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Fennell Dissertation

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# User Rev Content
1 chrisfen 2918 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
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4    
5     %% Created for Chris Fennell at 2006-04-26 09:45:27 -0400
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9    
10    
11     @STRING{acp = "Adv. Chem. Phys."}
12    
13     @STRING{cp = "Chem. Phys."}
14    
15     @STRING{cpl = "Chem. Phys. Lett."}
16    
17     @STRING{jacs = "J. Am. Chem. Soc."}
18    
19     @STRING{jcc = "J. Comput. Chem."}
20    
21     @STRING{jcp = "J. Chem. Phys."}
22    
23     @STRING{jml = "J. Mol. Liq."}
24    
25     @STRING{jpc = "J. Phys. Chem."}
26    
27     @STRING{jpca = "J. Phys. Chem. A"}
28    
29     @STRING{jpcb = "J. Phys. Chem. B"}
30    
31     @STRING{mp = "Mol. Phys."}
32    
33     @STRING{pccp = "Phys. Chem. Chem. Phys."}
34    
35     @STRING{pnas = "Proc. Natl. Acad. Sci. USA"}
36    
37     @STRING{pra = "Phys. Rev. A"}
38    
39     @STRING{prb = "Phys. Rev. B"}
40    
41     @STRING{pre = "Phys. Rev. E"}
42    
43     @STRING{prl = "Phys. Rev. Lett."}
44    
45     @STRING{rmp = "Rev. Mod. Phys."}
46    
47    
48     @article{Brodka04,
49     Author = {A. Br\'{o}dka},
50     Date-Added = {2006-04-26 09:41:52 -0400},
51     Date-Modified = {2006-04-26 09:43:52 -0400},
52     Doi = {10.1016/j.cplett.2004.10.086},
53     Journal = {Chem. Phys. Lett.},
54     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
55     Pages = {62-67},
56     Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
57     Volume = {400},
58     Year = {2004}}
59    
60     @article{deJoannis02,
61     Author = {J. {de Joannis} and A. Arnold and C. Holm},
62     Date-Added = {2006-04-26 09:40:15 -0400},
63     Date-Modified = {2006-04-26 09:45:19 -0400},
64     Doi = {10.1063/1.1491954},
65     Journal = {J. Chem. Phys.},
66     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
67     Number = {6},
68     Pages = {2503-2512},
69     Title = {Electrostatics in periodic slab geometries. II},
70     Volume = {117},
71     Year = {2002}}
72    
73     @article{Kawata01,
74     Author = {M. Kawata and M. Mikami},
75     Date-Added = {2006-04-26 09:38:01 -0400},
76     Date-Modified = {2006-04-26 09:40:11 -0400},
77     Journal = {Chem. Phys. Lett.},
78     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
79     Pages = {157-164},
80     Title = {Rapid calculation of two-dimensional Ewald summation},
81     Volume = {340},
82     Year = {2001}}
83    
84     @article{Arnold02,
85     Author = {A. Arnold and J. {de Joannis} and C. Holm},
86     Date-Added = {2006-04-26 09:36:09 -0400},
87     Date-Modified = {2006-04-26 09:37:52 -0400},
88     Doi = {10.1063/1.1491955},
89     Journal = {J. Chem. Phys.},
90     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
91     Number = {6},
92     Pages = {2496-2502},
93     Title = {Electrostatics in periodic slab geometries. I},
94     Volume = {117},
95     Year = {2002}}
96    
97     @article{Kolafa92,
98     Author = {J. Kolafa and J.~W. Perram},
99     Date-Added = {2006-03-21 09:41:58 -0500},
100     Date-Modified = {2006-03-21 09:42:47 -0500},
101     Journal = {Mol. Simul.},
102     Pages = {351-368},
103     Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
104     Volume = {9},
105     Year = {1992}}
106    
107     @article{Karasawa89,
108     Author = {N. Karasawa and W.~A. {Goddard III}},
109     Date-Added = {2006-03-21 09:11:44 -0500},
110     Date-Modified = {2006-03-21 09:13:00 -0500},
111     Journal = {J. Phys. Chem.},
112     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
113     Pages = {7320-7327},
114     Title = {Acceleration of Convergence for Lattice Sums},
115     Volume = {93},
116     Year = {1989}}
117    
118     @article{Roux99,
119     Author = {B. Roux and T. Simonson},
120     Date-Added = {2006-03-19 20:10:18 -0500},
121     Date-Modified = {2006-03-19 20:12:10 -0500},
122     Journal = {Biophys. Chem.},
123     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
124     Pages = {1-20},
125     Title = {Implicit solvent models},
126     Volume = {78},
127     Year = {1999}}
128    
129     @article{Rokhlin85,
130     Author = {V. Rokhlin},
131     Date-Added = {2006-03-19 20:02:25 -0500},
132     Date-Modified = {2006-03-19 20:04:19 -0500},
133     Doi = {10.1016/0021-9991(85)90002-6},
134     Journal = {J. Comput. Phys.},
135     Month = {September},
136     Number = {2},
137     Pages = {187-207},
138     Title = {Rapid solution of integral equations of classical potential theory},
139     Volume = {60},
140     Year = {1985}}
141    
142     @article{Grossfield00,
143     Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
144     Date-Added = {2006-03-19 19:52:19 -0500},
145     Date-Modified = {2006-03-19 19:54:14 -0500},
146     Journal = {Proteins},
147     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
148     Pages = {211-223},
149     Title = {Dipole Lattice Membrane Model for Protein Calculations},
150     Volume = {41},
151     Year = {2000}}
152    
153     @article{Born20,
154     Author = {M. Born},
155     Date-Added = {2006-03-19 18:05:01 -0500},
156     Date-Modified = {2006-03-19 18:07:42 -0500},
157     Journal = {Z. Physik},
158     Pages = {45-48},
159     Title = {Volumen und hydratationswame der ionen},
160     Volume = {1},
161     Year = {1920}}
162    
163     @article{Luty96,
164     Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
165     Date-Added = {2006-03-18 20:59:19 -0500},
166     Date-Modified = {2006-03-18 21:00:33 -0500},
167     Journal = {J. Phys. Chem.},
168     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
169     Number = {7},
170     Pages = {2581-2587},
