ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/fennellDissertation/dissertation.bib
Revision: 2973
Committed: Fri Aug 18 15:49:29 2006 UTC (18 years, 1 month ago) by chrisfen
File size: 96884 byte(s)
Log Message:
Chapter separation...

File Contents

# User Rev Content
1 chrisfen 2918 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3    
4    
5 chrisfen 2973 %% Created for Chris Fennell at 2006-08-16 10:43:59 -0400
6 chrisfen 2918
7    
8     %% Saved with string encoding Western (ASCII)
9    
10    
11 chrisfen 2957 @string{acp = {Adv. Chem. Phys.}}
12 chrisfen 2918
13 chrisfen 2957 @string{cp = {Chem. Phys.}}
14 chrisfen 2918
15 chrisfen 2957 @string{cpl = {Chem. Phys. Lett.}}
16 chrisfen 2918
17 chrisfen 2957 @string{jacs = {J. Am. Chem. Soc.}}
18 chrisfen 2918
19 chrisfen 2957 @string{jcc = {J. Comput. Chem.}}
20 chrisfen 2918
21 chrisfen 2957 @string{jcp = {J. Chem. Phys.}}
22 chrisfen 2918
23 chrisfen 2957 @string{jml = {J. Mol. Liq.}}
24 chrisfen 2918
25 chrisfen 2957 @string{jpc = {J. Phys. Chem.}}
26 chrisfen 2918
27 chrisfen 2957 @string{jpca = {J. Phys. Chem. A}}
28 chrisfen 2918
29 chrisfen 2957 @string{jpcb = {J. Phys. Chem. B}}
30 chrisfen 2918
31 chrisfen 2957 @string{mp = {Mol. Phys.}}
32 chrisfen 2918
33 chrisfen 2957 @string{pccp = {Phys. Chem. Chem. Phys.}}
34 chrisfen 2918
35 chrisfen 2957 @string{pnas = {Proc. Natl. Acad. Sci. USA}}
36 chrisfen 2918
37 chrisfen 2957 @string{pra = {Phys. Rev. A}}
38 chrisfen 2918
39 chrisfen 2957 @string{prb = {Phys. Rev. B}}
40 chrisfen 2918
41 chrisfen 2957 @string{pre = {Phys. Rev. E}}
42 chrisfen 2918
43 chrisfen 2957 @string{prl = {Phys. Rev. Lett.}}
44 chrisfen 2918
45 chrisfen 2957 @string{rmp = {Rev. Mod. Phys.}}
46 chrisfen 2918
47    
48 chrisfen 2973 @article{Aguado03,
49     Author = {A. Aguado and P.~A. Madden},
50     Date-Added = {2006-08-16 10:42:15 -0400},
51     Date-Modified = {2006-08-16 10:43:56 -0400},
52     Doi = {10.1063/1.1605941},
53     Journal = {J. Chem. Phys.},
54     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Aguado_MultipoleEwald_03.pdf},
55     Number = {14},
56     Pages = {7471-7483},
57     Title = {Ewald summation of electrostatic multipole interactions up to the quadrupolar level},
58     Volume = {119},
59     Year = {2003}}
60    
61     @article{Smith98,
62     Author = {W. Smith},
63     Date-Added = {2006-08-16 10:02:44 -0400},
64     Date-Modified = {2006-08-16 10:41:23 -0400},
65     Journal = {CCP5 Information Quarterly},
66     Number = {46},
67     Title = {Point multipoles in the \uppercase{E}wald summation (Revisited)},
68     Year = {1998}}
69    
70     @book{Stone02,
71     Author = {A.~J. Stone},
72     Date-Added = {2006-08-14 18:14:32 -0400},
73     Date-Modified = {2006-08-14 22:45:20 -0400},
74     Editor = {J.~S. Rowlinson},
75     Publisher = {Oxford University Press, Inc.},
76     Title = {The Theory of Intermolecular Forces},
77     Year = {2002}}
78    
79     @book{Hirschfelder67,
80     Author = {J.~O. Hirschfelder and C.~F. Curtiss and R.~B. Bird},
81     Date-Added = {2006-08-14 10:15:21 -0400},
82     Date-Modified = {2006-08-14 22:45:43 -0400},
83     Editor = {M.~G. Mayer},
84     Publisher = {John Wiley \& Sons, Inc.},
85     Title = {Molecular Theory of Gases and Liquids},
86     Year = {1967}}
87    
88 chrisfen 2971 @article{Ryckaert77,
89     Author = {J.-P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
90     Date-Added = {2006-08-06 17:05:44 -0400},
91     Date-Modified = {2006-08-06 17:08:35 -0400},
92     Doi = {10.1016/0021-9991(77)90098-5},
93     Journal = {J. Comput. Phys.},
94     Month = {March},
95     Number = {3},
96     Pages = {327-341},
97     Title = {Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of {\it n}-alkanes},
98     Volume = {23},
99     Year = {1977}}
100    
101     @article{Impey82,
102     Author = {R.~W. Impey and P.~A. Madden and I.~R. McDonald},
103     Date-Added = {2006-08-03 08:42:21 -0400},
104     Date-Modified = {2006-08-03 08:44:06 -0400},
105     Journal = {Mol. Phys.},
106     Number = {3},
107     Pages = {513-539},
108     Title = {Spectroscopic and transport properties of water: \uppercase{M}odel calculations and the interpretation of experimental results},
109     Volume = {46},
110     Year = {1982}}
111    
112     @article{Laasonen93,
113     Author = {K. Laasonen and M. Sprik and M. Parrinello and R. Car},
114     Date-Added = {2006-08-02 08:23:46 -0400},
115     Date-Modified = {2006-08-02 13:09:18 -0400},
116     Journal = {J. Chem. Phys.},
117     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Laasonen_AbInitioLiquidWater_93.pdf},
118     Number = {11},
119     Pages = {9080-9089},
120     Title = {``{\it \uppercase{A}b initio}" liquid water},
121     Volume = {99},
122     Year = {1993}}
123    
124     @article{Donchev06,
125     Author = {A.~G. Donchev and N.~G. Galkin and A.~A. Illarionov and O.~V. Khoruzhii and M.~A. Olevanov and M.~V. Subbotin and V.~I. Tarasov},
126     Date-Added = {2006-08-02 08:15:11 -0400},
127     Date-Modified = {2006-08-02 08:16:16 -0400},
128     Doi = {www.pnas.org/cgi/doi/10.1073/pnas.0602982103},
129     Journal = {Proc. Natl. Acad. Sci. USA},
130     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Donchev_QuantumWater_06.pdf},
131     Number = {23},
132     Pages = {8613-8617},
133     Title = {Water properties from first principles: \uppercase{S}imulations by a general-purpose quantum mechanical polarizable force field},
134     Volume = {103},
135     Year = {2006}}
136    
137     @article{Malmberg56,
138     Author = {G.~G. Malmberg and A.~A. Maryott},
139     Date-Added = {2006-08-01 17:19:00 -0400},
140     Date-Modified = {2006-08-02 13:16:04 -0400},
141     Journal = {J. Res. Natl. Bur. Stand.},
142     Number = {1},
143     Pages = {1-8},
144     Title = {Dielectric constant of Water from 0$^\circ$ to 100$^\circ$\uppercase{C}},
145     Volume = {56},
146     Year = {1956}}
147    
148     @article{Neumann80,
149     Author = {M. Neumann and O. Steinhauser},
150     Date-Added = {2006-08-01 17:17:52 -0400},
151     Date-Modified = {2006-08-01 17:18:51 -0400},
152     Journal = {Mol. Phys.},
153     Number = {2},
154     Pages = {437-454},
155     Title = {The influence of boundary conditions used in machine simulations on the structure of polar systems},
156     Volume = {39},
157     Year = {1980}}
158    
159     @article{Neumann83,
160     Author = {M. Neumann},
161     Date-Added = {2006-08-01 17:16:51 -0400},
162     Date-Modified = {2006-08-01 17:17:45 -0400},
163     Journal = {Mol. Phys.},
164     Number = {4},
165     Pages = {841-858},
166     Title = {Dipole moment fluctuation formulas in computer simulations of polar systems},
167     Volume = {50},
168     Year = {1983}}
169    
170     @article{Kell75,
171     Author = {G.~S. Kell},
172     Date-Added = {2006-08-01 16:05:09 -0400},
173     Date-Modified = {2006-08-02 13:17:29 -0400},
174     Journal = {J. Chem. Eng. Data},
175     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kell_CompressibilityAndExpansivityOfH2O_75.pdf},
176     Number = {1},
177     Pages = {91-105},
178     Title = {Density, Thermal Expansivity, and Compressibility of Liquid Water from 0$^\circ$ to 150$^\circ$\uppercase{C}: \uppercase{C}orrelations and Tables for Atmospheric Pressure and Saturation Reviewed and Expressed on 1968 Temperature Scale},
179     Volume = {20},
180     Year = {1975}}
181    
182     @article{Wagner02,
183     Author = {W. Wagner and A. Pru{\ss}},
184     Date-Added = {2006-08-01 16:02:31 -0400},
185     Date-Modified = {2006-08-02 13:16:50 -0400},
186     Journal = {J. Phys. Chem. Ref. Data},
187     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Wagner_ThermodynamicPropertiesOfH2O_03.pdf},
188     Number = {2},
189     Pages = {387-535},
190     Title = {The \uppercase{IAPWS} Formulation 1995 for the Thermodynamic Properties of Ordinary Water Substance for General and Scientific Use},
191     Volume = {31},
192     Year = {2002}}
193    
194     @article{Neumann84,
195     Author = {M. Neumann and O. Steinhauser and G.~S. Pawley},
196     Date-Added = {2006-07-31 10:22:39 -0400},
197     Date-Modified = {2006-07-31 10:24:17 -0400},
198     Journal = {Mol. Phys.},
199     Number = {1},
200     Pages = {97-113},
201     Title = {Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations},
202     Volume = {52},
203     Year = {1984}}
204    
205     @article{Neumann85,
206     Author = {M. Neumann},
207     Date-Added = {2006-07-31 10:19:17 -0400},
208     Date-Modified = {2006-08-02 13:17:58 -0400},
209     Journal = {J. Chem. Phys.},
210     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/DielectricConst./Neumann_H2ODielConst_85.pdf},
211     Number = {12},
212     Pages = {5663-5672},
213     Title = {The dielectric constant of water. \uppercase{C}omputer simulations with the \uppercase{MCY} potential},
214     Volume = {82},
215     Year = {1985}}
216    
217     @book{Berry00,
218     Address = {New York},
219     Author = {R. Stephen Berry and Stuart A. Rice and John Ross},
220     Date-Added = {2006-07-30 14:49:40 -0400},
221     Date-Modified = {2006-07-30 14:53:08 -0400},
222     Edition = {Second},
223     Editor = {Donald G. Truhlar},
224     Publisher = {Oxford University Press, Inc.},
225     Series = {Topics in Physical Chemistry},
226     Title = {Physical Chemistry},
227     Year = {2000}}
228    
229 chrisfen 2957 @article{Sorenson00,
230     Author = {J.~M. Sorenson and G. Hura and R.~M. Glaeser and T. Head-Gordon},
231     Date-Added = {2006-07-21 11:41:31 -0400},
232     Date-Modified = {2006-07-21 11:44:44 -0400},
233     Journal = {J. Chem. Phys.},
234     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayRadial_2000.pdf},
235     Number = {20},
236     Pages = {9149-9161},
237     Title = {What can x-ray scattering tell us about the radial distribution functions of water?},
238     Volume = {113},
239     Year = {2000}}
240    
241     @book{CRC80,
242     Address = {Boca Raton, FL},
243     Date-Added = {2006-07-21 09:20:17 -0400},
244     Date-Modified = {2006-07-21 09:20:17 -0400},
245     Edition = 60,
246     Editor = {R.~C. Weast},
247     Publisher = {CRC Press, Inc.},
248     Title = {CRC Handbook of Chemistry and Physics},
249     Year = 1980}
250    
251     @article{Shi06,
252     Author = {Q. Shi and S. Izvekov and G.~A. Voth},
253     Date-Added = {2006-07-20 15:28:29 -0400},
254     Date-Modified = {2006-07-20 15:29:45 -0400},
255     Doi = {10.1021/jp062700h},
256     Journal = {J. Phys. Chem. B},
257     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Shi_MixedAtomisticCGIonChannel_06.pdf},
258     Title = {Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel},
259     Year = {2006}}
260    
261     @article{Weis06,
262     Author = {J.-J. Weis and D. Levesque},
263     Date-Added = {2006-07-20 15:22:45 -0400},
264     Date-Modified = {2006-07-20 15:24:22 -0400},
265     Doi = {10.1063/1.2215614},
266     Journal = {J. Chem. Phys.},
267     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Weis_OrientationalOrderHardSphereDipole_06.pdf},
268     Number = {3},
269     Pages = {034504},
270     Title = {Orientational order in high density dipolar hard sphere fluids},
271     Volume = {125},
272     Year = {2006}}
273    
274     @article{Rick04,
275     Author = {S.~W. Rick},
276     Date-Added = {2006-07-18 10:49:48 -0400},
277     Date-Modified = {2006-07-18 14:23:07 -0400},
278     Doi = {10.1063/1.1652434},
279     Journal = {J. Chem. Phys.},
280     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Rick_TIP5P-Ew_04.pdf},
281     Number = {13},
282     Pages = {6085-6093},
283     Title = {A reoptimization of the five-site water potential (\uppercase{TIP5P}) for use with \uppercase{E}wald sums},
284     Volume = {120},
285     Year = {2004}}
286    
287     @article{Horn04,
288     Author = {H.~W. Horn and W.~C. Swope and J.~W. Pitera and J.~D. Madura and T.~J. Dick and G.~L. Hura and T. Head-Gordon},
289     Date-Added = {2006-07-18 10:18:42 -0400},
290     Date-Modified = {2006-07-18 14:21:48 -0400},
291     Doi = {10.1063/1.1683075},
292     Journal = {J. Chem. Phys.},
293     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Horn_TIP4P-Ew_04.pdf},
294     Number = {20},
295     Pages = {9665-9678},
296     Title = {Development of an improved four-site water model for biomolecular simulations: \uppercase{TIP4P-E}w},
297     Volume = {120},
298     Year = {2004}}
299    
300 chrisfen 2918 @article{Brodka04,
301     Author = {A. Br\'{o}dka},
302     Date-Added = {2006-04-26 09:41:52 -0400},
303 chrisfen 2957 Date-Modified = {2006-07-18 14:29:43 -0400},
304 chrisfen 2918 Doi = {10.1016/j.cplett.2004.10.086},
305     Journal = {Chem. Phys. Lett.},
306     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
307     Pages = {62-67},
308 chrisfen 2957 Title = {\uppercase{E}wald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
309 chrisfen 2918 Volume = {400},
310     Year = {2004}}
311    
312     @article{deJoannis02,
313     Author = {J. {de Joannis} and A. Arnold and C. Holm},
314     Date-Added = {2006-04-26 09:40:15 -0400},
315 chrisfen 2957 Date-Modified = {2006-07-18 14:35:47 -0400},
316     Doi = {10.1063/1.149195},
317 chrisfen 2918 Journal = {J. Chem. Phys.},
318     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
319     Number = {6},
320     Pages = {2503-2512},
321 chrisfen 2957 Title = {Electrostatics in periodic slab geometries. \uppercase{II}},
322 chrisfen 2918 Volume = {117},
323     Year = {2002}}
324    
325     @article{Kawata01,
326     Author = {M. Kawata and M. Mikami},
327     Date-Added = {2006-04-26 09:38:01 -0400},
328 chrisfen 2957 Date-Modified = {2006-07-18 14:31:24 -0400},
329 chrisfen 2918 Journal = {Chem. Phys. Lett.},
330     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
331     Pages = {157-164},
332 chrisfen 2957 Title = {Rapid calculation of two-dimensional \uppercase{E}wald summation},
333 chrisfen 2918 Volume = {340},
334     Year = {2001}}
335    
336     @article{Arnold02,
337     Author = {A. Arnold and J. {de Joannis} and C. Holm},
338     Date-Added = {2006-04-26 09:36:09 -0400},
339 chrisfen 2957 Date-Modified = {2006-07-18 14:29:18 -0400},
340     Doi = {10.1063/1.149195},
