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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 2610 by chrisfen, Mon Mar 13 14:22:15 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 2006-03-12 20:26:24 -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	<	}
48	>	@article{Steinbach94,
49	>	Author = {P.~J. Steinbach and B.~R. Brooks},
50	>	Date-Added = {2006-03-12 19:26:45 -0500},
51	>	Date-Modified = {2006-03-12 19:29:43 -0500},
52	>	Doi = {10.1002/jcc.540150702},
53	>	Journal = {J. Comput. Chem.},
54	>	Number = {7},
55	>	Pages = {667-683},
56	>	Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
57	>	Volume = {15},
58	>	Year = {1994}}
59
60	<	@Article{Zwanzig88,
61	<	author =       {R. Zwanzig},
62	<	title =        {Diffusion in rough potential},
63	<	journal =      {Proc. Natl. Acad. Sci. USA},
64	<	year =         1988,
65	<	volume =       85,
66	<	pages =        2029
67	<	}
60	>	@article{deLeeuw80,
61	>	Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
62	>	Date-Added = {2006-03-07 10:26:31 -0500},
63	>	Date-Modified = {2006-03-07 10:30:11 -0500},
64	>	Journal = {Proc. R. Soc. London Ser. A},
65	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
66	>	Number = {1752},
67	>	Pages = {27-56},
68	>	Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
69	>	Volume = {373},
70	>	Year = {1980}}
71
72	<	@Article{Stillinger95,
73	<	author =       {F.~H. Stillinger},
74	<	title =        {A Topographic View of Supercooled Liquids and Glass
75	<	Formation},
76	<	journal =      {Science},
77	<	year =         1995,
78	<	volume =       267,
79	<	pages =        {1935-1939}
80	<	}
72	>	@article{Essmann95,
73	>	Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
74	>	Date-Added = {2006-03-05 12:25:25 -0500},
75	>	Date-Modified = {2006-03-05 12:29:07 -0500},
76	>	Journal = {J. Chem. Phys.},
77	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
78	>	Number = {19},
79	>	Pages = {8577-8593},
80	>	Title = {A smooth particle mesh Ewald method},
81	>	Volume = {103},
82	>	Year = {1995}}
83
84	<	@InCollection{Angell85,
85	<	author =       {C.~A. Angell},
86	<	title =        {unknown},
87	<	booktitle =    {Relaxations in Complex Systems},
88	<	publisher =    {National Technical Information Service,
89	<	U.S. Department of Commerce},
90	<	year =         1985,
91	<	editor =       {K.~Ngai and G.~B. Wright},
92	<	address =      {Springfield, VA},
93	<	pages =        1
298	<	}
84	>	@article{Kast03,
85	>	Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
86	>	Date-Added = {2006-02-18 16:47:26 -0500},
87	>	Date-Modified = {2006-02-18 16:51:25 -0500},
88	>	Journal = {Chem. Phys. Lett.},
89	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
90	>	Pages = {398-404},
91	>	Title = {Integral equation theory for correcting truncation errors in molecular simulations},
92	>	Volume = {367},
93	>	Year = {2003}}
94
95	<	@Article{Bembenek96,
96	<	author =       {S.~D. Bembenek and B.~B. Laird},
97	<	title =        {The role of localization in glasses and supercooled liquids},
98	<	journal =      jcp,
99	<	year =         1996,
100	<	volume =       104,
101	<	pages =        5199
102	<	}
95	>	@article{Tobias01,
96	>	Author = {D.~J. Tobias},
97	>	Date-Added = {2006-02-15 11:28:58 -0500},
98	>	Date-Modified = {2006-02-15 11:32:16 -0500},
99	>	Journal = {Curr. Opin. Struct. Biol.},
100	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
101	>	Pages = {253-261},
102	>	Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
103	>	Volume = {11},
104	>	Year = {2001}}
105
106	<	@Article{Sun97,
107	<	author =       {X. Sun and W.~H. Miller},
108	<	title =        {Semiclassical initial value representation for
109	<	electronically nonadiabatic molecular dynamics},
110	<	journal =      jcp,
111	<	year =         1997,
112	<	volume =       106,
113	<	pages =        6346
114	<	}
106	>	@article{Zahn02,
107	>	Author = {D. Zahn and B. Schilling and S.~M. Kast},
108	>	Date-Added = {2006-02-15 09:21:27 -0500},
109	>	Date-Modified = {2006-02-15 09:24:07 -0500},
110	>	Journal = {J. Phys. Chem. B},
111	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
112	>	Number = {41},
113	>	Pages = {10725-10732},
114	>	Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
115	>	Volume = {106},
116	>	Year = {2002}}
117
118	<	@Article{Spath96,
119	<	author =       {B.~W. Spath and W.~H. Miller},
120	<	title =        {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
121	<	PROBABILITIES},
122	<	journal =      jcp,
123	<	year =         1996,