171     Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
172     Volume = {100},
173     Year = {1996}}
174    
175     @article{Rhee89,
176     Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
177     Date-Added = {2006-03-18 20:48:07 -0500},
178     Date-Modified = {2006-03-18 20:51:09 -0500},
179     Journal = {Phys. Rev. B},
180     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
181     Number = {1},
182     Pages = {36-42},
183     Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
184     Volume = {40},
185     Year = {1989}}
186    
187     @article{Hunenberger99a,
188     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
189     Date-Added = {2006-03-18 20:14:24 -0500},
190     Date-Modified = {2006-03-18 20:16:01 -0500},
191     Journal = {J. Chem. Phys.},
192     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
193     Number = {4},
194     Pages = {1856-1872},
195     Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
196     Volume = {110},
197     Year = {1999}}
198    
199     @article{Roberts95,
200     Author = {J.~E. Roberts and J. Schnitker},
201     Date-Added = {2006-03-18 20:12:23 -0500},
202     Date-Modified = {2006-03-18 20:13:36 -0500},
203     Journal = {J. Phys. Chem.},
204     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
205     Pages = {1322-1331},
206     Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
207     Volume = {99},
208     Year = {1995}}
209    
210     @article{Roberts94,
211     Author = {J.~E. Roberts and J. Schnitker},
212     Date-Added = {2006-03-18 20:10:37 -0500},
213     Date-Modified = {2006-03-18 20:12:19 -0500},
214     Journal = {J. Chem. Phys.},
215     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
216     Number = {6},
217     Pages = {5024-5031},
218     Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
219     Volume = {101},
220     Year = {1994}}
221    
222     @article{Yeh99,
223     Author = {I.-C. Yeh and M.~L. Berkowitz},
224     Date-Added = {2006-03-18 19:24:27 -0500},
225     Date-Modified = {2006-03-18 19:26:08 -0500},
226     Journal = {J. Chem. Phys.},
227     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
228     Number = {7},
229     Pages = {3155-3162},
230     Title = {Ewald summation for systems with slab geometry},
231     Volume = {111},
232     Year = {1999}}
233    
234     @article{Parry76,
235     Author = {D.~E. Parry},
236     Date-Added = {2006-03-18 19:11:01 -0500},
237     Date-Modified = {2006-03-18 19:14:01 -0500},
238     Journal = {Surf. Sci.},
239     Pages = {195},
240     Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
241     Volume = {54},
242     Year = {1976}}
243    
244     @article{Parry75,
245     Author = {D.~E. Parry},
246     Date-Added = {2006-03-18 19:08:40 -0500},
247     Date-Modified = {2006-03-18 19:16:14 -0500},
248     Journal = {Surf. Sci.},
249     Pages = {433-440},
250     Title = {The electrostatic potential in the surface region of an ionic crystal},
251     Volume = {49},
252     Year = {1975}}
253    
254     @article{deLeeuw79,
255     Author = {S.~W. {de Leeuw} and J.~W. Perram},
256     Date-Added = {2006-03-18 19:05:18 -0500},
257     Date-Modified = {2006-03-18 19:07:48 -0500},
258     Journal = {Mol. Phys.},
259     Pages = {1313-1327},
260     Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
261     Volume = {37},
262     Year = {1979}}
263    
264     @article{Heyes77,
265     Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
266     Date-Added = {2006-03-18 19:02:16 -0500},
267     Date-Modified = {2006-03-18 19:04:48 -0500},
268     Journal = {J. Chem. Soc., Faraday Trans. II},
269     Number = {7},
270     Pages = {1485-1496},
271     Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
272     Volume = {73},
273     Year = {1977}}
274    
275     @article{Spohr97,
276     Author = {E. Spohr},
277     Date-Added = {2006-03-18 18:51:02 -0500},
278     Date-Modified = {2006-03-18 18:52:21 -0500},
279     Journal = {J. Chem. Phys.},
280     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
281     Number = {16},
282     Pages = {6342-6348},
283     Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
284     Volume = {107},
285     Year = {1997}}
286    
287     @article{York94,
288     Author = {D. York and W. Yang},
289     Date-Added = {2006-03-18 11:52:58 -0500},
290     Date-Modified = {2006-03-18 11:54:19 -0500},
291     Journal = {J. Chem. Phys.},
292     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
293     Number = {4},
294     Pages = {3298-3300},
295     Title = {The fast Fourier Poisson method for calculating Ewald sums},
296     Volume = {101},
297     Year = {1994}}
298    
299     @article{Shimada93,
300     Author = {J. Shimada and H. Kaneko and T. Takada},
301     Date-Added = {2006-03-18 11:10:38 -0500},
302     Date-Modified = {2006-03-18 11:12:10 -0500},
303     Journal = {J. Comp. Chem.},
304     Pages = {867-78},
305     Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
306     Volume = {14},
307     Year = {1993}}
308    
309     @article{Luty94,
310     Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
311     Date-Added = {2006-03-18 10:37:17 -0500},
312     Date-Modified = {2006-03-18 11:09:55 -0500},
313     Journal = {Mol. Simul.},
314     Pages = {11-20},
315     Title = {A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic systems},
316     Volume = {14},
317     Year = {1994}}
318    
319     @book{Hockney81,
320     Address = {New York},
321     Author = {R.~W. Hockney and J.~W. Eastwood},
322     Date-Added = {2006-03-18 10:33:19 -0500},
323     Date-Modified = {2006-03-18 10:35:04 -0500},
324     Publisher = {McGraw-Hill},
325     Title = {Computer Simulation Using Particles},
326     Year = {1981}}
327    
328     @article{Sagui99,
329     Author = {C. Sagui and T.~A. Darden},