341 chrisfen 2918 Journal = {J. Chem. Phys.},
342     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
343     Number = {6},
344     Pages = {2496-2502},
345 chrisfen 2957 Title = {Electrostatics in periodic slab geometries. \uppercase{I}},
346 chrisfen 2918 Volume = {117},
347     Year = {2002}}
348    
349     @article{Kolafa92,
350     Author = {J. Kolafa and J.~W. Perram},
351     Date-Added = {2006-03-21 09:41:58 -0500},
352 chrisfen 2957 Date-Modified = {2006-07-18 14:41:10 -0400},
353 chrisfen 2918 Journal = {Mol. Simul.},
354     Pages = {351-368},
355 chrisfen 2957 Title = {Cutoff Errors in the \uppercase{E}wald Summation Formulae for Point Charge Systems},
356 chrisfen 2918 Volume = {9},
357     Year = {1992}}
358    
359     @article{Karasawa89,
360     Author = {N. Karasawa and W.~A. {Goddard III}},
361     Date-Added = {2006-03-21 09:11:44 -0500},
362     Date-Modified = {2006-03-21 09:13:00 -0500},
363     Journal = {J. Phys. Chem.},
364     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
365     Pages = {7320-7327},
366     Title = {Acceleration of Convergence for Lattice Sums},
367     Volume = {93},
368     Year = {1989}}
369    
370     @article{Roux99,
371     Author = {B. Roux and T. Simonson},
372     Date-Added = {2006-03-19 20:10:18 -0500},
373     Date-Modified = {2006-03-19 20:12:10 -0500},
374     Journal = {Biophys. Chem.},
375     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
376     Pages = {1-20},
377     Title = {Implicit solvent models},
378     Volume = {78},
379     Year = {1999}}
380    
381     @article{Rokhlin85,
382     Author = {V. Rokhlin},
383     Date-Added = {2006-03-19 20:02:25 -0500},
384     Date-Modified = {2006-03-19 20:04:19 -0500},
385     Doi = {10.1016/0021-9991(85)90002-6},
386     Journal = {J. Comput. Phys.},
387     Month = {September},
388     Number = {2},
389     Pages = {187-207},
390     Title = {Rapid solution of integral equations of classical potential theory},
391     Volume = {60},
392     Year = {1985}}
393    
394     @article{Grossfield00,
395     Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
396     Date-Added = {2006-03-19 19:52:19 -0500},
397     Date-Modified = {2006-03-19 19:54:14 -0500},
398     Journal = {Proteins},
399     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
400     Pages = {211-223},
401     Title = {Dipole Lattice Membrane Model for Protein Calculations},
402     Volume = {41},
403     Year = {2000}}
404    
405     @article{Born20,
406     Author = {M. Born},
407     Date-Added = {2006-03-19 18:05:01 -0500},
408     Date-Modified = {2006-03-19 18:07:42 -0500},
409     Journal = {Z. Physik},
410     Pages = {45-48},
411     Title = {Volumen und hydratationswame der ionen},
412     Volume = {1},
413     Year = {1920}}
414    
415     @article{Luty96,
416     Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
417     Date-Added = {2006-03-18 20:59:19 -0500},
418     Date-Modified = {2006-03-18 21:00:33 -0500},
419     Journal = {J. Phys. Chem.},
420     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
421     Number = {7},
422     Pages = {2581-2587},
423     Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
424     Volume = {100},
425     Year = {1996}}
426    
427     @article{Rhee89,
428     Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
429     Date-Added = {2006-03-18 20:48:07 -0500},
430 chrisfen 2957 Date-Modified = {2006-07-18 14:33:26 -0400},
431 chrisfen 2918 Journal = {Phys. Rev. B},
432     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
433     Number = {1},
434     Pages = {36-42},
435 chrisfen 2957 Title = {\uppercase{E}wald methods in molecular dynamics for systems of finite extent in one of three dimensions},
436 chrisfen 2918 Volume = {40},
437     Year = {1989}}
438    
439     @article{Hunenberger99a,
440     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
441     Date-Added = {2006-03-18 20:14:24 -0500},
442 chrisfen 2957 Date-Modified = {2006-07-18 15:03:36 -0400},
443 chrisfen 2918 Journal = {J. Chem. Phys.},
444     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
445     Number = {4},
446     Pages = {1856-1872},
447 chrisfen 2957 Title = {\uppercase{E}wald artifacts in computer simulations of ionic solvation and ion -- ion interaction: \uppercase{A} continuum electrostatics study},
448 chrisfen 2918 Volume = {110},
449     Year = {1999}}
450    
451     @article{Roberts95,
452     Author = {J.~E. Roberts and J. Schnitker},
453     Date-Added = {2006-03-18 20:12:23 -0500},
454 chrisfen 2957 Date-Modified = {2006-07-18 15:11:50 -0400},
455 chrisfen 2918 Journal = {J. Phys. Chem.},
456     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
457     Pages = {1322-1331},
458 chrisfen 2957 Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: $\mbox{A}$ Systematic Study},
459 chrisfen 2918 Volume = {99},
460     Year = {1995}}
461    
462     @article{Roberts94,
463     Author = {J.~E. Roberts and J. Schnitker},
464     Date-Added = {2006-03-18 20:10:37 -0500},
465     Date-Modified = {2006-03-18 20:12:19 -0500},
466     Journal = {J. Chem. Phys.},
467     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
468     Number = {6},
469     Pages = {5024-5031},
470     Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
471     Volume = {101},
472     Year = {1994}}
473    
474     @article{Yeh99,
475     Author = {I.-C. Yeh and M.~L. Berkowitz},
476     Date-Added = {2006-03-18 19:24:27 -0500},
477 chrisfen 2957 Date-Modified = {2006-07-18 14:34:09 -0400},
478 chrisfen 2918 Journal = {J. Chem. Phys.},
479     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
480     Number = {7},
481     Pages = {3155-3162},
482 chrisfen 2957 Title = {\uppercase{E}wald summation for systems with slab geometry},
483 chrisfen 2918 Volume = {111},
484     Year = {1999}}
485    
486     @article{Parry76,
487     Author = {D.~E. Parry},
488     Date-Added = {2006-03-18 19:11:01 -0500},
489 chrisfen 2957 Date-Modified = {2006-07-18 15:09:52 -0400},
490 chrisfen 2918 Journal = {Surf. Sci.},
491     Pages = {195},
492 chrisfen 2957 Title = {Errata: $\mbox{T}$he electrostatic potential in the surface region of an ionic crystal},
493 chrisfen 2918 Volume = {54},
494     Year = {1976}}
495    
496     @article{Parry75,
497     Author = {D.~E. Parry},
498     Date-Added = {2006-03-18 19:08:40 -0500},
499     Date-Modified = {2006-03-18 19:16:14 -0500},
500     Journal = {Surf. Sci.},
501     Pages = {433-440},
502     Title = {The electrostatic potential in the surface region of an ionic crystal},
503     Volume = {49},
504     Year = {1975}}
505    
506     @article{deLeeuw79,
507     Author = {S.~W. {de Leeuw} and J.~W. Perram},
508     Date-Added = {2006-03-18 19:05:18 -0500},
509     Date-Modified = {2006-03-18 19:07:48 -0500},
510     Journal = {Mol. Phys.},
511     Pages = {1313-1327},
512     Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
513     Volume = {37},
514     Year = {1979}}
515    
516     @article{Heyes77,
517     Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
518     Date-Added = {2006-03-18 19:02:16 -0500},
519     Date-Modified = {2006-03-18 19:04:48 -0500},
520     Journal = {J. Chem. Soc., Faraday Trans. II},
521     Number = {7},
522     Pages = {1485-1496},
523     Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
524     Volume = {73},
525     Year = {1977}}
526    
527     @article{Spohr97,
528     Author = {E. Spohr},
529     Date-Added = {2006-03-18 18:51:02 -0500},
530     Date-Modified = {2006-03-18 18:52:21 -0500},
531     Journal = {J. Chem. Phys.},
532     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
533     Number = {16},
534     Pages = {6342-6348},
535     Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
536     Volume = {107},
537     Year = {1997}}
538    
539     @article{York94,
540     Author = {D. York and W. Yang},
541     Date-Added = {2006-03-18 11:52:58 -0500},
542 chrisfen 2957 Date-Modified = {2006-07-18 14:34:21 -0400},
543 chrisfen 2918 Journal = {J. Chem. Phys.},
544     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
545     Number = {4},
546     Pages = {3298-3300},
547 chrisfen 2957 Title = {The fast Fourier Poisson method for calculating \uppercase{E}wald sums},
548 chrisfen 2918 Volume = {101},
549     Year = {1994}}
550    
551     @article{Shimada93,
552     Author = {J. Shimada and H. Kaneko and T. Takada},
553     Date-Added = {2006-03-18 11:10:38 -0500},
554     Date-Modified = {2006-03-18 11:12:10 -0500},
555     Journal = {J. Comp. Chem.},
556     Pages = {867-78},
557     Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
558     Volume = {14},
559     Year = {1993}}
560    
561     @article{Luty94,
562     Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
563     Date-Added = {2006-03-18 10:37:17 -0500},
564 chrisfen 2957 Date-Modified = {2006-07-18 14:31:50 -0400},
565 chrisfen 2918 Journal = {Mol. Simul.},
566     Pages = {11-20},
567 chrisfen 2957 Title = {A comparison of particle-particle particle-mesh and \uppercase{E}wald methods for calculating electrostatic interactions in periodic systems},
568 chrisfen 2918 Volume = {14},
569     Year = {1994}}
570    
571     @book{Hockney81,
572     Address = {New York},
573     Author = {R.~W. Hockney and J.~W. Eastwood},
574     Date-Added = {2006-03-18 10:33:19 -0500},
575     Date-Modified = {2006-03-18 10:35:04 -0500},
576     Publisher = {McGraw-Hill},
577     Title = {Computer Simulation Using Particles},
578     Year = {1981}}
579    
580     @article{Sagui99,
581     Author = {C. Sagui and T.~A. Darden},
582     Date-Added = {2006-03-17 18:27:01 -0500},
583 chrisfen 2957 Date-Modified = {2006-07-18 15:12:58 -0400},
584 chrisfen 2918 Journal = {Annu. Rev. Biophys. Biomol. Struct.},
585     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_electrostaticInBiomolecules_99.pdf},
586     Pages = {155-179},
587 chrisfen 2957 Title = {Molecular Dynamics Simulations of Biomolecules: $\mbox{L}$ong-Range Electrostatic Effects},
588 chrisfen 2918 Volume = {28},
589     Year = {1999}}
590    
591     @article{Perram88,
592     Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
593     Date-Added = {2006-03-17 13:42:04 -0500},
594     Date-Modified = {2006-03-17 13:59:01 -0500},
595     Journal = {Mol. Phys.},
596     Pages = {875-893},
597     Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
598     Volume = {65},
599     Year = {1988}}
600    
601     @article{Woodcock71,
602     Author = {L.~V. Woodcock and K. Singer},
603     Date-Added = {2006-03-17 11:14:17 -0500},
604 chrisfen 2957 Date-Modified = {2006-07-18 14:46:33 -0400},
605 chrisfen 2918 Journal = {Trans. Faraday Soc.},
606     Pages = {12-30},
607 chrisfen 2957 Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by $\mbox{Monte Carlo}$ Computation},
608 chrisfen 2918 Volume = {67},
609     Year = {1971}}
610    
611     @article{Smith81,
612     Author = {E.~R. Smith},
613     Date-Added = {2006-03-16 13:47:17 -0500},
614     Date-Modified = {2006-03-16 13:48:34 -0500},
615     Journal = {Proc. R. Soc. London Ser. A},
616     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
617     Pages = {475-505},
618     Title = {Electrostatic Energy in Ionic Crystals},
619     Volume = {375},
620     Year = {1981}}
621    
622     @article{Weber00,
623     Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
624     Date-Added = {2006-03-16 09:49:22 -0500},
625 chrisfen 2957 Date-Modified = {2006-07-18 15:18:48 -0400},
626 chrisfen 2918 Doi = {10.1021/jp9937757},
627     Journal = {J. Phys. Chem. B},
628     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
629     Number = {15},
630     Pages = {3668-3675},
631 chrisfen 2957 Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under \uppercase{E}wald Boundary Conditions: $\mbox{I}$nfluence of Artificial Periodicity on Peptide Conformation},
632 chrisfen 2918 Volume = {104},
633     Year = {2000}}
634    
635     @article{Hunenberger99b,
636     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
637     Date-Added = {2006-03-16 09:45:10 -0500},
638 chrisfen 2957 Date-Modified = {2006-07-18 15:03:59 -0400},
639 chrisfen 2918 Journal = {Biophys. Chem.},
640     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
641     Pages = {69-88},
642 chrisfen 2957 Title = {Effect of artificial periodicity in simulations of biomolecules under \uppercase{E}wald boundary conditions: \uppercase{A} continuum electrostatics study},
643 chrisfen 2918 Volume = {78},
644     Year = {1999}}
645    
646     @article{Petersen95,
647     Author = {H.~G. Petersen},
648     Date-Added = {2006-03-16 08:43:02 -0500},
649 chrisfen 2957 Date-Modified = {2006-07-18 14:33:13 -0400},
650 chrisfen 2918 Journal = {J. Chem. Phys.},
651     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
652     Month = {September},
653     Number = {9},
654     Pages = {3668-3679},
655 chrisfen 2957 Title = {Accuracy and efficiency of the particle mesh \uppercase{E}wald method},
656 chrisfen 2918 Volume = {103},
657     Year = {1995}}
658    
659     @article{Luty95,
660     Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
661     Date-Added = {2006-03-16 08:39:13 -0500},
662     Date-Modified = {2006-03-16 08:41:15 -0500},
663     Journal = {J. Chem. Phys.},
664     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
665     Number = {8},
666     Pages = {3014-3021},
667     Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
668     Volume = {103},
669     Year = {1995}}
670    
671     @article{Barker73,
672     Author = {J.~A. Barker and R.~O. Watts},
673     Date-Added = {2006-03-15 18:58:17 -0500},
674 chrisfen 2957 Date-Modified = {2006-07-18 14:44:12 -0400},
675 chrisfen 2918 Journal = {Mol. Phys.},
676     Pages = {789-792},
677 chrisfen 2957 Title = {$\mbox{Monte Carlo}$ studies of the dielectric properties of water-like models},
678 chrisfen 2918 Volume = {26},
679     Year = {1973}}
680    
681     @article{Adams79,
682     Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
683     Date-Added = {2006-03-15 17:46:36 -0500},
684     Date-Modified = {2006-03-15 17:48:04 -0500},
685     Journal = {Mol. Phys.},
686     Number = {2},
687     Pages = {387-400},
688     Title = {The computer simulation of polar liquids},