124	<	volume =       104,
125	<	pages =        95
126	<	}
118	>	@article{Wolf99,
119	>	Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
120	>	Date-Added = {2006-02-15 09:09:39 -0500},
121	>	Date-Modified = {2006-02-15 09:25:30 -0500},
122	>	Journal = {J. Chem. Phys.},
123	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
124	>	Number = {17},
125	>	Pages = {8255-8282},
126	>	Rating = {0},
127	>	Read = {No},
128	>	Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
129	>	Volume = {110},
130	>	Year = {1999}}
131
132	<	@Book{Warshel91,
133	<	author =       {Arieh Warshel},
134	<	title =        {Computer modeling of chemical reactions in enzymes
135	<	and solutions},
136	<	publisher =    {Wiley},
137	<	year =         1991,
335	<	address =      {New York}
336	<	}
132	>	@book{Berne90,
133	>	Address = {Malabar, Florida},
134	>	Author = {B.~J. Berne and R. Pecora},
135	>	Publisher = {Robert E. Krieger Publishing Company, Inc.},
136	>	Title = {Dynamic Light Scattering},
137	>	Year = 1990}
138
139	<	@Article{Vuilleumier97,
140	<	author =       {Rodolphe Vuilleumier and Daniel Borgis},
141	<	title =        {Molecular Dynamics of an excess proton in water
142	<	using a non-additive valence bond force field},
143	<	journal =      jpc,
144	<	year =         1997,
145	<	volume =       {in press}
345	<	}
139	>	@article{Evans77,
140	>	Author = {D.~J. Evans},
141	>	Journal = {Mol. Phys.},
142	>	Pages = {317-325},
143	>	Title = {On the representation of orientation space},
144	>	Volume = 34,
145	>	Year = 1977}
146
147	<	@Article{Kob95a,
148	<	author =       {W. Kob and H.~C. Andersen},
149	<	title =        {Testing mode-coupling theory for a supercooled
150	<	binary Lennard-Jones mixtures: The van Hove
151	<	corraltion function},
152	<	journal =      pre,
153	<	year =         1995,
354	<	volume =       51,
355	<	pages =        {4626-4641}
356	<	}
147	>	@article{Tuckerman92,
148	>	Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
149	>	Journal = jcp,
150	>	Pages = {1990-2001},
151	>	Title = {Reversible multiple time scale molecular dynamics},
152	>	Volume = 97,
153	>	Year = 1992}
154
155	<	@Article{Kob95b,
156	<	author =       {W. Kob and H.~C. Andersen},
157	<	title =        {Testing mode-coupling theory for a supercooled
158	<	binary Lennard-Jones mixtures. II. Intermediate
159	<	scattering function and dynamic susceptibility},
160	<	journal =      pre,
161	<	year =         1995,
162	<	volume =       52,
366	<	pages =        {4134-4153}
367	<	}
155	>	@book{Hansen86,
156	>	Address = {London},
157	>	Author = {J.~P. Hansen and I.~R. McDonald},
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1163	>	Year = 1986}
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1704	<	journal =      {Journal of Computational Physics},
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1706	<	volume =       23,
1707	<	pages =        {327-341}
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1706	>	Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
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1721	<	title =        {Analytical Mechanics},
1722	<	chapter =      10,
1723	<	publisher =    {Saunders College Publishing},
1724	<	address =      {},
1725	<	year =         1999,
1726	<	edition =      {6th}
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1722	>	Journal = {Biophysical Journal},
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1726	>	Year = 1999}
1727
1728	<	@Article{petrache00,
1729	<	author =       {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
1730	<	title =        {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1731	<	journal =      {Biophysical Journal},
1732	<	year =         2000,
1733	<	volume =       79,
1734	<	pages =        {3172-3192}
1735	<	}
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1731	>	Journal = {J. Phys. Chem. B},
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1735	>	Year = 2002}
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1740	<	journal =      {J. Chem. Phys.},
1741	<	year =         1988,
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1739	>	Date-Modified = {2006-02-15 10:29:36 -0500},
1740	>	Journal = {Biophysical Journal},
1741	>	Pages = {1537-1553},
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1744	>	Year = 2000}
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1748	<	title =        {Temperature-dependent self-diffusion coefficients of
1749	<	water and six selected molecular liquids for calibration