330     Date-Added = {2006-03-17 18:27:01 -0500},
331     Date-Modified = {2006-03-23 13:48:12 -0500},
332     Journal = {Annu. Rev. Biophys. Biomol. Struct.},
333     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_electrostaticInBiomolecules_99.pdf},
334     Pages = {155-179},
335     Title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic Effects},
336     Volume = {28},
337     Year = {1999}}
338    
339     @article{Perram88,
340     Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
341     Date-Added = {2006-03-17 13:42:04 -0500},
342     Date-Modified = {2006-03-17 13:59:01 -0500},
343     Journal = {Mol. Phys.},
344     Pages = {875-893},
345     Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
346     Volume = {65},
347     Year = {1988}}
348    
349     @article{Woodcock71,
350     Author = {L.~V. Woodcock and K. Singer},
351     Date-Added = {2006-03-17 11:14:17 -0500},
352     Date-Modified = {2006-03-17 11:16:52 -0500},
353     Journal = {Trans. Faraday Soc.},
354     Pages = {12-30},
355     Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by Monte Carlo Computation},
356     Volume = {67},
357     Year = {1971}}
358    
359     @article{Smith81,
360     Author = {E.~R. Smith},
361     Date-Added = {2006-03-16 13:47:17 -0500},
362     Date-Modified = {2006-03-16 13:48:34 -0500},
363     Journal = {Proc. R. Soc. London Ser. A},
364     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
365     Pages = {475-505},
366     Title = {Electrostatic Energy in Ionic Crystals},
367     Volume = {375},
368     Year = {1981}}
369    
370     @article{Weber00,
371     Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
372     Date-Added = {2006-03-16 09:49:22 -0500},
373     Date-Modified = {2006-03-16 09:51:17 -0500},
374     Doi = {10.1021/jp9937757},
375     Journal = {J. Phys. Chem. B},
376     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
377     Number = {15},
378     Pages = {3668-3675},
379     Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
380     Volume = {104},
381     Year = {2000}}
382    
383     @article{Hunenberger99b,
384     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
385     Date-Added = {2006-03-16 09:45:10 -0500},
386     Date-Modified = {2006-03-18 20:16:16 -0500},
387     Journal = {Biophys. Chem.},
388     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
389     Pages = {69-88},
390     Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
391     Volume = {78},
392     Year = {1999}}
393    
394     @article{Petersen95,
395     Author = {H.~G. Petersen},
396     Date-Added = {2006-03-16 08:43:02 -0500},
397     Date-Modified = {2006-03-16 08:44:32 -0500},
398     Journal = {J. Chem. Phys.},
399     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
400     Month = {September},
401     Number = {9},
402     Pages = {3668-3679},
403     Title = {Accuracy and efficiency of the particle mesh Ewald method},
404     Volume = {103},
405     Year = {1995}}
406    
407     @article{Luty95,
408     Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
409     Date-Added = {2006-03-16 08:39:13 -0500},
410     Date-Modified = {2006-03-16 08:41:15 -0500},
411     Journal = {J. Chem. Phys.},
412     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
413     Number = {8},
414     Pages = {3014-3021},
415     Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
416     Volume = {103},
417     Year = {1995}}
418    
419     @article{Barker73,
420     Author = {J.~A. Barker and R.~O. Watts},
421     Date-Added = {2006-03-15 18:58:17 -0500},
422     Date-Modified = {2006-03-18 11:36:56 -0500},
423     Journal = {Mol. Phys.},
424     Pages = {789-792},
425     Title = {Monte Carlo studies of the dielectric properties of water-like models},
426     Volume = {26},
427     Year = {1973}}
428    
429     @article{Adams79,
430     Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
431     Date-Added = {2006-03-15 17:46:36 -0500},
432     Date-Modified = {2006-03-15 17:48:04 -0500},
433     Journal = {Mol. Phys.},
434     Number = {2},
435     Pages = {387-400},
436     Title = {The computer simulation of polar liquids},
437     Volume = {38},
438     Year = {1979}}
439    
440     @article{Rahman71,
441     Author = {A. Rahman and F.~H. Stillinger},
442     Date-Added = {2006-03-15 17:04:53 -0500},
443     Date-Modified = {2006-03-15 17:07:29 -0500},
444     Journal = {J. Chem. Phys.},
445     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
446     Month = {October},
447     Number = {7},
448     Pages = {3336-3359},
449     Title = {Molecular Dynamics Study of Liquid Water},
450     Volume = {55},
451     Year = {1971}}
452    
453     @article{Andrea83,
454     Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
455     Date-Added = {2006-03-15 15:16:12 -0500},
456     Date-Modified = {2006-03-15 15:18:10 -0500},
457     Journal = {J. Chem. Phys.},
458     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
459     Number = {9},
460     Pages = {4576-4584},
461     Title = {The role of long ranged forces in determining the structure and properties of liquid water},
462     Volume = {79},
463     Year = {1983}}
464    
465     @article{Brush66,
466     Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
467     Date-Added = {2006-03-13 16:55:39 -0500},
468     Date-Modified = {2006-03-13 17:01:15 -0500},
469     Journal = {J. Chem. Phys.},
470     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
471     Month = {September},
472     Number = {6},
473     Pages = {2102-2118},
474     Title = {Monte Carlo Study of a One-Component Plasma. I},
475     Volume = {45},
476     Year = {1966}}
477    
478     @article{Ewald21,
479     Author = {P.~P. Ewald},
480     Date-Added = {2006-03-13 13:32:04 -0500},
481     Date-Modified = {2006-03-16 22:39:27 -0500},
482     Journal = {Ann. Physik},