689     Volume = {38},
690     Year = {1979}}
691    
692     @article{Rahman71,
693     Author = {A. Rahman and F.~H. Stillinger},
694     Date-Added = {2006-03-15 17:04:53 -0500},
695     Date-Modified = {2006-03-15 17:07:29 -0500},
696     Journal = {J. Chem. Phys.},
697     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
698     Month = {October},
699     Number = {7},
700     Pages = {3336-3359},
701     Title = {Molecular Dynamics Study of Liquid Water},
702     Volume = {55},
703     Year = {1971}}
704    
705     @article{Andrea83,
706     Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
707     Date-Added = {2006-03-15 15:16:12 -0500},
708     Date-Modified = {2006-03-15 15:18:10 -0500},
709     Journal = {J. Chem. Phys.},
710     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
711     Number = {9},
712     Pages = {4576-4584},
713     Title = {The role of long ranged forces in determining the structure and properties of liquid water},
714     Volume = {79},
715     Year = {1983}}
716    
717     @article{Brush66,
718     Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
719     Date-Added = {2006-03-13 16:55:39 -0500},
720 chrisfen 2957 Date-Modified = {2006-07-18 14:48:59 -0400},
721 chrisfen 2918 Journal = {J. Chem. Phys.},
722     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
723     Month = {September},
724     Number = {6},
725     Pages = {2102-2118},
726 chrisfen 2957 Title = {$\mbox{Monte Carlo}$ Study of a One-Component Plasma. \uppercase{I}},
727 chrisfen 2918 Volume = {45},
728     Year = {1966}}
729    
730     @article{Ewald21,
731     Author = {P.~P. Ewald},
732     Date-Added = {2006-03-13 13:32:04 -0500},
733     Date-Modified = {2006-03-16 22:39:27 -0500},
734     Journal = {Ann. Physik},
735     Pages = {253-287},
736     Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
737     Volume = {64},
738     Year = {1921}}
739    
740     @article{Jones56,
741     Author = {R.~E. Jones and D.~H. Templeton},
742     Date-Added = {2006-03-13 13:25:58 -0500},
743 chrisfen 2957 Date-Modified = {2006-07-18 14:24:50 -0400},
744 chrisfen 2918 Journal = {J. Chem. Phys.},
745     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
746     Number = {5},
747     Pages = {1062-1063},
748 chrisfen 2957 Title = {Optimum Atomic Shape for \uppercase{B}ertaut Series},
749 chrisfen 2918 Volume = {25},
750     Year = {1956}}
751    
752     @article{Heyes81,
753     Author = {D.~M. Heyes},
754     Date-Added = {2006-03-13 13:12:45 -0500},
755     Date-Modified = {2006-03-13 13:14:27 -0500},
756     Journal = {J. Chem. Phys.},
757     Keywords = {Empty Keywords},
758     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
759     Number = {3},
760     Pages = {1924-1929},
761     Title = {Electrostatic potentials and fields in infinite point charge lattices},
762     Volume = {74},
763     Year = {1981}}
764    
765     @article{Steinbach94,
766     Author = {P.~J. Steinbach and B.~R. Brooks},
767     Date-Added = {2006-03-12 19:26:45 -0500},
768     Date-Modified = {2006-03-12 19:29:43 -0500},
769     Doi = {10.1002/jcc.540150702},
770     Journal = {J. Comput. Chem.},
771     Number = {7},
772     Pages = {667-683},
773     Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
774     Volume = {15},
775     Year = {1994}}
776    
777     @article{deLeeuw80,
778     Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
779     Date-Added = {2006-03-07 10:26:31 -0500},
780 chrisfen 2957 Date-Modified = {2006-07-18 14:52:02 -0400},
781 chrisfen 2918 Journal = {Proc. R. Soc. London Ser. A},
782     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
783     Number = {1752},
784     Pages = {27-56},
785 chrisfen 2957 Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. \uppercase{I. L}attice Sums and Dielectric Constants},
786 chrisfen 2918 Volume = {373},
787     Year = {1980}}
788    
789     @article{Essmann95,
790     Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
791     Date-Added = {2006-03-05 12:25:25 -0500},
792 chrisfen 2957 Date-Modified = {2006-07-18 14:30:21 -0400},
793 chrisfen 2918 Journal = {J. Chem. Phys.},
794     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
795     Number = {19},
796     Pages = {8577-8593},
797 chrisfen 2957 Title = {A smooth particle mesh \uppercase{E}wald method},
798 chrisfen 2918 Volume = {103},
799     Year = {1995}}
800    
801     @article{Kast03,
802     Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
803     Date-Added = {2006-02-18 16:47:26 -0500},
804     Date-Modified = {2006-02-18 16:51:25 -0500},
805     Journal = {Chem. Phys. Lett.},
806     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
807     Pages = {398-404},
808     Title = {Integral equation theory for correcting truncation errors in molecular simulations},
809     Volume = {367},
810     Year = {2003}}
811    
812     @article{Tobias01,
813     Author = {D.~J. Tobias},
814     Date-Added = {2006-02-15 11:28:58 -0500},
815 chrisfen 2957 Date-Modified = {2006-07-18 15:21:08 -0400},
816 chrisfen 2918 Journal = {Curr. Opin. Struct. Biol.},
817     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
818     Pages = {253-261},
819 chrisfen 2957 Title = {Electrostatics calculations: $\mbox{R}$ecent methodological advances and applications to membranes},
820 chrisfen 2918 Volume = {11},
821     Year = {2001}}
822    
823     @article{Zahn02,
824     Author = {D. Zahn and B. Schilling and S.~M. Kast},
825     Date-Added = {2006-02-15 09:21:27 -0500},
826 chrisfen 2957 Date-Modified = {2006-07-18 15:19:05 -0400},
827 chrisfen 2918 Journal = {J. Phys. Chem. B},
828     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
829     Number = {41},
830     Pages = {10725-10732},
831 chrisfen 2957 Title = {Enhancement of the \uppercase{W}olf Damped Coulomb Potential: $\mbox{S}$tatic, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
832 chrisfen 2918 Volume = {106},
833     Year = {2002}}
834    
835     @article{Wolf99,
836     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
837     Date-Added = {2006-02-15 09:09:39 -0500},
838 chrisfen 2957 Date-Modified = {2006-07-17 12:28:56 -0400},
839 chrisfen 2918 Journal = {J. Chem. Phys.},
840     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
841     Number = {17},
842     Pages = {8255-8282},
843     Rating = {0},
844     Read = {No},
845 chrisfen 2957 Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
846 chrisfen 2918 Volume = {110},
847     Year = {1999}}
848    
849     @book{Berne90,
850     Address = {Malabar, Florida},
851     Author = {B.~J. Berne and R. Pecora},
852     Publisher = {Robert E. Krieger Publishing Company, Inc.},
853     Title = {Dynamic Light Scattering},
854     Year = 1990}
855    
856     @article{Evans77,
857     Author = {D.~J. Evans},
858     Journal = {Mol. Phys.},
859     Pages = {317-325},
860     Title = {On the representation of orientation space},
861     Volume = 34,
862     Year = 1977}
863    
864     @article{Tuckerman92,
865     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
866     Journal = jcp,
867     Pages = {1990-2001},
868     Title = {Reversible multiple time scale molecular dynamics},
869     Volume = 97,
870     Year = 1992}
871    
872     @book{Hansen86,
873     Address = {London},
874     Author = {J.~P. Hansen and I.~R. McDonald},
875     Chapter = 7,
876     Pages = {199-206},
877     Publisher = {Academic Press},
878     Title = {Theory of Simple Liquids},
879     Year = 1986}
880    
881     @article{Angelani98,
882     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
883 chrisfen 2957 Date-Modified = {2006-07-18 14:59:40 -0400},
884 chrisfen 2918 Journal = prl,
885     Number = 21,
886     Pages = {4648-4651},
887 chrisfen 2957 Title = {Connected Network of Minima as a Model Glass: \uppercase{L}ong Time Dynamics},
888 chrisfen 2918 Volume = 81,
889     Year = 1998}
890    
891     @article{Stillinger82,
892     Author = {F.~H. Stillinger and T.~A. Weber},
893     Journal = pra,
894     Number = 2,
895     Pages = {978-989},
896     Title = {Hidden structure in liquids},
897     Volume = 25,
898     Year = 1982}
899    
900     @article{Stillinger83,
901     Author = {F.~H. Stillinger and T.~A. Weber},
902     Journal = pra,
903     Number = 4,
904     Pages = {2408-2416},
905     Title = {Dynamics of structural transitions in liquids},
906     Volume = 28,
907     Year = 1983}
908    
909     @article{Weber84,
910     Author = {T.~A. Weber and F.~H. Stillinger},
911     Journal = jcp,
912     Number = 6,
913     Pages = {2742-2746},
914     Title = {The effect of density on the inherent structure in liquids},
915     Volume = 80,
916     Year = 1984}
917    
918     @article{Stillinger85,
919     Author = {F.~H. Stillinger and T.~A. Weber},
920     Journal = jcp,
921     Number = 9,
922     Pages = {4767-4775},
923     Title = {Inherent structure theory of liquids in the hard-sphere limit},
924     Volume = 83,
925     Year = 1985}
926    
927     @article{Stillinger98,
928     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
929     Journal = {Nature},
930     Pages = {554-557},
931     Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
932     Volume = 393,
933     Year = 1998}
934    
935     @article{Parkhurst75a,
936     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
937 chrisfen 2957 Date-Modified = {2006-07-18 14:50:48 -0400},
938 chrisfen 2918 Journal = jcp,
939     Number = 6,
940     Pages = {2698-2704},
941 chrisfen 2957 Title = {Dense liquids. \uppercase{I. T}he effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
942 chrisfen 2918 Volume = 63,
943     Year = 1975}
944    
945     @article{Parkhurst75b,
946     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
947 chrisfen 2957 Date-Modified = {2006-07-18 14:51:04 -0400},
948 chrisfen 2918 Journal = jcp,
949     Number = 6,
950     Pages = {2705-2709},
951 chrisfen 2957 Title = {Dense liquids. \uppercase{II. T}he effect of density and temperature on viscosity of tetramethylsilane and benzene},
952 chrisfen 2918 Volume = 63,
953     Year = 1975}
954    
955     @article{Forester97,
956     Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
957     Journal = {J. Chem. Soc. - Faraday Transactions},
958     Pages = {613-619},
959     Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
960     Volume = 93,
961     Year = 1997}
962    
963     @article{Tieleman98,
964     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
965     Journal = {Biophys. J.},
966     Pages = {2786-2801},
967     Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
968     Volume = 74,
969     Year = 1998}
970    
971     @article{Cascales98,
972     Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
973 chrisfen 2957 Date-Modified = {2006-07-18 15:01:21 -0400},
974 chrisfen 2918 Journal = {J. Phys. Chem. B},
975     Pages = {625-631},
976 chrisfen 2957 Title = {Anaesthetic mechanism on a model biological membrane: \uppercase{A} molecular dynamics simulation study},
977 chrisfen 2918 Volume = 102,
978     Year = 1998}
979    
980     @article{Bassolino95,
981     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
982     Journal = {J. Am. Chem. Soc.},
983     Pages = {4118-4129},
984     Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
985     Volume = 117,
986     Year = 1995}
987    
988     @article{Alper95,
989     Author = {H.~E. Alper and T.~R. Stouch},
990     Journal = {J. Phys. Chem.},
991     Pages = {5724-5731},
992     Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
993     Volume = 99,
994     Year = 1995}
995    
996     @article{Sok92,
997     Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
998     Journal = {J. Chem. Phys.},
999     Pages = {4699-4704},
1000     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
1001     Volume = 96,
1002     Year = 1992}
1003    
1004     @article{Rabani99,
1005     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1006     Journal = prl,
1007     Pages = {3649},
1008     Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
1009     Volume = 82,
1010     Year = {1999}}
1011    
1012     @article{Rabani97,
1013     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1014 chrisfen 2957 Date-Modified = {2006-07-18 15:11:37 -0400},
1015 chrisfen 2918 Journal = {J. Chem. Phys.},
1016     Pages = {6867-6876},
1017 chrisfen 2957 Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: $\mbox{C}$age correlations},
1018 chrisfen 2918 Volume = 107,
1019     Year = 1997}
1020    
1021     @article{Gezelter99,
1022     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1023     Journal = jcp,
1024     Pages = 3444,
1025     Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
1026     Volume = 110,
1027     Year = 1999}
1028    
1029     @article{Gezelter98,
1030     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1031     Date-Modified = {2006-02-15 10:18:42 -0500},
1032     Journal = jcp,
1033     Pages = 4695,
1034     Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
1035     Volume = 109,
1036     Year = 1998}
1037    
1038     @article{Gezelter97,
1039     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1040     Journal = jcp,
1041     Pages = 4618,
1042     Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
1043     Volume = 107,
1044     Year = 1997}
1045    
1046     @article{Zwanzig83,
1047     Author = {R. Zwanzig},
1048     Journal = jcp,
1049     Pages = {4507-4508},
1050     Title = {On the relation between self-diffusion and viscosity of liquids},
1051     Volume = 79,
1052     Year = 1983}
1053    
1054     @article{Zwanzig88,
1055     Author = {R. Zwanzig},
1056     Journal = {Proc. Natl. Acad. Sci. USA},
1057     Pages = 2029,
1058     Title = {Diffusion in rough potential},
1059     Volume = 85,
1060     Year = 1988}
1061    
1062     @article{Stillinger95,
1063     Author = {F.~H. Stillinger},
1064     Journal = {Science},
1065     Pages = {1935-1939},
1066     Title = {A Topographic View of Supercooled Liquids and Glass Formation},
1067     Volume = 267,
1068     Year = 1995}
1069    
1070     @incollection{Angell85,
1071     Address = {Springfield, VA},
1072     Author = {C.~A. Angell},
1073     Booktitle = {Relaxations in Complex Systems},
1074     Editor = {K.~Ngai and G.~B. Wright},