1750	<	in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1751	<	journal =      {Phys. Chem. Chem. Phys.},
1752	<	year =         2000,
1753	<	volume =       2,
2031	<	pages =        {4740-4742},
2032	<	}
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1748	>	Date-Modified = {2006-02-15 10:29:58 -0500},
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1750	>	Pages = {3636-3645},
1751	>	Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
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1756	<	author =       {C. Zannoni},
1757	<	title =        {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1758	<	booktitle =    {The Molecular Dynamics of Liquid Crstals},
1759	<	pages =        {139-169},
1760	<	publisher =    {Kluwer Academic Publishers},
1761	<	year =         1994,
1762	<	editor =       {G.~R. Luckhurst and C.~A. Veracini},
2042	<	chapter =      6
2043	<	}
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1757	>	Date-Modified = {2006-02-15 10:28:28 -0500},
1758	>	Journal = {J. Phys. Chem. B},
1759	>	Pages = {750-760},
1760	>	Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
1761	>	Volume = 108,
1762	>	Year = 2004}
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1764	+	@article{Andersen83,
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1766	+	Date-Modified = {2006-02-15 10:08:20 -0500},
1767	+	Journal = {Journal of Computational Physics},
1768	+	Pages = {24-34},
1769	+	Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1770	+	Volume = 52,
1771	+	Year = 1983}
1772
1773	<	@Article{melchionna93,
1774	<	author =       {S. Melchionna and G. Ciccotti and B.~L. Holian},
1775	<	title =        {Hoover {\sc npt} dynamics for systems varying in shape and size},
1776	<	journal =      {Molecular Physics},
1777	<	year =         1993,
1778	<	volume =       78,
1779	<	pages =        {533-544}
1780	<	}
1773	>	@article{Hura00,
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1779	>	Volume = 113,
1780	>	Year = 2000}
1781
1782	+	@article{Ryckaert77,
1783	+	Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1784	+	Date-Modified = {2006-02-15 10:31:44 -0500},
1785	+	Journal = {Journal of Computational Physics},
1786	+	Pages = {327-341},
1787	+	Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1788	+	Volume = 23,
1789	+	Year = 1977}
1790
1791	+	@inbook{Fowles99,
1792	+	Author = {G.~R. Fowles and G.~L. Cassiday},
1793	+	Chapter = 10,
1794	+	Date-Modified = {2006-02-15 10:18:00 -0500},
1795	+	Edition = {6th},
1796	+	Publisher = {Saunders College Publishing},
1797	+	Title = {Analytical Mechanics},
1798	+	Year = 1999}
1799
1800	<	@Article{Fennell04,
1801	<	author =       {C.~J. Fennell and J.~D. Gezelter},
1802	<	title =        {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1803	<	journal =      jcp,
1804	<	year =         2004,
1805	<	volume =       120,
1806	<	number =       19,
1807	<	pages =        {9175-9184}
2065	<	}
1800	>	@article{Petrache00,
1801	>	Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
1802	>	Date-Modified = {2006-02-15 10:30:24 -0500},
1803	>	Journal = {Biophysical Journal},
1804	>	Pages = {3172-3192},
1805	>	Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1806	>	Volume = 79,
1807	>	Year = 2000}
1808
1809	<	@Article{klein01,
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1811	<	title =        {A coarse Grain Model for Phospholipid Simulations},
1812	<	journal =      {J. Phys. Chem. B},
1813	<	year =         2001,
1814	<	volume =       105,
1815	<	pages =        {4464-4470}
1816	<	}
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1810	>	Author = {E. Egberts and H.~J.~C. Berendsen},
1811	>	Date-Modified = {2006-02-15 10:16:43 -0500},
1812	>	Journal = {J. Chem. Phys.},
1813	>	Pages = {3718-3732},
1814	>	Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
1815	>	Volume = 89,
1816	>	Year = 1988}
1817
1818	+	@article{Holz00,
1819	+	Author = {M. Holz and S.~R. Heil and A. Sacco},
1820	+	Journal = {Phys. Chem. Chem. Phys.},
1821	+	Pages = {4740-4742},
1822	+	Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1823	+	Volume = 2,
1824	+	Year = 2000}
1825
1826	<	@Article{marrink03:vesicles,
1827	<	author =       {S.~J. Marrink and A.~E. Mark},
1828	<	title =        {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1829	<	journal =      {J. Am. Chem. Soc.},
1830	<	year =         2003,
1831	<	volume =       125,
1832	<	pages =        {15233-15242}
1833	<	}
1826	>	@incollection{Zannoni94,
1827	>	Author = {C. Zannoni},