483     Pages = {253-287},
484     Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
485     Volume = {64},
486     Year = {1921}}
487    
488     @article{Jones56,
489     Author = {R.~E. Jones and D.~H. Templeton},
490     Date-Added = {2006-03-13 13:25:58 -0500},
491     Date-Modified = {2006-03-13 13:27:15 -0500},
492     Journal = {J. Chem. Phys.},
493     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
494     Number = {5},
495     Pages = {1062-1063},
496     Title = {Optimum Atomic Shape for Bertaut Series},
497     Volume = {25},
498     Year = {1956}}
499    
500     @article{Heyes81,
501     Author = {D.~M. Heyes},
502     Date-Added = {2006-03-13 13:12:45 -0500},
503     Date-Modified = {2006-03-13 13:14:27 -0500},
504     Journal = {J. Chem. Phys.},
505     Keywords = {Empty Keywords},
506     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
507     Number = {3},
508     Pages = {1924-1929},
509     Title = {Electrostatic potentials and fields in infinite point charge lattices},
510     Volume = {74},
511     Year = {1981}}
512    
513     @article{Steinbach94,
514     Author = {P.~J. Steinbach and B.~R. Brooks},
515     Date-Added = {2006-03-12 19:26:45 -0500},
516     Date-Modified = {2006-03-12 19:29:43 -0500},
517     Doi = {10.1002/jcc.540150702},
518     Journal = {J. Comput. Chem.},
519     Number = {7},
520     Pages = {667-683},
521     Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
522     Volume = {15},
523     Year = {1994}}
524    
525     @article{deLeeuw80,
526     Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
527     Date-Added = {2006-03-07 10:26:31 -0500},
528     Date-Modified = {2006-03-07 10:30:11 -0500},
529     Journal = {Proc. R. Soc. London Ser. A},
530     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
531     Number = {1752},
532     Pages = {27-56},
533     Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
534     Volume = {373},
535     Year = {1980}}
536    
537     @article{Essmann95,
538     Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
539     Date-Added = {2006-03-05 12:25:25 -0500},
540     Date-Modified = {2006-03-23 13:47:48 -0500},
541     Journal = {J. Chem. Phys.},
542     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
543     Number = {19},
544     Pages = {8577-8593},
545     Title = {A smooth particle mesh Ewald method},
546     Volume = {103},
547     Year = {1995}}
548    
549     @article{Kast03,
550     Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
551     Date-Added = {2006-02-18 16:47:26 -0500},
552     Date-Modified = {2006-02-18 16:51:25 -0500},
553     Journal = {Chem. Phys. Lett.},
554     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
555     Pages = {398-404},
556     Title = {Integral equation theory for correcting truncation errors in molecular simulations},
557     Volume = {367},
558     Year = {2003}}
559    
560     @article{Tobias01,
561     Author = {D.~J. Tobias},
562     Date-Added = {2006-02-15 11:28:58 -0500},
563     Date-Modified = {2006-02-15 11:32:16 -0500},
564     Journal = {Curr. Opin. Struct. Biol.},
565     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
566     Pages = {253-261},
567     Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
568     Volume = {11},
569     Year = {2001}}
570    
571     @article{Zahn02,
572     Author = {D. Zahn and B. Schilling and S.~M. Kast},
573     Date-Added = {2006-02-15 09:21:27 -0500},
574     Date-Modified = {2006-02-15 09:24:07 -0500},
575     Journal = {J. Phys. Chem. B},
576     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
577     Number = {41},
578     Pages = {10725-10732},
579     Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
580     Volume = {106},
581     Year = {2002}}
582    
583     @article{Wolf99,
584     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
585     Date-Added = {2006-02-15 09:09:39 -0500},
586     Date-Modified = {2006-02-15 09:25:30 -0500},
587     Journal = {J. Chem. Phys.},
588     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
589     Number = {17},
590     Pages = {8255-8282},
591     Rating = {0},
592     Read = {No},
593     Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
594     Volume = {110},
595     Year = {1999}}
596    
597     @book{Berne90,
598     Address = {Malabar, Florida},
599     Author = {B.~J. Berne and R. Pecora},
600     Publisher = {Robert E. Krieger Publishing Company, Inc.},
601     Title = {Dynamic Light Scattering},
602     Year = 1990}
603    
604     @article{Evans77,
605     Author = {D.~J. Evans},
606     Journal = {Mol. Phys.},
607     Pages = {317-325},
608     Title = {On the representation of orientation space},
609     Volume = 34,
610     Year = 1977}
611    
612     @article{Tuckerman92,
613     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
614     Journal = jcp,
615     Pages = {1990-2001},
616     Title = {Reversible multiple time scale molecular dynamics},
617     Volume = 97,
618     Year = 1992}
619    
620     @book{Hansen86,
621     Address = {London},
622     Author = {J.~P. Hansen and I.~R. McDonald},
623     Chapter = 7,
624     Pages = {199-206},
625     Publisher = {Academic Press},
626     Title = {Theory of Simple Liquids},
627     Year = 1986}
628    
629     @article{Angelani98,
630     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
631     Journal = prl,
632     Number = 21,
633     Pages = {4648-4651},
634     Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
635     Volume = 81,
636     Year = 1998}
637    
638     @article{Stillinger82,
639     Author = {F.~H. Stillinger and T.~A. Weber},
640     Journal = pra,
641     Number = 2,
642     Pages = {978-989},
643     Title = {Hidden structure in liquids},
644     Volume = 25,
645     Year = 1982}
646    
647     @article{Stillinger83,