1075     Pages = 1,
1076     Publisher = {National Technical Information Service, U.S. Department of Commerce},
1077     Title = {unknown},
1078     Year = 1985}
1079    
1080     @article{Bembenek96,
1081     Author = {S.~D. Bembenek and B.~B. Laird},
1082     Journal = jcp,
1083     Pages = 5199,
1084     Title = {The role of localization in glasses and supercooled liquids},
1085     Volume = 104,
1086     Year = 1996}
1087    
1088     @article{Sun97a,
1089     Author = {X. Sun and W.~H. Miller},
1090     Date-Modified = {2006-02-15 10:33:35 -0500},
1091     Journal = jcp,
1092     Pages = 6346,
1093     Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
1094     Volume = 106,
1095     Year = 1997}
1096    
1097     @article{Spath96,
1098     Author = {B.~W. Spath and W.~H. Miller},
1099     Journal = jcp,
1100     Pages = 95,
1101     Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
1102     Volume = 104,
1103     Year = 1996}
1104    
1105     @book{Warshel91,
1106     Address = {New York},
1107     Author = {Arieh Warshel},
1108     Publisher = {Wiley},
1109     Title = {Computer modeling of chemical reactions in enzymes and solutions},
1110     Year = 1991}
1111    
1112     @article{Vuilleumier97,
1113     Author = {Rodolphe Vuilleumier and Daniel Borgis},
1114     Journal = jpc,
1115     Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
1116     Volume = {in press},
1117     Year = 1997}
1118    
1119     @article{Kob95a,
1120     Author = {W. Kob and H.~C. Andersen},
1121 chrisfen 2957 Date-Modified = {2006-07-18 15:04:56 -0400},
1122 chrisfen 2918 Journal = pre,
1123     Pages = {4626-4641},
1124 chrisfen 2957 Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones} mixtures: \uppercase{T}he van \uppercase{H}ove corraltion function},
1125 chrisfen 2918 Volume = 51,
1126     Year = 1995}
1127    
1128     @article{Kob95b,
1129     Author = {W. Kob and H.~C. Andersen},
1130 chrisfen 2957 Date-Modified = {2006-07-18 14:50:19 -0400},
1131 chrisfen 2918 Journal = pre,
1132     Pages = {4134-4153},
1133 chrisfen 2957 Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones}$ mixtures. \uppercase{II. I}ntermediate scattering function and dynamic susceptibility},
1134 chrisfen 2918 Volume = 52,
1135     Year = 1995}
1136    
1137     @inproceedings{Gotze89,
1138     Address = {Amsterdam},
1139     Author = {W. G{\"{o}}tze},
1140     Booktitle = {Liquids, Freezing and Glass Transitions},
1141     Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
1142     Pages = {287-503},
1143     Publisher = {North-Holland},
1144     Title = {Aspects of Structural Glass Transitions},
1145     Volume = {I},
1146     Year = 1989}
1147    
1148     @article{Sun97b,
1149     Author = {X. Sun and W.~H. Miller},
1150     Date-Modified = {2006-02-15 10:33:29 -0500},
1151     Journal = jcp,
1152     Pages = 916,
1153     Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
1154     Year = 1997}
1155    
1156     @article{Keshavamurthy94,
1157     Author = {S. Keshavamurthy and W.~H. Miller},
1158     Journal = cpl,
1159     Pages = 189,
1160     Title = {ivr},
1161     Volume = 218,
1162     Year = 1994}
1163    
1164     @article{Billing75,
1165     Author = {G.~D. Billing},
1166     Journal = cpl,
1167     Pages = 391,
1168     Title = {ehrenfest},
1169     Volume = 30,
1170     Year = 1975}
1171    
1172     @article{Chang90,
1173     Author = {Y.-T. Chang and W.~H. Miller},
1174     Journal = jpc,
1175     Pages = {5884-5888},
1176     Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
1177     Volume = 94,
1178     Year = 1990}
1179    
1180     @article{Shor94,
1181     Author = {P.W. Shor},
1182 chrisfen 2957 Date-Modified = {2006-07-18 15:13:14 -0400},
1183 chrisfen 2918 Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
1184     Pages = {124-134},
1185 chrisfen 2957 Title = {Algorithms for quantum computation: $\mbox{D}$iscrete logarithms and factoring},
1186 chrisfen 2918 Year = 1994}
1187    
1188     @article{Feynman82,
1189     Author = {R.~P. Feynman},
1190     Journal = {Int. J. Theor. Phys.},
1191     Pages = {467-488},
1192     Title = {Simulating physics with computers},
1193     Volume = 21,
1194     Year = 1982}
1195    
1196     @article{Grover97,
1197     Author = {L.~K. Grover},
1198     Journal = prl,
1199     Pages = {4709-4712},
1200     Title = {Quantum computers can search arbitrarily large databases by a single query},
1201     Volume = 79,
1202     Year = 1997}
1203    
1204     @article{Chuang98,
1205     Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
1206     Journal = prl,
1207     Pages = {3408-3411},
1208     Title = {Experimental Implementation of Fast Quantum Searching},
1209     Volume = 80,
1210     Year = 1998}
1211    
1212     @article{Monroe95,
1213     Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
1214     Journal = prl,
1215     Pages = 4714,
1216     Title = {Demonstration of a fundamental quantum logic gate},
1217     Volume = 75,
1218     Year = 1995}
1219    
1220     @article{Lent93,
1221     Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
1222     Journal = {Nanotechnology},
1223     Pages = {49-57},
1224     Title = {Quantum Cellular Automata},
1225     Volume = 4,
1226     Year = 1993}
1227    
1228     @article{Barenco95,
1229     Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
1230     Journal = {Phys. Rev. A},
1231     Pages = {3457-3467},
1232     Title = {elementary gates for quantum computation},
1233     Volume = 52,
1234     Year = 1995}
1235    
1236     @article{Reinot97,
1237     Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
1238     Date-Modified = {2006-02-15 10:31:21 -0500},
1239     Journal = jcp,
1240     Pages = {457-466},
1241     Title = {Electronic dephasing and electron-phonon coupling of aluminum phthalocyanine tetrasulphonate in hyperquenched and annealed glassy films of ethanol and methanol over a broad temperature range},
1242     Volume = 106,
1243     Year = 1997}
1244    
1245     @article{Laflamme96,
1246     Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
1247     Journal = prl,
1248     Pages = 77,
1249     Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
1250     Volume = 98,
1251     Year = 1996}
1252    
1253     @article{Shor95,
1254     Author = {P.~W. Shor},
1255     Journal = {Phys. Rev. A},
1256     Pages = {2493-2496},
1257     Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
1258     Volume = 52,
1259     Year = 1995}
1260    
1261     @article{Calderbank96,
1262     Author = {A.~R. Calderbank and P.~W. Shor},
1263     Journal = {Phys. Rev. A},
1264     Pages = {1098-1105},
1265     Title = {Good quantum error-correcting codes exist},
1266     Volume = 54,
1267     Year = 1996}
1268    
1269     @article{Steane96,
1270     Author = {A.~M. Steane},
1271     Journal = prl,
1272     Pages = {793-797},
1273     Title = {Error correcting codes in quantum theory},
1274     Volume = 77,
1275     Year = 1996}
1276    
1277     @article{Gezelter95,
1278     Author = {J.~D. Gezelter and W.~H. Miller},
1279     Journal = jcp,
1280     Pages = {7868-7876},
1281     Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
1282     Volume = 103,
1283     Year = 1995}
1284    
1285     @article{Chakrabarti92,
1286     Author = {A.~C. Chakrabarti and D.~W. Deamer},
1287     Journal = {Biochimica et Biophysica Acta},
1288     Pages = {171-177},
1289     Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
1290     Volume = 1111,
1291     Year = 1992}
1292    
1293     @article{Paula96,
1294     Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
1295     Journal = {Biophys. J.},
1296     Pages = {339-348},
1297     Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
1298     Volume = 70,
1299     Year = 1996}
1300    
1301     @article{Little96,
1302     Author = {H.~J. Little},
1303     Journal = {Pharmacology \& Therapeutics},
1304     Pages = {37-58},
1305     Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
1306     Volume = 69,
1307     Year = 1996}
1308    
1309     @article{McKinnon92,
1310     Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
1311     Journal = jpc,
1312     Pages = {10497-10506},
1313     Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
1314     Volume = 96,
1315     Year = 1992}
1316    
1317     @article{Venable93,
1318     Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
1319 chrisfen 2957 Date-Modified = {2006-07-18 15:17:14 -0400},
1320 chrisfen 2918 Journal = {Science},
1321     Pages = {223-226},
1322 chrisfen 2957 Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: $\mbox{A}$n Investigation of Membrane Fluidity},
1323 chrisfen 2918 Volume = 262,
1324     Year = 1993}
1325    
1326     @article{Essmann99,
1327     Author = {U. Essmann and M.~L. Berkowitz},
1328     Journal = {Biophys. J.},
1329     Pages = {2081-2089},
1330     Title = {Dynamical properties of phospholipid bilayers from computer simulation},
1331     Volume = 76,
1332     Year = 1999}
1333    
1334     @article{Tu98,
1335     Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
1336 chrisfen 2957 Date-Modified = {2006-07-18 15:16:12 -0400},
1337 chrisfen 2918 Journal = {Biophys. J.},
1338     Pages = {2123-2134},
1339 chrisfen 2957 Title = {Effects of anesthetics on the structure of a phospholipid bilayer: $\mbox{M}$olecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
1340 chrisfen 2918 Volume = 75,
1341     Year = 1998}
1342    
1343     @article{Pomes96,
1344     Author = {R. Pomes and B. Roux},
1345 chrisfen 2957 Date-Modified = {2006-07-18 15:10:47 -0400},
1346 chrisfen 2918 Journal = {Biophys. J.},
1347     Pages = {19-39},
1348 chrisfen 2957 Title = {Structure and dynamics of a proton wire: $\mbox{A}$ theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
1349 chrisfen 2918 Volume = 71,
1350     Year = 1996}
1351    
1352     @article{Duwez60,
1353     Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
1354     Journal = {J. Appl. Phys.},
1355     Pages = {1136-1137},
1356     Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
1357     Volume = 31,
1358     Year = 1960}
1359    
1360     @article{Peker93,
1361     Author = {A. Peker and W.~L. Johnson},
1362     Journal = {Appl. Phys. Lett.},
1363     Pages = {2342-2344},
1364     Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
1365     Volume = 63,
1366     Year = 1993}
1367    
1368     @article{ChoiYim97,
1369     Author = {H. Choi-Yim and W.~L. Johnson},
1370     Journal = {Appl. Phys. Lett.},
1371     Pages = {3808-3810},
1372     Title = {Bulk metallic glass matrix composites},
1373     Volume = 71,
1374     Year = 1997}
1375    
1376     @article{Sun96,
1377     Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
1378     Journal = {J. Mater. Res.},
1379     Pages = {2738-2743},
1380     Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
1381     Volume = 11,
1382     Year = 1996}
1383    
1384     @article{Heller93,
1385     Author = {H. Heller and M. Schaefer and K. Schulten},
1386     Journal = jpc,
1387     Pages = {8343-8360},
1388     Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
1389     Volume = 97,
1390     Year = 1993}
1391    
1392     @article{Kushick76,
1393     Author = {J. Kushick and B.~J. Berne},
1394     Journal = jcp,
1395     Pages = {1362-1367},
1396     Title = {Computer Simulation of anisotropic molecular fluids},
1397     Volume = 64,
1398     Year = 1976}
1399    
1400     @article{Berardi96,
1401     Author = {R. Berardi and S. Orlandi and C Zannoni},
1402     Journal = cpl,
1403     Pages = {357-362},
1404     Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
1405     Volume = 261,
1406     Year = 1996}
1407    
1408     @article{Berardi99,
1409     Author = {R. Berardi and S. Orlandi and C. Zannoni},
1410 chrisfen 2957 Date-Modified = {2006-07-18 14:44:37 -0400},
1411 chrisfen 2918 Journal = {Int. J. Mod. Phys. C},
1412     Pages = {477-484},
1413 chrisfen 2957 Title = {$\mbox{Monte Carlo}$ simulations of rod-like $\mbox{Gay-Berne}$ mesogens with transverse dipoles},
1414 chrisfen 2918 Volume = 10,
1415     Year = 1999}
1416    
1417     @article{Pasterny00,
1418     Author = {K. Pasterny and E. Gwozdz and A. Brodka},
1419 chrisfen 2957 Date-Modified = {2006-07-18 15:10:06 -0400},
1420 chrisfen 2918 Journal = {J. Mol. Liq.},
1421     Pages = {173-184},
1422 chrisfen 2957 Title = {Properties of a model liquid crystal: $\mbox{Polar Gay-Berne}$ particles},
1423 chrisfen 2918 Volume = 85,
1424     Year = 2000}
1425    
1426     @article{Jorgensen83,
1427     Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
1428     Journal = jcp,
1429     Pages = {926-935},
1430     Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
1431     Volume = 79,
1432     Year = 1983}
1433    
1434     @article{Berardi98,
1435     Author = {R. Berardi and C. Fava and C. Zannoni},
1436     Journal = cpl,
1437     Pages = {8-14},
1438     Title = {A Gay-Berne potential for dissimilar biaxial particles},
1439     Volume = 297,
1440     Year = 1998}
1441    
1442     @article{Luckhurst90,
1443     Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
1444 chrisfen 2957 Date-Modified = {2006-07-18 14:54:27 -0400},
1445 chrisfen 2918 Journal = {Liquid Crystals},
1446     Pages = {451-464},
1447 chrisfen 2957 Title = {Computer simulation studies of anisotropic systems {XIX}. \uppercase{M}esophases formed by the $\mbox{Gay-Berne}$ model mesogen},
1448 chrisfen 2918 Volume = 8,
1449     Year = 1990}
1450    
1451     @article{Gay81,
1452     Author = {J.~G. Gay and B.~J. Berne},
1453     Journal = jcp,
1454     Pages = {3316-3319},
1455     Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
1456     Volume = 74,
1457     Year = 1981}
1458    
1459     @article{Berne72,
1460     Author = {B.~J. Berne and P. Pechukas},
1461     Journal = jcp,
1462     Pages = {4213-4216},
1463     Title = {Gaussian Model Potentials for Molecular Interactions},
1464     Volume = 56,
1465     Year = 1972}
1466    
1467     @article{Perram96,
1468     Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
1469 chrisfen 2957 Date-Modified = {2006-07-18 15:10:36 -0400},
1470 chrisfen 2918 Journal = pre,
1471     Pages = {6565-6572},
1472 chrisfen 2957 Title = {Ellipsoid contact potential: $\mbox{T}$heory and relation to overlap potentials},