1828	>	Booktitle = {The Molecular Dynamics of Liquid Crstals},
1829	>	Chapter = 6,
1830	>	Date-Modified = {2006-02-15 10:12:36 -0500},
1831	>	Editor = {G.~R. Luckhurst and C.~A. Veracini},
1832	>	Pages = {139-169},
1833	>	Publisher = {Kluwer Academic Publishers},
1834	>	Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1835	>	Year = 1994}
1836
1837	<	@Article{FletcherReeves,
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1839	<	title =        {Function minimization by conjugate gradients},
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1842	<	volume =       7,
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2094	<	}
1837	>	@article{Melchionna93,
1838	>	Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
1839	>	Date-Modified = {2006-02-15 10:28:54 -0500},
1840	>	Journal = {Molecular Physics},
1841	>	Pages = {533-544},
1842	>	Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
1843	>	Volume = 78,
1844	>	Year = 1993}
1845
1846	<	@Article{PolakRibiere,
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1848	<	title =        {Note sur la convergence de methodes de directions conjugees},
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1850	<	year =         1969,
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1852	<	pages =        {35-43}
1853	<	}
1846	>	@article{Fennell04,
1847	>	Author = {C.~J. Fennell and J.~D. Gezelter},
1848	>	Date-Modified = {2006-02-15 09:08:04 -0500},
1849	>	Journal = jcp,
1850	>	Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
1851	>	Number = 19,
1852	>	Pages = {9175-9184},
1853	>	Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1854	>	Volume = 120,
1855	>	Year = 2004}
1856
1857	<	@article{Voter:87,
1858	<	Author = {A.F. Voter and S.P. Chen},
1857	>	@article{Klein01,
1858	>	Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
1859	>	Date-Modified = {2006-02-15 10:27:22 -0500},
1860	>	Journal = {J. Phys. Chem. B},
1861	>	Pages = {4464-4470},
1862	>	Title = {A Coarse Grain Model for Phospholipid Simulations},
1863	>	Volume = 105,
1864	>	Year = 2001}
1865	>
1866	>	@article{Marrink03,
1867	>	Author = {S.~J. Marrink and A.~E. Mark},
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1869	>	Journal = {J. Am. Chem. Soc.},
1870	>	Pages = {15233-15242},
1871	>	Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1872	>	Volume = 125,
1873	>	Year = 2003}
1874	>
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1878	>	Journal = {Comput. J.},
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1881	>	Title = {Function minimization by conjugate gradients},
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1886	>	Author = {E. Polak and G. Ribiere},
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1888	>	Journal = {Rev. Fr. Inform. Rech. Oper.},
1889	>	Pages = {35-43},
1890	>	Title = {Note sur la convergence de methodes de directions conjugees},
1891	>	Volume = {16-R1},
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1904		Author = {Bruce Hendrickson and Steve Plimpton},
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1906		Journal = {Journal of Parallel and Distributed Computing},
1907		Pages = {15-25},
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1909		Volume = {27},
1910		Year = {1995}}
1911
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1914	+	Author = {S.~J. Plimpton and B.~A. Hendrickson},
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1916	+	Date-Modified = {2006-02-15 10:30:42 -0500},
1917	+	Editor = {J. Broughton and P. Bristowe and J. Newsam},
1918	+	Pages = 37,
1919	+	Publisher = {Materials Research Society},
1920	+	Series = {MRS Proceedings},
1921	+	Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
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2125	<	title =        {Parallel Molecular Dynamics With the Embedded Atom Method},
2126	<	booktitle =    {Materials Theory and Modelling},
2127	<	pages =        37,
2128	<	year =         1993,
2129	<	editor =       {J. Broughton and P. Bristowe and J. Newsam},
2130	<	volume =       291,
2131	<	series =       {MRS Proceedings},
2132	<	address =      {Pittsburgh, PA},
2133	<	publisher =    {Materials Research Society}
2134	<	}
2135	<
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1925	>	@article{Voter95a,
1926	>	Author = {A.~F. Voter},
1927	>	Date-Modified = {2006-02-15 10:35:27 -0500},
1928		Journal = {Intermetallic Compounds: Principles and Practice},
1929		Pages = {77},
1930		Title = {The Embedded-Atom Method},
1931		Volume = {1},
1932		Year = {1995}}
1933