648     Author = {F.~H. Stillinger and T.~A. Weber},
649     Journal = pra,
650     Number = 4,
651     Pages = {2408-2416},
652     Title = {Dynamics of structural transitions in liquids},
653     Volume = 28,
654     Year = 1983}
655    
656     @article{Weber84,
657     Author = {T.~A. Weber and F.~H. Stillinger},
658     Journal = jcp,
659     Number = 6,
660     Pages = {2742-2746},
661     Title = {The effect of density on the inherent structure in liquids},
662     Volume = 80,
663     Year = 1984}
664    
665     @article{Stillinger85,
666     Author = {F.~H. Stillinger and T.~A. Weber},
667     Journal = jcp,
668     Number = 9,
669     Pages = {4767-4775},
670     Title = {Inherent structure theory of liquids in the hard-sphere limit},
671     Volume = 83,
672     Year = 1985}
673    
674     @article{Stillinger98,
675     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
676     Journal = {Nature},
677     Pages = {554-557},
678     Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
679     Volume = 393,
680     Year = 1998}
681    
682     @article{Parkhurst75a,
683     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
684     Journal = jcp,
685     Number = 6,
686     Pages = {2698-2704},
687     Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
688     Volume = 63,
689     Year = 1975}
690    
691     @article{Parkhurst75b,
692     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
693     Journal = jcp,
694     Number = 6,
695     Pages = {2705-2709},
696     Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
697     Volume = 63,
698     Year = 1975}
699    
700     @article{Forester97,
701     Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
702     Journal = {J. Chem. Soc. - Faraday Transactions},
703     Pages = {613-619},
704     Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
705     Volume = 93,
706     Year = 1997}
707    
708     @article{Tieleman98,
709     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
710     Journal = {Biophys. J.},
711     Pages = {2786-2801},
712     Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
713     Volume = 74,
714     Year = 1998}
715    
716     @article{Cascales98,
717     Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
718     Journal = {J. Phys. Chem. B},
719     Pages = {625-631},
720     Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
721     Volume = 102,
722     Year = 1998}
723    
724     @article{Bassolino95,
725     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
726     Journal = {J. Am. Chem. Soc.},
727     Pages = {4118-4129},
728     Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
729     Volume = 117,
730     Year = 1995}
731    
732     @article{Alper95,
733     Author = {H.~E. Alper and T.~R. Stouch},
734     Journal = {J. Phys. Chem.},
735     Pages = {5724-5731},
736     Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
737     Volume = 99,
738     Year = 1995}
739    
740     @article{Sok92,
741     Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
742     Journal = {J. Chem. Phys.},
743     Pages = {4699-4704},
744     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
745     Volume = 96,
746     Year = 1992}
747    
748     @article{Rabani99,
749     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
750     Journal = prl,
751     Pages = {3649},
752     Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
753     Volume = 82,
754     Year = {1999}}
755    
756     @article{Rabani97,
757     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
758     Journal = {J. Chem. Phys.},
759     Pages = {6867-6876},
760     Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
761     Volume = 107,
762     Year = 1997}
763    
764     @article{Gezelter99,
765     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
766     Journal = jcp,
767     Pages = 3444,
768     Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
769     Volume = 110,
770     Year = 1999}
771    
772     @article{Gezelter98,
773     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
774     Date-Modified = {2006-02-15 10:18:42 -0500},
775     Journal = jcp,
776     Pages = 4695,
777     Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
778     Volume = 109,
779     Year = 1998}
780    
781     @article{Gezelter97,
782     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
783     Journal = jcp,
784     Pages = 4618,
785     Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
786     Volume = 107,
787     Year = 1997}
788    
789     @article{Zwanzig83,
790     Author = {R. Zwanzig},
791     Journal = jcp,
792     Pages = {4507-4508},
793     Title = {On the relation between self-diffusion and viscosity of liquids},
794     Volume = 79,
795     Year = 1983}
796    
797     @article{Zwanzig88,
798     Author = {R. Zwanzig},
799     Journal = {Proc. Natl. Acad. Sci. USA},
800     Pages = 2029,
801     Title = {Diffusion in rough potential},
802     Volume = 85,
803     Year = 1988}
804    
805     @article{Stillinger95,
806     Author = {F.~H. Stillinger},
807     Journal = {Science},
808     Pages = {1935-1939},
809     Title = {A Topographic View of Supercooled Liquids and Glass Formation},
810     Volume = 267,
811     Year = 1995}
812    
813     @incollection{Angell85,
814     Address = {Springfield, VA},
815     Author = {C.~A. Angell},
816     Booktitle = {Relaxations in Complex Systems},
817     Editor = {K.~Ngai and G.~B. Wright},
818     Pages = 1,
819     Publisher = {National Technical Information Service, U.S. Department of Commerce},
820     Title = {unknown},
821     Year = 1985}
822    
823     @article{Bembenek96,
824     Author = {S.~D. Bembenek and B.~B. Laird},
825     Journal = jcp,
826     Pages = 5199,
827     Title = {The role of localization in glasses and supercooled liquids},
828     Volume = 104,