1473 chrisfen 2918 Volume = 54,
1474     Year = 1996}
1475    
1476     @article{Cornell95,
1477     Author = {W.~D. Cornell and P. Cieplak and C.~I. Bayly and I.~R. Gould and K.~M. {Merz, Jr.} and D.~M. Ferguson and D.~C. Spellmeyer and T. Fox and J.~W. Caldwell and P.~A. Kollman},
1478     Journal = jacs,
1479     Pages = {5179-5197},
1480     Title = {A second generation force field for the simulation of proteins and nucleic acids},
1481     Volume = 117,
1482     Year = 1995}
1483    
1484     @article{Brooks83,
1485     Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
1486 chrisfen 2957 Date-Modified = {2006-07-18 15:00:32 -0400},
1487 chrisfen 2918 Journal = {J. Comp. Chem.},
1488     Pages = {187-217},
1489 chrisfen 2957 Title = {\uppercase{CHARMM: A} Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
1490 chrisfen 2918 Volume = 4,
1491     Year = 1983}
1492    
1493     @incollection{MacKerell98,
1494     Address = {New York},
1495     Author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and and M. Karplus},
1496     Booktitle = {The Encyclopedia of Computational Chemistry},
1497 chrisfen 2957 Date-Modified = {2006-07-18 15:06:36 -0400},
1498 chrisfen 2918 Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1499     Pages = {271-277},
1500     Publisher = {John Wiley \& Sons},
1501 chrisfen 2957 Title = {$\mbox{CHARMM: T}$he Energy Function and Its Parameterization with an Overview of the Program},
1502 chrisfen 2918 Volume = 1,
1503     Year = 1998}
1504    
1505     @incollection{Jorgensen98a,
1506     Address = {New York},
1507     Author = {W.~L. Jorgensen},
1508     Booktitle = {The Encyclopedia of Computational Chemistry},
1509     Date-Modified = {2006-02-15 10:21:45 -0500},
1510     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1511     Pages = {1986-1989},
1512     Publisher = {John Wiley \& Sons},
1513     Title = {OPLS Force Fields},
1514     Volume = 3,
1515     Year = 1998}
1516    
1517     @article{Rabani00,
1518     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1519     Date-Modified = {2006-02-15 10:30:55 -0500},
1520     Journal = prl,
1521     Pages = 467,
1522     Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
1523     Volume = 85,
1524     Year = 2000}
1525    
1526     @book{Cevc87,
1527     Address = {New York},
1528     Author = {G. Cevc and D. Marsh},
1529     Publisher = {John Wiley \& Sons},
1530     Title = {Phospholipid Bilayers},
1531     Year = 1987}
1532    
1533     @article{Janiak79,
1534     Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
1535     Journal = {J. Biol. Chem.},
1536     Pages = {6068-6078},
1537     Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
1538     Volume = 254,
1539     Year = 1979}
1540    
1541     @article{Mazur92,
1542     Author = {E. Mazur},
1543 chrisfen 2957 Date-Modified = {2006-07-18 14:55:07 -0400},
1544 chrisfen 2918 Journal = {Optics and Photonics News},
1545     Pages = 38,
1546 chrisfen 2957 Title = {Qualitative vs. Quantititative Thinking: \uppercase{A}re we teaching the right thing?},
1547 chrisfen 2918 Volume = 3,
1548     Year = 1992}
1549    
1550     @book{Mazur97,
1551     Address = {New Jersey},
1552     Author = {Eric Mazur},
1553 chrisfen 2957 Date-Modified = {2006-07-18 15:07:06 -0400},
1554 chrisfen 2918 Publisher = {Prentice Hall},
1555 chrisfen 2957 Title = {Peer Instruction: $\mbox{A}$ User's Manual},
1556 chrisfen 2918 Year = 1997}
1557    
1558     @article{Wigner55,
1559     Author = {E.~P. Wigner},
1560     Journal = {Annals of Mathematics},
1561     Pages = {548-564},
1562     Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
1563     Volume = 62,
1564     Year = 1955}
1565    
1566     @article{Gaukel98,
1567     Author = {C. Gaukel and H.~R. Schober},
1568     Journal = {Solid State Comm.},
1569     Pages = {1-5},
1570     Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
1571     Volume = 107,
1572     Year = 1998}
1573    
1574     @article{Qi99,
1575     Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
1576     Journal = prb,
1577     Number = 5,
1578     Pages = {3527-3533},
1579     Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
1580     Volume = 59,
1581     Year = 1999}
1582    
1583     @article{Khorunzhy97,
1584     Author = {A. Khorunzhy and G.~J. Rodgers},
1585     Journal = {J. Math. Phys.},
1586     Pages = {3300-3320},
1587     Title = {Eigenvalue distribution of large dilute random matrices},
1588     Volume = 38,
1589     Year = 1997}
1590    
1591     @article{Rodgers88,
1592     Author = {G.~J. Rodgers and A. Bray},
1593     Journal = {Phys. Rev. B},
1594     Pages = 355703562,
1595     Title = {Density of States of a Sparse Random Matrix},
1596     Volume = 37,
1597     Year = 1988}
1598    
1599     @article{Rodgers90,
1600     Author = {G.~J. Rodgers and C. {De Dominicis}},
1601     Journal = {J. Phys. A: Math. Gen.},
1602     Pages = {1567-1573},
1603     Title = {Density of states of sparse random matrices},
1604     Volume = 23,
1605     Year = 1990}
1606    
1607     @inproceedings{Barker80,
1608     Author = {J.~A. Barker},
1609     Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
1610     Editor = {D. Ceperley},
1611     Pages = {45-6},
1612     Series = {NRCC Workshop Proceedings},
1613     Title = {Reaction field method for polar fluids},
1614     Volume = 9,
1615     Year = 1980}
1616    
1617     @article{Smith82,
1618     Author = {W. Smith},
1619 chrisfen 2957 Date-Modified = {2006-07-18 14:33:49 -0400},
1620 chrisfen 2918 Journal = {CCP5 Quarterly},
1621     Pages = {13-25},
1622 chrisfen 2957 Title = {Point multipoles in the \uppercase{E}wald summation},
1623 chrisfen 2918 Volume = 4,
1624     Year = 1982}
1625    
1626     @article{Daw84,
1627     Author = {M.~S. Daw and M.~I. Baskes},
1628 chrisfen 2957 Date-Modified = {2006-07-18 15:01:56 -0400},
1629 chrisfen 2918 Journal = prb,
1630     Number = 12,
1631     Pages = {6443-6453},
1632 chrisfen 2957 Title = {Embedded-atom method: \uppercase{D}erivation and application to impurities, surfaces, and other defects in metals},
1633 chrisfen 2918 Volume = 29,
1634     Year = 1984}
1635    
1636     @article{Sutton90,
1637     Author = {A.~P. Sutton and J. Chen},
1638     Date-Modified = {2006-02-15 10:33:48 -0500},
1639     Journal = {Phil. Mag. Lett.},
1640     Pages = {139-146},
1641     Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
1642     Volume = 61,
1643     Year = 1990}
1644    
1645     @article{Lu97,
1646     Author = {J. Lu and J.~A. Szpunar},
1647     Journal = {Phil. Mag. A},
1648     Pages = {1057-1066},
1649     Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
1650     Volume = {75},
1651     Year = {1997}}
1652    
1653     @article{Shlesinger99,
1654     Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
1655     Journal = {Am. J. Phys.},
1656     Pages = {1253-1259},
1657     Title = {Above, below, and beyond Brownian motion},
1658     Volume = 67,
1659     Year = 1999}
1660    
1661     @article{Klafter96,
1662     Author = {J. Klafter and M. Shlesinger and G. Zumofen},
1663     Journal = {Physics Today},
1664     Pages = {33-39},
1665     Title = {Beyond Brownian Motion},
1666     Volume = 49,
1667     Year = 1996}
1668    
1669     @article{Blumen83,
1670     Author = {A. Blumen and J. Klafter and G. Zumofen},
1671     Journal = {Phys. Rev. B},
1672     Pages = {3429-3435},
1673     Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
1674     Volume = 27,
1675     Year = 1983}
1676    
1677     @article{Klafter94,
1678     Author = {J. Klafter and G. Zumofen},
1679     Journal = jpc,
1680     Pages = {7366-7370},
1681     Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
1682     Volume = 98,
1683     Year = 1994}
1684    
1685     @article{Dzugutov92,
1686     Author = {M. Dzugutov},
1687     Journal = pra,
1688     Pages = {R2984-R2987},
1689     Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
1690     Volume = 46,
1691     Year = 1992}
1692    
1693     @article{Moore94,
1694     Author = {P. Moore and T. Keyes},
1695 chrisfen 2957 Date-Modified = {2006-07-18 15:07:46 -0400},
1696 chrisfen 2918 Journal = jcp,
1697     Pages = 6709,
1698 chrisfen 2957 Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: $\mbox{V}$elocity Correlation Functions and Self-Diffusion Constants},
1699 chrisfen 2918 Volume = 100,
1700     Year = 1994}
1701    
1702     @article{Seeley89,
1703     Author = {G. Seeley and T. Keyes},
1704     Journal = jcp,
1705     Pages = {5581-5586},
1706     Title = {Normal-mode analysis of liquid-state dynamics},
1707     Volume = 91,
1708     Year = 1989}
1709    
1710     @article{Madan90,
1711     Author = {B. Madan and T. Keyes and G. Seeley},
1712     Journal = jcp,
1713     Pages = {7565-7569},
1714     Title = {Diffusion in supercooled liquids via normal mode analysis},
1715     Volume = 92,
1716     Year = 1990}
1717    
1718     @article{Madan91,
1719     Author = {B. Madan and T. Keyes and G. Seeley},
1720     Journal = jcp,
1721     Pages = {6762-6769},
1722     Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
1723     Volume = 94,
1724     Year = 1991}
1725    
1726     @article{Buchner92,
1727     Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
1728 chrisfen 2957 Date-Modified = {2006-07-18 14:49:51 -0400},
1729 chrisfen 2918 Journal = jcp,
1730     Pages = {8522-8535},
1731 chrisfen 2957 Title = {The short-time dynamics of molecular liquids. \uppercase{I}nstantaneous-normal-mode theory},
1732 chrisfen 2918 Volume = 97,
1733     Year = 1992}
1734    
1735     @article{Wan94,
1736     Author = {Yi. Wan and R.~M. Stratt},
1737     Journal = jcp,
1738     Pages = {5123-5138},
1739     Title = {Liquid theory for the instantaneous normal modes of a liquid},
1740     Volume = 100,
1741     Year = 1994}
1742    
1743     @article{Stratt95,
1744     Author = {R.~M. Stratt},
1745     Journal = {Acc. Chem. Res.},
1746     Pages = {201-207},
1747     Title = {The instantaneous normal modes of liquids},
1748     Volume = 28,
1749     Year = 1995}
1750    
1751     @article{Nitzan95,
1752     Author = {G.~V. Vijayadamodar and A. Nitzan},
1753     Journal = jcp,
1754     Pages = {2169-2177},
1755     Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
1756     Volume = 103,
1757     Year = 1995}
1758    
1759     @article{Ribeiro98,
1760     Author = {M.~C.~C. Ribeiro and P.~A. Madden},
1761     Journal = jcp,
1762     Pages = {3256-3263},
1763     Title = {Unstable Modes in Ionic Melts},
1764     Volume = 108,
1765     Year = 1998}
1766    
1767     @article{Keyes98,
1768     Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
1769 chrisfen 2957 Date-Modified = {2006-07-18 14:53:08 -0400},
1770 chrisfen 2918 Journal = jcp,
1771     Pages = {4693-4694},
1772 chrisfen 2957 Title = {Comment on a critique of the instantaneous normal mode (\uppercase{INM}) approach to diffusion},
1773 chrisfen 2918 Volume = 109,
1774     Year = 1998}
1775    
1776     @article{Alemany98,
1777     Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
1778 chrisfen 2957 Date-Modified = {2006-07-18 14:58:53 -0400},
1779 chrisfen 2918 Journal = jcp,
1780     Pages = {5175-5176},
1781 chrisfen 2957 Title = {Transport coefficients of liquid transition metals: \uppercase{A} computer simulation study using the embedded atom model},
1782 chrisfen 2918 Volume = 109,
1783     Year = 1998}
1784    
1785     @article{Belonoshko00,
1786     Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
1787     Journal = prb,
1788     Pages = {3838-3844},
1789     Title = {Quasi ab initio molecular dynamic study of Cu melting},
1790     Volume = 61,
1791     Year = 2000}
1792    
1793     @article{Banhart92,
1794     Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1795     Journal = prb,
1796     Pages = {9968-9975},
1797     Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1798     Volume = 46,
1799     Year = 1992}
1800    
1801     @article{Wendt78,
1802     Author = {H. Wendt and F.~F. Abraham},
1803     Journal = prl,
1804     Pages = 1244,
1805     Volume = 41,
1806     Year = 1978}
1807    
1808     @article{Lewis91,
1809     Author = {L.~J. Lewis},
1810     Journal = prb,
1811     Pages = {4245-4254},
1812     Title = {Atomic dynamics through the glass transition},
1813     Volume = 44,
1814     Year = 1991}
1815    
1816     @article{Liu92,
1817     Author = {R.~S. Liu and D.~W. Qi and S. Wang},
1818     Journal = prb,
1819     Pages = {451-453},
1820     Title = {Subpeaks of structure factors for rapidly quenched metals},
1821     Volume = 45,
1822     Year = 1992}
1823    
1824     @article{Anheuser94,
1825     Author = {K. Anheuser and J.P. Northover},
1826     Journal = {Brit. Num. J.},
1827     Pages = 22,
1828     Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
1829     Volume = 64,
1830     Year = 1994}
1831    
1832     @article{Pense92,
1833     Author = {A. W. Pense},
1834     Journal = {Mat. Char.},
1835     Pages = 213,
1836     Title = {The Decline and Fall of the Roman Denarius},
1837     Volume = 29,
1838     Year = 1992}
1839    
1840     @article{Ngai81,
1841     Author = {K.~L. Ngai and F.-S. Liu},
1842     Journal = prb,
1843     Pages = {1049-1065},
1844     Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1845     Volume = 24,
1846     Year = 1981}
1847    
1848     @unpublished{Truhlar00,
1849     Author = {D.~G. Truhlar and A. Kohen},
1850     Date-Modified = {2006-02-15 16:35:52 -0500},
1851     Note = {private correspondence},
1852     Year = {2000}}
1853    
1854     @article{Truhlar78,
1855     Author = {Donald G. Truhlar},
1856     Journal = {J. Chem. Ed.},
1857     Pages = 309,
1858     Title = {Interpretation of the Activation Energy},
1859     Volume = 55,
1860     Year = 1978}
1861    
1862     @book{Tolman27,
1863     Address = {New York},
1864     Author = {R. C. Tolman},
1865     Pages = {260-270},
1866     Publisher = {Chemical Catalog Co.},
1867     Title = {Statistical Mechanics with Applications to Physics and Chemistry},
1868     Year = 1927}
1869    
1870     @article{Tolman20,
1871     Author = {R. C. Tolman},
1872     Journal = jacs,
1873     Pages = 2506,
1874     Title = {Statistical Mechanics Applied to Chemical Kinetics},