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1935		Author = {H. Heller and H. Grubmuller and K. Schulten},
1936	+	Date-Modified = {2006-02-15 10:19:02 -0500},
1937		Journal = {Molecular Simulation},
1938		Pages = {133},
1939		Title = {Molecular dynamics simulation on a parallel computer},
1940		Volume = {5},
1941		Year = {1990}}
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1943	<	@Book{Fox88,
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1948	<	volume =       {I},
1949	<	address =      {Englewood Cliffs, NJ}
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1943	>	@book{Fox88,
1944	>	Address = {Englewood Cliffs, NJ},
1945	>	Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
1946	>	Publisher = {Prentice-Hall},
1947	>	Title = {Solving Promblems on Concurrent Processors},
1948	>	Volume = {I},
1949	>	Year = 1988}
1950
1951	<	@Article{Gromacs,
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1955	>	Pages = {43-56},
1956	>	Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
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1960	<	@Article{Gromacs3,
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1965	>	Title = {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
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1978
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2003	>	Publisher = {Reidel},
2004	>	Title = {Simple Point Charge Water},
2005	>	Year = 1981}
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2008	+	Author = {M.~W. Mahoney and W.~L. Jorgensen},
2009	+	Journal = jcp,
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2011	+	Pages = {8910-8922},
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2469	<	}
2235	>	@article{Stillinger74,
2236	>	Author = {F.~H. Stillinger and A. Rahman},
2237	>	Journal = jcp,
2238	>	Number = 4,
2239	>	Pages = {1545-1557},
2240	>	Title = {Improved simulation of liquid water by molecular dynamics},
2241	>	Volume = 60,
2242	>	Year = 1974}
2243
2244	<	@Article{Li96,
2245	<	author =       {H. Li and R. Helling and C. Tang and N. Wingreen},
2246	<	title =        {Emergence of Preferred Structures in a Simple Model of Protein Folding},
2247	<	journal =      {Science},
2248	<	year =         1996,
2249	<	volume =       273,
2250	<	pages =        {666-669}
2251	<	}
2244	>	@article{Caldwell95,
2245	>	Author = {J.~W. Caldwell and P.~A. Kollman},
2246	>	Journal = jpc,
2247	>	Number = 16,
2248	>	Pages = {6208-6219},
2249	>	Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2250	>	Volume = 99,
2251	>	Year = 1995}
2252
2253	<	@Article{Stillinger74,
2254	<	author =       {F.~H. Stillinger and A. Rahman},
2255	<	title =        {Improved simulation of liquid water by molecular dynamics},
2256	<	journal =      jcp,
2257	<	year =         1974,
2258	<	volume =       60,
2259	<	number =       4,
2260	<	pages =        {1545-1557}
2261	<	}
2253	>	@article{Urbic00,
2254	>	Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2255	>	Date-Modified = {2006-02-15 10:34:30 -0500},
2256	>	Journal = jcp,
2257	>	Number = 6,
2258	>	Pages = {2843-2848},
2259	>	Title = {A two-dimensional model of water: Therory and computer simulations},
2260	>	Volume = 112,
2261	>	Year = 2000}
2262
2263	<	@Article{Caldwell95,
2264	<	author =       {J.~W. Caldwell and P.~A. Kollman},
2265	<	title =        {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2266	<	journal =      jpc,
2267	<	year =         1995,
2268	<	volume =       99,
2269	<	number =       16,
2270	<	pages =        {6208-6219}
2498	<	}
2499	<
2500	<	@Article{Dill00,
2501	<	author =       {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2502	<	title =        {A two-dimensional model of water: Therory and computer simulations},
2503	<	journal =      jcp,
2504	<	year =         2000,
2505	<	volume =       112,
2506	<	number =       6,
2507	<	pages =        {2843-2848}
2508	<	}
2509	<
2510	<	@Article{Yang04,
2511	<	author =       {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2512	<	title =        {Ice Tessellation on a Hydroxylated Silica Surface},
2513	<	journal =      prl,
2514	<	year =         2004,
2515	<	volume =       92,
2516	<	number =       14,
2517	<	pages =        146102
2518	<	}
2519	<
2263	>	@article{Yang04,
2264	>	Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2265	>	Journal = prl,
2266	>	Number = 14,
2267	>	Pages = 146102,
2268	>	Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2269	>	Volume = 92,
2270	>	Year = 2004}

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