829     Year = 1996}
830    
831     @article{Sun97a,
832     Author = {X. Sun and W.~H. Miller},
833     Date-Modified = {2006-02-15 10:33:35 -0500},
834     Journal = jcp,
835     Pages = 6346,
836     Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
837     Volume = 106,
838     Year = 1997}
839    
840     @article{Spath96,
841     Author = {B.~W. Spath and W.~H. Miller},
842     Journal = jcp,
843     Pages = 95,
844     Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
845     Volume = 104,
846     Year = 1996}
847    
848     @book{Warshel91,
849     Address = {New York},
850     Author = {Arieh Warshel},
851     Publisher = {Wiley},
852     Title = {Computer modeling of chemical reactions in enzymes and solutions},
853     Year = 1991}
854    
855     @article{Vuilleumier97,
856     Author = {Rodolphe Vuilleumier and Daniel Borgis},
857     Journal = jpc,
858     Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
859     Volume = {in press},
860     Year = 1997}
861    
862     @article{Kob95a,
863     Author = {W. Kob and H.~C. Andersen},
864     Journal = pre,
865     Pages = {4626-4641},
866     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
867     Volume = 51,
868     Year = 1995}
869    
870     @article{Kob95b,
871     Author = {W. Kob and H.~C. Andersen},
872     Journal = pre,
873     Pages = {4134-4153},
874     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
875     Volume = 52,
876     Year = 1995}
877    
878     @inproceedings{Gotze89,
879     Address = {Amsterdam},
880     Author = {W. G{\"{o}}tze},
881     Booktitle = {Liquids, Freezing and Glass Transitions},
882     Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
883     Pages = {287-503},
884     Publisher = {North-Holland},
885     Title = {Aspects of Structural Glass Transitions},
886     Volume = {I},
887     Year = 1989}
888    
889     @article{Sun97b,
890     Author = {X. Sun and W.~H. Miller},
891     Date-Modified = {2006-02-15 10:33:29 -0500},
892     Journal = jcp,
893     Pages = 916,
894     Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
895     Year = 1997}
896    
897     @article{Keshavamurthy94,
898     Author = {S. Keshavamurthy and W.~H. Miller},
899     Journal = cpl,
900     Pages = 189,
901     Title = {ivr},
902     Volume = 218,
903     Year = 1994}
904    
905     @article{Billing75,
906     Author = {G.~D. Billing},
907     Journal = cpl,
908     Pages = 391,
909     Title = {ehrenfest},
910     Volume = 30,
911     Year = 1975}
912    
913     @article{Chang90,
914     Author = {Y.-T. Chang and W.~H. Miller},
915     Journal = jpc,
916     Pages = {5884-5888},
917     Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
918     Volume = 94,
919     Year = 1990}
920    
921     @article{Shor94,
922     Author = {P.W. Shor},
923     Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
924     Pages = {124-134},
925     Title = {Algorithms for quantum computation: discrete logarithms and factoring},
926     Year = 1994}
927    
928     @article{Feynman82,
929     Author = {R.~P. Feynman},
930     Journal = {Int. J. Theor. Phys.},
931     Pages = {467-488},
932     Title = {Simulating physics with computers},
933     Volume = 21,
934     Year = 1982}
935    
936     @article{Grover97,
937     Author = {L.~K. Grover},
938     Journal = prl,
939     Pages = {4709-4712},
940     Title = {Quantum computers can search arbitrarily large databases by a single query},
941     Volume = 79,
942     Year = 1997}
943    
944     @article{Chuang98,
945     Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
946     Journal = prl,
947     Pages = {3408-3411},
948     Title = {Experimental Implementation of Fast Quantum Searching},
949     Volume = 80,
950     Year = 1998}
951    
952     @article{Monroe95,
953     Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
954     Journal = prl,
955     Pages = 4714,
956     Title = {Demonstration of a fundamental quantum logic gate},
957     Volume = 75,
958     Year = 1995}
959    
960     @article{Lent93,
961     Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
962     Journal = {Nanotechnology},
963     Pages = {49-57},
964     Title = {Quantum Cellular Automata},
965     Volume = 4,
966     Year = 1993}
967    
968     @article{Barenco95,
969     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},
970     Journal = {Phys. Rev. A},
971     Pages = {3457-3467},
972     Title = {elementary gates for quantum computation},
973     Volume = 52,
974     Year = 1995}
975    
976     @article{Reinot97,
977     Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
978     Date-Modified = {2006-02-15 10:31:21 -0500},
979     Journal = jcp,
980     Pages = {457-466},
981     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},
982     Volume = 106,
983     Year = 1997}
984    
985     @article{Laflamme96,
986     Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
987     Journal = prl,
988     Pages = 77,
989     Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
990     Volume = 98,
991     Year = 1996}
992    
993     @article{Shor95,
994     Author = {P.~W. Shor},
995     Journal = {Phys. Rev. A},
996     Pages = {2493-2496},
997     Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
998     Volume = 52,
999     Year = 1995}
1000    
1001     @article{Calderbank96,
1002     Author = {A.~R. Calderbank and P.~W. Shor},
1003     Journal = {Phys. Rev. A},
1004     Pages = {1098-1105},
1005     Title = {Good quantum error-correcting codes exist},
1006     Volume = 54,
1007     Year = 1996}
1008    
1009     @article{Steane96,
1010     Author = {A.~M. Steane},
1011     Journal = prl,
1012     Pages = {793-797},
1013     Title = {Error correcting codes in quantum theory},
1014     Volume = 77,
1015     Year = 1996}
1016    
1017     @article{Gezelter95,