1875     Volume = 42,
1876     Year = 1920}
1877    
1878     @article{Ediger96,
1879     Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
1880     Date-Modified = {2006-02-15 10:16:35 -0500},
1881     Journal = jpc,
1882     Pages = 13200,
1883     Title = {Supercooled Liquids and Glasses},
1884     Volume = 100,
1885     Year = 1996}
1886    
1887     @inbook{Blumen86,
1888     Address = {Amsterdam},
1889     Author = {A. Blumen and J. Klafter and G. Zumofen},
1890     Chapter = {Reactions in Disordered Media Modelled by Fractals},
1891     Editor = {Luciano Peitronero and E. Tosatti},
1892     Pages = 399,
1893     Publisher = {North-Holland},
1894     Series = {International Symposium on Fractals in Physics},
1895     Title = {Fractals in Physics},
1896     Year = 1986}
1897    
1898     @article{Shlesinger84,
1899     Author = {M.~F. Shlesinger and E.~W. Montroll},
1900     Journal = {Proc. Natl. Acad. Sci. USA},
1901     Pages = {1280-1283},
1902     Title = {On the Williams-Watts function of dielectric relaxation},
1903     Volume = 81,
1904     Year = 1984}
1905    
1906     @article{Klafter86,
1907     Author = {J. Klafter and M.~F. Shlesinger},
1908     Journal = {Proc. Natl. Acad. Sci. USA},
1909     Pages = {848-851},
1910     Title = {On the relationship among three theories of relaxation in disordered systems},
1911     Volume = 83,
1912     Year = 1986}
1913    
1914     @article{Li01,
1915     Author = {Z. Li and M. Lieberman and W. Hill},
1916 chrisfen 2957 Date-Modified = {2006-07-18 15:05:41 -0400},
1917 chrisfen 2918 Journal = {Langmuir},
1918     Pages = {4887-4894},
1919 chrisfen 2957 Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: \uppercase{U}mbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
1920 chrisfen 2918 Volume = 17,
1921     Year = 2001}
1922    
1923     @article{Evans93,
1924     Author = {J.~W. Evans},
1925     Date-Modified = {2006-02-15 10:17:03 -0500},
1926     Journal = rmp,
1927     Pages = {1281-1329},
1928     Title = {Random and Cooperative Sequential Adsorption},
1929     Volume = 65,
1930     Year = 1993}
1931    
1932     @article{Dwyer1977,
1933     Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1934     Journal = {Surf. Sci.},
1935     Pages = 617,
1936     Volume = 64,
1937     Year = 1977}
1938    
1939     @article{Macritche78,
1940     Author = {F. MacRitche},
1941     Date-Modified = {2006-02-15 10:27:37 -0500},
1942     Journal = {Adv. Protein Chem.},
1943     Pages = 283,
1944     Volume = 32,
1945     Year = 1978}
1946    
1947     @article{Feder80,
1948     Author = {J. Feder},
1949     Date-Modified = {2006-02-15 10:17:21 -0500},
1950     Journal = {J. Theor. Biol.},
1951     Pages = 237,
1952     Volume = 87,
1953     Year = 1980}
1954    
1955     @article{Ramsden93,
1956     Author = {J.~J. Ramsden},
1957     Date-Modified = {2006-02-15 10:31:03 -0500},
1958     Journal = prl,
1959     Pages = 295,
1960     Volume = 71,
1961     Year = 1993}
1962    
1963     @article{Egelhoff89,
1964     Author = {W.~F. Egelhoff and I. Jacob},
1965     Date-Modified = {2006-02-15 10:16:54 -0500},
1966     Journal = prl,
1967     Pages = 921,
1968     Volume = 62,
1969     Year = 1989}
1970    
1971     @article{Viot92a,
1972     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1973 chrisfen 2957 Date-Modified = {2006-07-18 14:57:12 -0400},
1974 chrisfen 2918 Journal = jpc,
1975     Pages = {5212-5218},
1976 chrisfen 2957 Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. \uppercase{J}AMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1977 chrisfen 2918 Volume = 97,
1978     Year = 1992}
1979    
1980     @article{Viot92b,
1981     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1982     Date-Modified = {2006-02-15 10:12:57 -0500},
1983     Journal = {Physica A},
1984     Pages = {248-252},
1985     Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
1986     Volume = 191,
1987     Year = 1992}
1988    
1989     @article{Dobson1987,
1990     Author = {B.~W. Dobson},
1991     Journal = prb,
1992     Pages = 1068,
1993     Volume = 36,
1994     Year = 1987}
1995    
1996     @article{Boyer95,
1997     Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1998     Date-Modified = {2006-02-15 10:15:52 -0500},
1999     Journal = jcp,
2000     Pages = 1607,
2001     Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
2002     Volume = 103,
2003     Year = 1995}
2004    
2005     @article{Viot92c,
2006     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
2007     Date-Modified = {2006-02-15 10:13:03 -0500},
2008     Journal = {Physica A},
2009     Pages = {248-252},
2010     Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
2011     Volume = 191,
2012     Year = 1992}
2013    
2014     @article{Ricci94,
2015     Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
2016     Date-Modified = {2006-02-15 10:31:32 -0500},
2017     Journal = jcp,
2018     Pages = 9164,
2019     Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
2020     Volume = 101,
2021     Year = 1994}
2022    
2023     @article{Semmler98,
2024     Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
2025     Date-Modified = {2006-02-15 10:14:46 -0500},
2026     Journal = {Langmuir},
2027     Pages = {5127-5132},
2028     Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
2029     Volume = 14,
2030     Year = 1998}
2031    
2032     @article{Solomon86,
2033     Author = {H. Solomon and H. Weiner},
2034     Date-Modified = {2006-02-15 10:10:38 -0500},
2035     Journal = {Comm. Statistics A},
2036     Pages = {2571-2607},
2037     Title = {A REVIEW OF THE PACKING PROBLEM},
2038     Volume = 15,
2039     Year = 1986}
2040    
2041     @article{Bonnier93,
2042     Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
2043     Date-Modified = {2006-02-15 10:08:35 -0500},
2044     Journal = {Physica A},
2045     Pages = {1-10},
2046     Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
2047     Volume = 198,
2048     Year = 1993}
2049    
2050     @book{Frenkel96,
2051     Address = {New York},
2052     Author = {D. Frenkel and B. Smit},
2053 chrisfen 2957 Date-Modified = {2006-07-18 15:02:21 -0400},
2054 chrisfen 2918 Publisher = {Academic Press},
2055 chrisfen 2957 Title = {Understanding Molecular Simulation: \uppercase{F}rom Algorithms to Applications},
2056 chrisfen 2918 Year = 1996}
2057    
2058     @article{Dullweber1997,
2059     Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
2060     Journal = jcp,
2061     Number = 15,
2062     Pages = {5840-5851},
2063     Title = {Symplectic splitting methods for rigid body molecular dynamics},
2064     Volume = 107,
2065     Year = 1997}
2066    
2067     @article{Martin98,
2068     Author = {M. Martin and J.~I. Siepmann},
2069 chrisfen 2957 Date-Modified = {2006-07-18 14:54:51 -0400},
2070 chrisfen 2918 Journal = jpcB,
2071     Pages = {2569-2577},
2072 chrisfen 2957 Title = {Transferable Potentials for Phase Equilibria. 1. \uppercase{U}nited-Atom Description of n-Alkanes},
2073 chrisfen 2918 Volume = 102,
2074     Year = 1998}
2075    
2076     @article{Marrink01a,
2077     Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
2078     Date-Modified = {2006-02-15 10:28:09 -0500},
2079     Journal = jacs,
2080     Pages = {8638-8639},
2081     Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
2082     Volume = 123,
2083     Year = 2001}
2084    
2085     @article{Liu96b,
2086     Author = {Y. Liu and T. Ichiye},
2087 chrisfen 2957 Date-Modified = {2006-07-18 15:06:06 -0400},
2088 chrisfen 2918 Journal = jpc,
2089     Pages = {2723-2730},
2090 chrisfen 2957 Title = {Soft sticky dipole potential for liquid water: \uppercase{a} new model},
2091 chrisfen 2918 Volume = 100,
2092     Year = 1996}
2093    
2094     @article{Liu96a,
2095     Author = {Y. Liu and T. Ichiye},
2096     Date-Modified = {2006-02-15 10:27:01 -0500},
2097     Journal = {Chem. Phys. Lett.},
2098     Pages = {334-340},
2099     Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
2100     Volume = 256,
2101     Year = 1996}
2102    
2103     @article{Chandra99,
2104     Author = {A. Chandra and T. Ichiye},
2105 chrisfen 2957 Date-Modified = {2006-07-18 15:01:30 -0400},
2106 chrisfen 2918 Journal = {J. Chem. Phys.},
2107     Number = 6,
2108     Pages = {2701-2709},
2109 chrisfen 2957 Title = {Dynamical properties of the soft sticky dipole model of water: \uppercase{M}olecular dynamics simulation},
2110 chrisfen 2918 Volume = 111,
2111     Year = 1999}
2112    
2113     @book{Allen87,
2114     Address = {New York},
2115     Author = {M.~P. Allen and D.~J. Tildesley},
2116     Date-Modified = {2006-02-15 10:08:08 -0500},
2117     Publisher = {Oxford University Press},
2118     Title = {Computer Simulations of Liquids},
2119     Year = 1987}
2120    
2121     @book{Leach01,
2122     Address = {Harlow, England},
2123     Author = {A.~R. Leach},
2124 chrisfen 2957 Date-Modified = {2006-07-18 15:19:59 -0400},
2125 chrisfen 2918 Edition = {2nd},
2126     Publisher = {Pearson Educated Limited},
2127     Title = {Molecular Modeling: Principles and Applications},
2128     Year = 2001}
2129    
2130     @article{Katsaras00,
2131     Author = {J. Katsaras and S. Tristram-Nagle and Y. Liu and R.~L. Headrick and E. Fontes and P.~C. Mason and J.~F. Nagle},
2132     Date-Modified = {2006-02-15 10:21:52 -0500},
2133     Journal = {Physical Review E},
2134     Number = 5,
2135     Pages = {5668-5677},
2136     Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
2137     Volume = 61,
2138     Year = 2000}
2139    
2140     @article{Sengupta00,
2141     Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
2142     Date-Modified = {2006-02-15 10:32:00 -0500},
2143     Journal = {Europhysics Letters},
2144     Number = 6,
2145     Pages = {722-728},
2146     Title = {Novel structural Features of the ripple phase of phospholipids},
2147     Volume = 49,
2148     Year = 2000}
2149    
2150     @article{Venable00,
2151     Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
2152     Date-Modified = {2006-02-15 10:11:19 -0500},
2153     Journal = jcp,
2154     Number = 10,
2155     Pages = {4822-4832},
2156     Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
2157     Volume = 112,
2158     Year = 2000}
2159    
2160     @article{Lindahl00,
2161     Author = {E. Lindahl and O. Edholm},
2162     Date-Modified = {2006-02-15 10:26:05 -0500},
2163     Journal = {Biophysical Journal},
2164     Month = {July},
2165     Pages = {426-433},
2166     Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
2167     Volume = 79,
2168     Year = 2000}
2169    
2170     @article{Saiz02,
2171     Author = {L. Saiz and M. Klein},
2172     Date-Modified = {2006-02-15 10:31:50 -0500},
2173     Journal = jcp,
2174     Number = 7,
2175     Pages = {3052-3057},
2176     Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
2177     Volume = 116,
2178     Year = 2002}
2179    
2180     @article{Stevens95,
2181     Author = {M.~J. Stevens and G.~S. Grest},
2182     Date-Modified = {2006-02-15 10:10:47 -0500},
2183     Journal = {Physical Review E},
2184     Number = 6,
2185     Pages = {5976-5983},
2186     Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
2187     Volume = 51,
2188     Year = 1995}
2189    
2190     @article{Darden93,
2191     Author = {T. Darden and D. York and L. Pedersen},
2192 chrisfen 2957 Date-Modified = {2006-07-18 15:01:45 -0400},
2193 chrisfen 2918 Journal = {J. Chem. Phys.},
2194     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
2195     Number = 12,
2196     Pages = {10089-10092},
2197 chrisfen 2957 Title = {Particle mesh \uppercase{E}wald: \uppercase{A}n $\uppercase{N} \log \uppercase{N}$ method for \uppercase{E}wald sums in large systems},
2198 chrisfen 2918 Volume = 98,
2199     Year = 1993}
2200    
2201     @article{Goetz98,
2202     Author = {R. Goetz and R. Lipowsky},
2203 chrisfen 2957 Date-Modified = {2006-07-18 15:03:05 -0400},
2204 chrisfen 2918 Journal = {J. Chem. Phys.},
2205     Number = 17,
2206     Pages = 7397,
2207 chrisfen 2957 Title = {Computer simulations of bilayer membranes: \uppercase{S}elf-assembly and interfacial tension},
2208 chrisfen 2918 Volume = 108,
2209     Year = 1998}
2210    
2211     @article{Marrink01b,
2212     Author = {S.~J. Marrink and A.~E. Mark},
2213     Date-Modified = {2006-02-15 10:28:01 -0500},
2214     Journal = {Journal of Physical Chemistry B},
2215     Pages = {6122-6127},
2216     Title = {Effect of undulations on surface tension in simulated bilayers},
2217     Volume = 105,
2218     Year = 2001}
2219    
2220     @article{Metropolis49,
2221     Author = {N. Metropolis and S. Ulam},
2222     Date-Modified = {2006-02-15 10:29:03 -0500},
2223     Journal = {J. Am. Stat. Ass.},
2224     Pages = {335-341},
2225     Title = {The $\mbox{Monte Carlo}$ Method},
2226     Volume = 44,
2227     Year = 1949}
2228    
2229     @article{Metropolis53,
2230     Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
2231     Date-Modified = {2006-03-09 10:44:24 -0500},
2232     Journal = {J. Chem. Phys.},
2233     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
2234     Pages = {1087-1092},
2235     Title = {Equation of State Calculations by Fast Computing Machines},
2236     Volume = 21,
2237     Year = 1953}
2238    
2239     @article{Born12,
2240     Author = {M. Born and Th. Von~Karman},
2241     Date-Modified = {2006-02-15 10:08:50 -0500},
2242     Journal = {Physik Z.},
2243     Number = {297-309},
2244     Title = {Uber Schwingungen in Raumgittern},
2245     Volume = 13,
2246     Year = 1912}
2247    
2248     @book{Chandler87,
2249     Author = {David Chandler},
2250     Date-Modified = {2006-02-15 10:09:20 -0500},
2251     Publisher = {Oxford University Press},
2252     Title = {Introduction to Modern Statistical Mechanics},
2253     Year = 1987}
2254    
2255     @article{Pearlman95,
2256     Author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman},
2257 chrisfen 2957 Date-Modified = {2006-07-18 14:56:08 -0400},
2258 chrisfen 2918 Journal = {Computer Physics Communications},
2259     Pages = {1-41},
2260 chrisfen 2957 Title = {\uppercase{AMBER}, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules},
2261 chrisfen 2918 Volume = 91,
2262     Year = 1995}
2263    
2264     @book{Goldstein01,
