2399	>	Publisher = {Reidel},
2400	>	Title = {Simple Point Charge Water},
2401	>	Year = 1981}
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2404	+	Author = {M.~W. Mahoney and W.~L. Jorgensen},
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2406	+	Number = 20,
2407	+	Pages = {8910-8922},
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2420	>	Year = 2005}
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2434	<	journal =      {J. Comp. Chem.},
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2490	<	@Article{Caldwell95,
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2664	>	Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2665	>	Volume = 92,
2666	>	Year = 2004}

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