1018     Author = {J.~D. Gezelter and W.~H. Miller},
1019     Journal = jcp,
1020     Pages = {7868-7876},
1021     Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
1022     Volume = 103,
1023     Year = 1995}
1024    
1025     @article{Chakrabarti92,
1026     Author = {A.~C. Chakrabarti and D.~W. Deamer},
1027     Journal = {Biochimica et Biophysica Acta},
1028     Pages = {171-177},
1029     Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
1030     Volume = 1111,
1031     Year = 1992}
1032    
1033     @article{Paula96,
1034     Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
1035     Journal = {Biophys. J.},
1036     Pages = {339-348},
1037     Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
1038     Volume = 70,
1039     Year = 1996}
1040    
1041     @article{Little96,
1042     Author = {H.~J. Little},
1043     Journal = {Pharmacology \& Therapeutics},
1044     Pages = {37-58},
1045     Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
1046     Volume = 69,
1047     Year = 1996}
1048    
1049     @article{McKinnon92,
1050     Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
1051     Journal = jpc,
1052     Pages = {10497-10506},
1053     Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
1054     Volume = 96,
1055     Year = 1992}
1056    
1057     @article{Venable93,
1058     Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
1059     Journal = {Science},
1060     Pages = {223-226},
1061     Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
1062     Volume = 262,
1063     Year = 1993}
1064    
1065     @article{Essmann99,
1066     Author = {U. Essmann and M.~L. Berkowitz},
1067     Journal = {Biophys. J.},
1068     Pages = {2081-2089},
1069     Title = {Dynamical properties of phospholipid bilayers from computer simulation},
1070     Volume = 76,
1071     Year = 1999}
1072    
1073     @article{Tu98,
1074     Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
1075     Journal = {Biophys. J.},
1076     Pages = {2123-2134},
1077     Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
1078     Volume = 75,
1079     Year = 1998}
1080    
1081     @article{Pomes96,
1082     Author = {R. Pomes and B. Roux},
1083     Journal = {Biophys. J.},
1084     Pages = {19-39},
1085     Title = {Structure and dynamics of a proton wire: A theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
1086     Volume = 71,
1087     Year = 1996}
1088    
1089     @article{Duwez60,
1090     Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
1091     Journal = {J. Appl. Phys.},
1092     Pages = {1136-1137},
1093     Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
1094     Volume = 31,
1095     Year = 1960}
1096    
1097     @article{Peker93,
1098     Author = {A. Peker and W.~L. Johnson},
1099     Journal = {Appl. Phys. Lett.},
1100     Pages = {2342-2344},
1101     Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
1102     Volume = 63,
1103     Year = 1993}
1104    
1105     @article{ChoiYim97,
1106     Author = {H. Choi-Yim and W.~L. Johnson},
1107     Journal = {Appl. Phys. Lett.},
1108     Pages = {3808-3810},
1109     Title = {Bulk metallic glass matrix composites},
1110     Volume = 71,
1111     Year = 1997}
1112    
1113     @article{Sun96,
1114     Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
1115     Journal = {J. Mater. Res.},
1116     Pages = {2738-2743},
1117     Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
1118     Volume = 11,
1119     Year = 1996}
1120    
1121     @article{Heller93,
1122     Author = {H. Heller and M. Schaefer and K. Schulten},
1123     Journal = jpc,
1124     Pages = {8343-8360},
1125     Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
1126     Volume = 97,
1127     Year = 1993}
1128    
1129     @article{Kushick76,
1130     Author = {J. Kushick and B.~J. Berne},
1131     Journal = jcp,
1132     Pages = {1362-1367},
1133     Title = {Computer Simulation of anisotropic molecular fluids},
1134     Volume = 64,
1135     Year = 1976}
1136    
1137     @article{Berardi96,
1138     Author = {R. Berardi and S. Orlandi and C Zannoni},
1139     Journal = cpl,
1140     Pages = {357-362},
1141     Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
1142     Volume = 261,
1143     Year = 1996}
1144    
1145     @article{Berardi99,
1146     Author = {R. Berardi and S. Orlandi and C. Zannoni},
1147     Journal = {Int. J. Mod. Phys. C},
1148     Pages = {477-484},
1149     Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
1150     Volume = 10,
1151     Year = 1999}
1152    
1153     @article{Pasterny00,
1154     Author = {K. Pasterny and E. Gwozdz and A. Brodka},
1155     Date-Modified = {2006-02-15 10:29:47 -0500},
1156     Journal = {J. Mol. Liq.},
1157     Pages = {173-184},
1158     Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
1159     Volume = 85,
1160     Year = 2000}
1161    
1162     @article{Jorgensen83,
1163     Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
1164     Journal = jcp,
1165     Pages = {926-935},
1166     Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
1167     Volume = 79,
1168     Year = 1983}
1169    
1170     @article{Berardi98,
1171     Author = {R. Berardi and C. Fava and C. Zannoni},
1172     Journal = cpl,
1173     Pages = {8-14},
1174     Title = {A Gay-Berne potential for dissimilar biaxial particles},
1175     Volume = 297,
1176     Year = 1998}
1177    
1178     @article{Luckhurst90,
1179     Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
1180     Journal = {Liquid Crystals},
1181     Pages = {451-464},
1182     Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the Gay-Berne model mesogen},
1183     Volume = 8,
1184     Year = 1990}
1185    
1186     @article{Gay81,
1187     Author = {J.~G. Gay and B.~J. Berne},
1188     Journal = jcp,
1189     Pages = {3316-3319},