2265     Address = {San Francisco},
2266     Author = {H. Goldstein and C. Poole and J. Safko},
2267     Edition = {3rd},
2268     Publisher = {Addison Wesley},
2269     Title = {Classical Mechanics},
2270     Year = 2001}
2271    
2272     @article{Bratko85,
2273     Author = {D. Bratko and L. Blum and A. Luzar},
2274     Journal = jcp,
2275     Number = 12,
2276     Pages = {6367-6370},
2277     Title = {A simple model for the intermolecular potential of water},
2278     Volume = 83,
2279     Year = 1985}
2280    
2281     @article{Bratko95,
2282     Author = {L. Blum and F. Vericat and D. Bratko},
2283 chrisfen 2957 Date-Modified = {2006-07-18 15:00:02 -0400},
2284 chrisfen 2918 Journal = jcp,
2285     Number = 3,
2286     Pages = {1461-1462},
2287 chrisfen 2957 Title = {Towards an analytical model of water: \uppercase{T}he octupolar model},
2288 chrisfen 2918 Volume = 102,
2289     Year = 1995}
2290    
2291     @article{Tan03,
2292     Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
2293     Journal = cpl,
2294     Pages = {646-652},
2295     Title = {A temperature of maximum density in soft sticky dipole water},
2296     Volume = 376,
2297     Year = 2003}
2298    
2299     @article{Soper86,
2300     Author = {A.~K. Soper and M.~G. Phillips},
2301     Journal = cp,
2302     Number = 1,
2303     Pages = {47-60},
2304     Title = {A new determination of the structure of water at 298K},
2305     Volume = 107,
2306     Year = 1986}
2307    
2308     @article{Plimpton95,
2309     Author = {S. Plimpton},
2310     Date-Modified = {2006-02-15 10:30:31 -0500},
2311     Journal = {J. Comp. Phys.},
2312     Pages = {1-19},
2313     Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
2314     Volume = 117,
2315     Year = 1995}
2316    
2317     @article{Tartaglino02,
2318     Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
2319 chrisfen 2957 Date-Modified = {2006-07-18 15:14:01 -0400},
2320 chrisfen 2918 Journal = prb,
2321     Pages = 241406,
2322 chrisfen 2957 Title = {Bending strain-driven modification of surface resconstructions: $\mbox{Au}$(111)},
2323 chrisfen 2918 Volume = 65,
2324     Year = 2002}
2325    
2326     @article{Ercolessi88,
2327     Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
2328 chrisfen 2957 Date-Modified = {2006-07-18 14:52:08 -0400},
2329 chrisfen 2918 Journal = {Philosophical Magazine A},
2330     Pages = {213-226},
2331 chrisfen 2957 Title = {Simulation of Gold in the Glue Model},
2332 chrisfen 2918 Volume = 58,
2333     Year = 1988}
2334    
2335     @article{Finnis84,
2336     Author = {M.~W Finnis and J.~E. Sinclair},
2337     Journal = {Phil. Mag. A},
2338     Pages = {45-55},
2339     Title = {A Simple Empirical N-Body Potential for Transition-Metals},
2340     Volume = 50,
2341     Year = 1984}
2342    
2343     @article{Foiles86,
2344     Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
2345     Date-Modified = {2006-02-15 10:17:44 -0500},
2346     Journal = prb,
2347     Number = 12,
2348     Pages = 7983,
2349     Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2350     Volume = 33,
2351     Year = 1986}
2352    
2353     @article{Daw93,
2354     Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
2355     Date-Modified = {2006-02-15 10:16:13 -0500},
2356     Journal = {Mat. Sci. Rep.},
2357     Pages = {251-310},
2358     Title = {The embededd-atom method},
2359     Volume = 9,
2360     Year = 1993}
2361    
2362     @article{Johnson89,
2363     Author = {R.~A. Johnson},
2364     Date-Modified = {2006-02-15 10:21:36 -0500},
2365     Journal = prb,
2366     Number = 17,
2367     Pages = 12554,
2368     Title = {Alloy models with the embedded-atom method},
2369     Volume = 39,
2370     Year = 1989}
2371    
2372     @article{Kol97,
2373     Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
2374     Date-Modified = {2006-02-15 10:24:53 -0500},
2375     Journal = jcp,
2376     Number = 7,
2377     Pages = {2580-2588},
2378     Title = {A symplectic method for rigid-body molecular simulation},
2379     Volume = 107,
2380     Year = 1997}
2381    
2382     @article{Hoover85,
2383     Author = {W.~G. Hoover},
2384 chrisfen 2957 Date-Modified = {2006-07-18 15:03:15 -0400},
2385 chrisfen 2918 Journal = pra,
2386     Pages = 1695,
2387 chrisfen 2957 Title = {Canonical dynamics: \uppercase{E}quilibrium phase-space distributions},
2388 chrisfen 2918 Volume = 31,
2389     Year = 1985}
2390    
2391     @article{Roux91,
2392     Author = {B. Roux and M. Karplus},
2393 chrisfen 2957 Date-Modified = {2006-07-18 15:12:04 -0400},
2394 chrisfen 2918 Journal = jpc,
2395     Number = 15,
2396     Pages = {4856-4868},
2397 chrisfen 2957 Title = {Ion transport in a Gramicidin-like channel: $\mbox{D}$ynamics and mobility},
2398 chrisfen 2918 Volume = 95,
2399     Year = 1991}
2400    
2401     @article{Marrink94,
2402     Author = {S.~J Marrink and H.~J.~C. Berendsen},
2403     Journal = jpc,
2404     Number = 15,
2405     Pages = {4155-4168},
2406     Title = {Simulation of water transport through a lipid membrane},
2407     Volume = 98,
2408     Year = 1994}
2409    
2410     @article{Daw89,
2411     Author = {Murray~S. Daw},
2412 chrisfen 2957 Date-Modified = {2006-07-18 15:02:06 -0400},
2413 chrisfen 2918 Journal = {Physical Review B},
2414     Pages = {7441-7452},
2415 chrisfen 2957 Title = {Model of metallic cohesion: \uppercase{T}he embedded-atom method},
2416 chrisfen 2918 Volume = 39,
2417     Year = 1989}
2418    
2419     @inbook{Voter95b,
2420     Author = {A.~F. Voter},
2421     Chapter = 4,
2422     Date-Modified = {2006-02-15 10:35:07 -0500},
2423     Editor = {J.~H. Westbrook and R.~L. Fleischer},
2424     Pages = 77,
2425     Publisher = {John Wiley and Sons Ltd},
2426     Title = {Intermetallic Compounds: Principles and Practice},
2427     Volume = 1,
2428     Year = 1995}
2429    
2430     @article{Marrink02,
2431     Author = {S.~J. Marrink and D.~P. Teileman},
2432     Date-Modified = {2006-02-15 10:28:20 -0500},
2433     Journal = {Biophysical Journal},
2434     Pages = {2386-2392},
2435     Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
2436     Volume = 83,
2437     Year = 2002}
2438    
2439     @article{Sum03,
2440     Author = {A.~K. Sum and J.~J. de~Pablo},
2441     Date-Modified = {2006-02-15 10:11:01 -0500},
2442     Journal = {Biophysical Journal},
2443     Pages = {3636-3645},
2444     Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2445     Volume = 85,
2446     Year = 2003}
2447    
2448     @article{Gomez03,
2449     Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
2450     Date-Modified = {2006-02-15 10:17:14 -0500},
2451     Journal = {Eur. Biophys. J.},
2452     Pages = {217-227},
2453     Title = {Setting up and optimization of membrane protein simulations},
2454     Volume = 31,
2455     Year = 2002}
2456    
2457     @article{Smondyrev99,
2458     Author = {A.~M. Smondyrev and M.~L. Berkowitz},
2459     Date-Modified = {2006-02-15 10:10:29 -0500},
2460     Journal = {Biophysical Journal},
2461     Pages = {2472-2478},
2462     Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
2463     Volume = 76,
2464     Year = 1999}
2465    
2466     @article{Nina02,
2467     Author = {M. Nina and T. Simonson},
2468 chrisfen 2957 Date-Modified = {2006-07-18 15:08:00 -0400},
2469 chrisfen 2918 Journal = {J. Phys. Chem. B},
2470     Pages = {3696-3705},
2471 chrisfen 2957 Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: $\mbox{C}$omparison between Continuum Reaction Field and Particle-Mesh \uppercase{E}wald Electrostatic Treatments},
2472 chrisfen 2918 Volume = 106,
2473     Year = 2002}
2474    
2475     @article{Norberg00,
2476     Author = {J. Norberg and L. Nilsson},
2477     Date-Modified = {2006-02-15 10:29:36 -0500},
2478     Journal = {Biophysical Journal},
2479     Pages = {1537-1553},
2480     Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2481     Volume = 79,
2482     Year = 2000}
2483    
2484     @article{Patra03,
2485     Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2486 chrisfen 2957 Date-Modified = {2006-07-18 15:10:24 -0400},
2487 chrisfen 2918 Journal = {Biophysical Journal},
2488     Pages = {3636-3645},
2489 chrisfen 2957 Title = {Molecular Dynamics Simulations of Lipid Bilayers: $\mbox{M}$ajor Artifacts Due to Truncating Electrostatic Interactions},
2490 chrisfen 2918 Volume = 84,
2491     Year = 2003}
2492    
2493     @article{Marrink04,
2494     Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
2495     Date-Modified = {2006-02-15 10:28:28 -0500},
2496     Journal = {J. Phys. Chem. B},
2497     Pages = {750-760},
2498     Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
2499     Volume = 108,
2500     Year = 2004}
2501    
2502     @article{Andersen83,
2503     Author = {H.~C. Andersen},
2504 chrisfen 2957 Date-Modified = {2006-07-18 14:59:26 -0400},
2505 chrisfen 2918 Journal = {Journal of Computational Physics},
2506     Pages = {24-34},
2507 chrisfen 2957 Title = {\uppercase{RATTLE: A} Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
2508 chrisfen 2918 Volume = 52,
2509     Year = 1983}
2510    
2511     @article{Hura00,
2512     Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
2513 chrisfen 2957 Date-Modified = {2006-07-21 11:45:15 -0400},
2514 chrisfen 2918 Journal = {J. Chem. Phys.},
2515 chrisfen 2957 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayH2O_2000.pdf},
2516 chrisfen 2918 Pages = {9140-9148},
2517     Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
2518     Volume = 113,
2519     Year = 2000}
2520    
2521     @inbook{Fowles99,
2522     Author = {G.~R. Fowles and G.~L. Cassiday},
2523     Chapter = 10,
2524     Date-Modified = {2006-02-15 10:18:00 -0500},
2525     Edition = {6th},
2526     Publisher = {Saunders College Publishing},
2527     Title = {Analytical Mechanics},
2528     Year = 1999}
2529    
2530     @article{Petrache00,
2531     Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2532     Date-Modified = {2006-02-15 10:30:24 -0500},
2533     Journal = {Biophysical Journal},
2534     Pages = {3172-3192},
2535     Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2536     Volume = 79,
2537     Year = 2000}
2538    
2539     @article{Egberts88,
2540     Author = {E. Egberts and H.~J.~C. Berendsen},
2541     Date-Modified = {2006-02-15 10:16:43 -0500},
2542     Journal = {J. Chem. Phys.},
2543     Pages = {3718-3732},
2544     Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
2545     Volume = 89,
2546     Year = 1988}
2547    
2548     @article{Holz00,
2549     Author = {M. Holz and S.~R. Heil and A. Sacco},
2550 chrisfen 2971 Date-Modified = {2006-08-06 14:07:16 -0400},
2551 chrisfen 2918 Journal = {Phys. Chem. Chem. Phys.},
2552 chrisfen 2971 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Holz_SelfDiffusionOfWaterFromNMR_00.pdf},
2553 chrisfen 2918 Pages = {4740-4742},
2554 chrisfen 2971 Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1$\uppercase{h nmr pfg} measurements},
2555 chrisfen 2918 Volume = 2,
2556     Year = 2000}
2557    
2558     @incollection{Zannoni94,
2559     Author = {C. Zannoni},
2560     Booktitle = {The Molecular Dynamics of Liquid Crstals},
2561     Chapter = 6,
2562     Date-Modified = {2006-02-15 10:12:36 -0500},
2563     Editor = {G.~R. Luckhurst and C.~A. Veracini},
2564     Pages = {139-169},
2565     Publisher = {Kluwer Academic Publishers},
2566     Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
2567     Year = 1994}
2568    
2569     @article{Melchionna93,
2570     Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
2571 chrisfen 2957 Date-Modified = {2006-07-20 08:41:04 -0400},
2572 chrisfen 2918 Journal = {Molecular Physics},
2573 chrisfen 2957 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Melchionna_HooverNVTandNPT_93.pdf},
2574 chrisfen 2918 Pages = {533-544},
2575 chrisfen 2957 Title = {Hoover \uppercase{$NPT$} dynamics for systems varying in shape and size},
2576 chrisfen 2918 Volume = 78,
2577     Year = 1993}
2578    
2579     @article{Fennell04,
2580     Author = {C.~J. Fennell and J.~D. Gezelter},
2581 chrisfen 2957 Date-Modified = {2006-07-18 14:20:59 -0400},
2582 chrisfen 2918 Journal = jcp,
2583     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
2584     Number = 19,
2585     Pages = {9175-9184},
2586 chrisfen 2957 Title = {On the structural and transport properties of the soft sticky dipole (\uppercase{SSD}) and related single point water models},
2587 chrisfen 2918 Volume = 120,
2588     Year = 2004}
2589    
2590     @article{Klein01,
2591     Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
2592     Date-Modified = {2006-02-15 10:27:22 -0500},
2593     Journal = {J. Phys. Chem. B},
2594     Pages = {4464-4470},
2595     Title = {A Coarse Grain Model for Phospholipid Simulations},
2596     Volume = 105,
2597     Year = 2001}
2598    
2599     @article{Marrink03,
2600     Author = {S.~J. Marrink and A.~E. Mark},
2601     Date-Modified = {2006-03-16 09:54:52 -0500},
2602     Journal = {J. Am. Chem. Soc.},
2603     Pages = {15233-15242},
2604     Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2605     Volume = 125,
2606     Year = 2003}
2607    
2608     @article{Fletcher64,
2609     Author = {R. Fletcher and C.~M. Reeves},
2610     Date-Modified = {2006-02-15 10:17:34 -0500},
2611     Journal = {Comput. J.},
2612     Number = 2,
2613     Pages = {149-154},
2614     Title = {Function minimization by conjugate gradients},
2615     Volume = 7,
2616     Year = 1964}
2617    
2618     @article{Polak69,
2619     Author = {E. Polak and G. Ribiere},
2620     Date-Modified = {2006-02-15 10:14:00 -0500},
2621     Journal = {Rev. Fr. Inform. Rech. Oper.},
2622     Pages = {35-43},
2623     Title = {Note sur la convergence de methodes de directions conjugees},
2624     Volume = {16-R1},
2625     Year = 1969}
2626    
2627     @article{Voter87,
2628     Author = {A.~F. Voter and S.~P. Chen},
2629     Date-Modified = {2006-02-15 10:35:19 -0500},
2630     Journal = {Mat. Res. Soc. Symp. Proc.},
2631     Pages = {175},
2632     Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
2633     Volume = {82},
2634     Year = {1987}}
2635    
2636     @article{Hendrickson95,
2637     Author = {Bruce Hendrickson and Steve Plimpton},
2638     Date-Modified = {2006-02-15 10:19:11 -0500},
2639     Journal = {Journal of Parallel and Distributed Computing},
2640     Pages = {15-25},
2641     Title = {Parallel Many-body Simulations without All-to-All Communication},
2642     Volume = {27},
2643     Year = {1995}}
2644    
2645     @inproceedings{Paradyn93,
2646     Address = {Pittsburgh, PA},
2647     Author = {S.~J. Plimpton and B.~A. Hendrickson},
2648     Booktitle = {Materials Theory and Modelling},
2649     Date-Modified = {2006-02-15 10:30:42 -0500},
2650     Editor = {J. Broughton and P. Bristowe and J. Newsam},
2651     Pages = 37,
2652     Publisher = {Materials Research Society},
2653     Series = {MRS Proceedings},
2654     Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
2655     Volume = 291,
2656     Year = 1993}
2657    
2658     @article{Voter95a,
2659     Author = {A.~F. Voter},
2660     Date-Modified = {2006-02-15 10:35:27 -0500},
2661     Journal = {Intermetallic Compounds: Principles and Practice},
2662     Pages = {77},
2663     Title = {The Embedded-Atom Method},
2664     Volume = {1},
2665     Year = {1995}}
2666    
2667     @article{Heller90,
2668     Author = {H. Heller and H. Grubmuller and K. Schulten},
2669     Date-Modified = {2006-02-15 10:19:02 -0500},
2670     Journal = {Molecular Simulation},
2671     Pages = {133},
2672     Title = {Molecular dynamics simulation on a parallel computer},
2673     Volume = {5},
2674     Year = {1990}}
2675    
2676     @book{Fox88,
2677     Address = {Englewood Cliffs, NJ},
2678     Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
2679     Publisher = {Prentice-Hall},
2680     Title = {Solving Promblems on Concurrent Processors},
2681     Volume = {I},
2682     Year = 1988}
2683    
2684     @article{Berendsen95,
2685     Author = {H.~J.~C. Berendsen and D. van~der~Spoel and R. van~Drunen},
2686 chrisfen 2957 Date-Modified = {2006-07-18 14:59:51 -0400},
2687 chrisfen 2918 Journal = {Comp. Phys. Comm.},
2688     Pages = {43-56},
2689 chrisfen 2957 Title = {\uppercase{GROMACS: A} message-passing parallel molecular dynamics implementation},
2690 chrisfen 2918 Volume = 91,
2691     Year = 1995}
2692    
2693     @article{Lindahl01,
2694     Author = {E. Lindahl and B. Hess and D. van~der~Spoel},
2695 chrisfen 2957 Date-Modified = {2006-07-18 14:53:59 -0400},
2696 chrisfen 2918 Journal = {J. Mol. Mod.},
2697     Pages = {306-317},
2698 chrisfen 2957 Title = {\uppercase{GROMACS 3.0: A} package for molecular simulation and trajectory analysis},
2699 chrisfen 2918 Volume = 7,
2700     Year = 2001}
2701    
2702     @article{Smith96,
2703     Author = {W. Smith and T. Forester},
2704 chrisfen 2957 Date-Modified = {2006-07-18 14:56:36 -0400},
2705 chrisfen 2918 Journal = {J. Molec. Graphics.},
2706     Number = 3,
2707     Pages = {136-141},
2708 chrisfen 2957 Title = {\uppercase{DL_POLY_2.0: A} general-purpose parallel molecular dynamics simulation package},
2709 chrisfen 2918 Volume = 14,
2710     Year = 1996}
2711    
2712     @article{Ponder87,
2713     Author = {J.~W. Ponder and F.~M. Richards},
2714     Date-Modified = {2006-02-15 10:13:45 -0500},
2715     Journal = {J. Comp. Chem.},
2716     Number = 7,
2717     Pages = {1016-1024},
2718     Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
2719     Volume = 8,
2720     Year = 1987}
2721    
2722     @article{Berendsen87,
2723     Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
2724     Journal = jpc,
2725     Pages = {6269-6271},
2726     Title = {The Missing Term in Effective Pair Potentials},
2727     Volume = 91,
2728     Year = 1987}
2729    
2730     @incollection{Berendsen81,
2731     Address = {Dordrecht},
2732     Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
2733     Booktitle = {Intermolecular Forces},
2734 chrisfen 2971 Date-Modified = {2006-08-02 13:23:53 -0400},
2735 chrisfen 2918 Editor = {B. Pullman},
2736 chrisfen 2971 Pages = {331-342},
2737 chrisfen 2918 Publisher = {Reidel},
2738     Title = {Simple Point Charge Water},
2739     Year = 1981}
2740    
2741     @article{Mahoney00,
2742     Author = {M.~W. Mahoney and W.~L. Jorgensen},
2743     Journal = jcp,
2744     Number = 20,
2745     Pages = {8910-8922},
2746     Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
2747     Volume = 112,
2748     Year = 2000}
2749    
2750     @article{Meineke05,
2751     Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2752 chrisfen 2957 Date-Modified = {2006-07-18 15:22:51 -0400},
2753 chrisfen 2918 Journal = {J. Comp. Chem.},
2754     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
2755     Pages = {252-271},
2756 chrisfen 2957 Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2757 chrisfen 2918 Volume = 26,
2758     Year = 2005}
2759    
2760     @article{Baez95a,
2761     Author = {L.~A. B\`{a}ez and P. Clancy},
2762     Journal = mp,
2763     Number = 3,
2764     Pages = {385-396},
2765     Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
2766     Volume = 86,
2767     Year = 1995}
2768    
2769     @article{Baez95b,
2770     Author = {L.~A. B\`{a}ez and P. Clancy},
2771     Journal = jcp,
2772     Number = 22,
2773     Pages = {9744-9755},
2774     Title = {Phase equilibria in extended simple point charge ice-water systems},
2775     Volume = 103,
2776     Year = 1995}
2777    
2778     @article{Davidson84,
2779     Author = {E.~R. Davidson and K. Morokuma},
2780     Journal = jcp,
2781     Number = 8,
2782     Pages = {3741-3742},
2783     Title = {A proposed antiferroelectric structure for proton ordered ice Ih},
2784     Volume = 81,
2785     Year = 1984}
2786    
2787     @article{Sanz04,
2788     Author = {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
2789     Journal = prl,
2790     Number = 25,
2791     Pages = 255701,
2792     Title = {Phase Diagram of Water from Computer Simulation},
2793     Volume = 92,
2794     Year = 2004}
2795    
2796     @article{Onsager36,
2797     Author = {L. Onsager},
2798 chrisfen 2971 Date-Modified = {2006-08-02 10:49:57 -0400},
2799 chrisfen 2918 Journal = jacs,
2800 chrisfen 2971 Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Onsager_electMoments_36.pdf},
2801 chrisfen 2918 Pages = {1486-1493},
2802     Title = {Electric Moments of Molecules in Liquids},
2803     Volume = 58,
2804     Year = 1936}
2805    
2806     @article{Matsumoto02,
2807     Author = {M. Matsumoto and S. Saito and I. Ohimine},
2808     Journal = {Nature (London)},
2809     Pages = {409-413},
2810     Title = {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
2811     Volume = 416,
2812     Year = 2002}
2813    
2814     @article{Yamada02,
2815     Author = {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
2816     Journal = prl,
2817     Number = 19,
2818     Pages = 195701,
2819     Title = {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
2820     Volume = 88,
2821     Year = 2002}
2822    
2823     @article{Wallqvist95,
2824     Author = {A. Wallqvist and B.~J. Berne},
2825     Journal = jpc,
2826     Pages = {2885-2892},
2827     Title = {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
2828     Volume = 99,
2829     Year = 1995}
2830    
2831     @article{Vlot99,
2832     Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
2833 chrisfen 2957 Date-Modified = {2006-07-18 15:18:07 -0400},
2834 chrisfen 2918 Journal = jcp,
2835     Number = 1,
2836     Pages = {55-61},
2837 chrisfen 2957 Title = {Free energy calculations on systems of rigid molecules: $\mbox{A}$n application to the $\mbox{TIP4P}$ model of $\mbox{H}_2$\mbox{O}$},
2838 chrisfen 2918 Volume = 110,
2839     Year = 1999}
2840    
2841     @article{Gao00,
2842     Author = {G.~T. Gao and X.~C. Zeng and H. Tanaka},
2843 chrisfen 2957 Date-Modified = {2006-07-18 15:02:44 -0400},
2844 chrisfen 2918 Journal = jcp,
2845     Number = 19,
2846     Pages = {8534-8538},
2847 chrisfen 2957 Title = {The melting temperature of proton-disordered hexagonal ice: \uppercase{A} computer simulation of 4-site transferable intermolecular potential model of water},
2848 chrisfen 2918 Volume = 112,
2849     Year = 2000}
2850    
2851     @article{Bizid87,
2852     Author = {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
2853 chrisfen 2957 Date-Modified = {2006-07-18 14:51:30 -0400},
2854 chrisfen 2918 Journal = jcp,
2855     Number = 4,
2856     Pages = {2225-2230},
2857 chrisfen 2957 Title = {Structure of high-density amorphous water. \uppercase{I. X}-ray diffraction study},
2858 chrisfen 2918 Volume = 87,
2859     Year = 1987}
2860    
2861     @article{Quintana92,
2862     Author = {J. Quintana and A.~D.~J. Haymet},
2863 chrisfen 2957 Date-Modified = {2006-07-18 15:11:19 -0400},
2864 chrisfen 2918 Journal = cpl,
2865     Number = 3,
2866     Pages = {273-277},
2867 chrisfen 2957 Title = {The chemical potential of water: $\mbox{m}$olecular dynamics computer simulation of the $\mbox{CF and SPC}$ models},
2868 chrisfen 2918 Volume = 189,
2869     Year = 1992}
2870    
2871     @article{Mezei92,
2872     Author = {M. Mezei},
2873     Journal = {J. Comput. Chem.},
2874     Pages = 651,
2875     Title = {Don't Remember},
2876     Volume = 13,
2877     Year = 1992}
2878    
2879     @article{Widom63,
2880     Author = {B. Widom},
2881     Journal = jcp,
2882     Pages = 2808,
2883     Title = {Particle insertion},
2884     Volume = 39,
2885     Year = 1963}
2886    
2887     @article{Clancy94,
2888     Author = {L.~A. B\'{a}ez and P. Clancy},
2889     Journal = jcp,
2890     Number = 11,
2891     Pages = {9837-9840},
2892     Title = {Existence of a density maximum in extended simple point charge water},
2893     Volume = 101,
2894     Year = 1994}
2895    
2896     @article{Jorgensen98b,
2897     Author = {W.~L. Jorgensen and C. Jenson},
2898 chrisfen 2957 Date-Modified = {2006-07-18 15:04:13 -0400},
2899 chrisfen 2918 Journal = jcc,
2900     Number = 10,
2901     Pages = {1179-1186},
2902 chrisfen 2957 Title = {Temperature Dependence of $\mbox{TIP3P, SPC, and TIP4P}$ Water from $\mbox{NPT Monte Carlo}$ Simulations: \uppercase{S}eeking Temperatures of Maximum Density},
2903 chrisfen 2918 Volume = 19,
2904     Year = 1998}
2905    
2906     @article{Mahoney01,
2907     Author = {M.~W. Mahoney and W.~L. Jorgensen},
2908     Journal = jcp,
2909     Number = 1,
2910     Pages = {363-366},
2911     Title = {Diffusion constant of the TIP5P model of liquid water},
2912     Volume = 114,
2913     Year = 2001}
2914    
2915     @article{Rahman75,
2916     Author = {A. Rahman and F.~H. Stillinger and H.~L. Lemberg},
2917     Journal = jcp,
2918     Number = 12,
2919     Pages = {5223-5230},
2920     Title = {Study of a central force model for liquid water by molecular dynamics},
2921     Volume = 63,
2922     Year = 1975}
2923    
2924 chrisfen 2957 @article{vanderSpoel98,
2925 chrisfen 2918 Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
2926 chrisfen 2957 Date-Modified = {2006-07-18 15:14:10 -0400},
2927 chrisfen 2918 Journal = jcp,
2928     Number = 24,
2929     Pages = {10220-10230},
2930 chrisfen 2957 Title = {A systematic study of water models for molecular simulation: $\mbox{D}$erivation of water models optimized for use with a reaction field},
2931 chrisfen 2918 Volume = 108,
2932     Year = 1998}
2933    
2934     @article{Gallagher03,
2935     Author = {K.~R. Gallagher and K.~A. Sharp},
2936     Journal = jacs,
2937     Pages = 9853,
2938     Title = {A New Angle on Heat Capacity Changes in Hydrophobic Solvation},
2939     Volume = 125,
2940     Year = 2003}
2941    
2942     @article{Frenkel84,
2943     Author = {D. Frenkel and A.~J.~C. Ladd},
2944 chrisfen 2957 Date-Modified = {2006-07-18 14:52:23 -0400},
2945 chrisfen 2918 Journal = jcp,
2946     Number = 7,
2947     Pages = {3188-3193},
2948 chrisfen 2957 Title = {New $\mbox{Monte Carlo}$ method to compute the free energy of arbitrary solids. \uppercase{A}pplication to the fcc and hcp phases of hard spheres},
2949 chrisfen 2918 Volume = 81,
2950     Year = 1984}
2951    
2952     @article{Hermens88,
2953     Author = {J. Hermans and A. Pathiaseril and A. Anderson},
2954 chrisfen 2957 Date-Modified = {2006-07-18 14:52:38 -0400},
2955 chrisfen 2918 Journal = jacs,
2956     Pages = {5982-5986},
2957 chrisfen 2957 Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. \uppercase{A}pplication to Water Models},
2958 chrisfen 2918 Volume = 110,
2959     Year = 1988}
2960    
2961     @article{Meijer90,
2962     Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2963 chrisfen 2957 Date-Modified = {2006-07-18 14:46:17 -0400},
2964 chrisfen 2918 Journal = jcp,
2965     Number = 12,
2966     Pages = {7570-7575},
2967 chrisfen 2957 Title = {Location of melting point at 300 \uppercase{K} of nitrogen by $\mbox{Monte Carlo}$ simulation},
2968 chrisfen 2918 Volume = 92,
2969     Year = 1990}
2970    
2971     @article{Li96,
2972     Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
2973     Journal = {Science},
2974     Pages = {666-669},
2975     Title = {Emergence of Preferred Structures in a Simple Model of Protein Folding},
2976     Volume = 273,
2977     Year = 1996}
2978    
2979     @article{Stillinger74,
2980     Author = {F.~H. Stillinger and A. Rahman},
2981     Journal = jcp,
2982     Number = 4,
2983     Pages = {1545-1557},
2984     Title = {Improved simulation of liquid water by molecular dynamics},
2985     Volume = 60,
2986     Year = 1974}
2987    
2988     @article{Caldwell95,
2989     Author = {J.~W. Caldwell and P.~A. Kollman},
2990     Journal = jpc,
2991     Number = 16,
2992     Pages = {6208-6219},
2993     Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2994     Volume = 99,
2995     Year = 1995}
2996    
2997     @article{Urbic00,
2998     Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2999 chrisfen 2957 Date-Modified = {2006-07-18 15:16:53 -0400},
3000 chrisfen 2918 Journal = jcp,
3001     Number = 6,
3002     Pages = {2843-2848},
3003 chrisfen 2957 Title = {A two-dimensional model of water: $\mbox{T}$heory and computer simulations},
3004 chrisfen 2918 Volume = 112,
3005     Year = 2000}
3006    
3007     @article{Yang04,
3008     Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
3009     Journal = prl,
3010     Number = 14,
3011     Pages = 146102,
3012     Title = {Ice Tessellation on a Hydroxylated Silica Surface},
3013     Volume = 92,
3014     Year = 2004}