1190     Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
1191     Volume = 74,
1192     Year = 1981}
1193    
1194     @article{Berne72,
1195     Author = {B.~J. Berne and P. Pechukas},
1196     Journal = jcp,
1197     Pages = {4213-4216},
1198     Title = {Gaussian Model Potentials for Molecular Interactions},
1199     Volume = 56,
1200     Year = 1972}
1201    
1202     @article{Perram96,
1203     Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
1204     Journal = pre,
1205     Pages = {6565-6572},
1206     Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
1207     Volume = 54,
1208     Year = 1996}
1209    
1210     @article{Cornell95,
1211     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},
1212     Journal = jacs,
1213     Pages = {5179-5197},
1214     Title = {A second generation force field for the simulation of proteins and nucleic acids},
1215     Volume = 117,
1216     Year = 1995}
1217    
1218     @article{Brooks83,
1219     Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
1220     Journal = {J. Comp. Chem.},
1221     Pages = {187-217},
1222     Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
1223     Volume = 4,
1224     Year = 1983}
1225    
1226     @incollection{MacKerell98,
1227     Address = {New York},
1228     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},
1229     Booktitle = {The Encyclopedia of Computational Chemistry},
1230     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1231     Pages = {271-277},
1232     Publisher = {John Wiley \& Sons},
1233     Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
1234     Volume = 1,
1235     Year = 1998}
1236    
1237     @incollection{Jorgensen98a,
1238     Address = {New York},
1239     Author = {W.~L. Jorgensen},
1240     Booktitle = {The Encyclopedia of Computational Chemistry},
1241     Date-Modified = {2006-02-15 10:21:45 -0500},
1242     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1243     Pages = {1986-1989},
1244     Publisher = {John Wiley \& Sons},
1245     Title = {OPLS Force Fields},
1246     Volume = 3,
1247     Year = 1998}
1248    
1249     @article{Rabani00,
1250     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1251     Date-Modified = {2006-02-15 10:30:55 -0500},
1252     Journal = prl,
1253     Pages = 467,
1254     Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
1255     Volume = 85,
1256     Year = 2000}
1257    
1258     @book{Cevc87,
1259     Address = {New York},
1260     Author = {G. Cevc and D. Marsh},
1261     Publisher = {John Wiley \& Sons},
1262     Title = {Phospholipid Bilayers},
1263     Year = 1987}
1264    
1265     @article{Janiak79,
1266     Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
1267     Journal = {J. Biol. Chem.},
1268     Pages = {6068-6078},
1269     Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
1270     Volume = 254,
1271     Year = 1979}
1272    
1273     @book{Tobias90,
1274     Address = {Tucson},
1275     Author = {Sheila Tobias},
1276     Publisher = {Research Corp.},
1277     Title = {They're not Dumb. They're Different: Stalking the Second Tier},
1278     Year = 1990}
1279    
1280     @article{Mazur92,
1281     Author = {E. Mazur},
1282     Journal = {Optics and Photonics News},
1283     Pages = 38,
1284     Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing?},
1285     Volume = 3,
1286     Year = 1992}
1287    
1288     @book{Mazur97,
1289     Address = {New Jersey},
1290     Author = {Eric Mazur},
1291     Publisher = {Prentice Hall},
1292     Title = {Peer Instruction: A User's Manual},
1293     Year = 1997}
1294    
1295     @article{Wigner55,
1296     Author = {E.~P. Wigner},
1297     Journal = {Annals of Mathematics},
1298     Pages = {548-564},
1299     Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
1300     Volume = 62,
1301     Year = 1955}
1302    
1303     @article{Gaukel98,
1304     Author = {C. Gaukel and H.~R. Schober},
1305     Journal = {Solid State Comm.},
1306     Pages = {1-5},
1307     Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
1308     Volume = 107,
1309     Year = 1998}
1310    
1311     @article{Qi99,
1312     Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
1313     Journal = prb,
1314     Number = 5,
1315     Pages = {3527-3533},
1316     Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
1317     Volume = 59,
1318     Year = 1999}
1319    
1320     @article{Khorunzhy97,
1321     Author = {A. Khorunzhy and G.~J. Rodgers},
1322     Journal = {J. Math. Phys.},
1323     Pages = {3300-3320},
1324     Title = {Eigenvalue distribution of large dilute random matrices},
1325     Volume = 38,
1326     Year = 1997}
1327    
1328     @article{Rodgers88,
1329     Author = {G.~J. Rodgers and A. Bray},
1330     Journal = {Phys. Rev. B},
1331     Pages = 355703562,
1332     Title = {Density of States of a Sparse Random Matrix},
1333     Volume = 37,
1334     Year = 1988}
1335    
1336     @article{Rodgers90,
1337     Author = {G.~J. Rodgers and C. {De Dominicis}},
1338     Journal = {J. Phys. A: Math. Gen.},
1339     Pages = {1567-1573},
1340     Title = {Density of states of sparse random matrices},
1341     Volume = 23,
1342     Year = 1990}
1343    
1344     @inproceedings{Barker80,
1345     Author = {J.~A. Barker},
1346     Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
1347     Editor = {D. Ceperley},
1348     Pages = {45-6},
1349     Series = {NRCC Workshop Proceedings},
1350     Title = {Reaction field method for polar fluids},
1351     Volume = 9,
1352     Year = 1980}
1353    
1354     @article{Smith82,
1355     Author = {W. Smith},
1356     Journal = {CCP5 Quarterly},
1357     Pages = {13-25},
1358     Title = {Point multipoles in the Ewald summation},
1359     Volume = 4,
1360     Year = 1982}
1361    
1362     @article{Daw84,
1363     Author = {M.~S. Daw and M.~I. Baskes},
1364     Journal = prb,
1365     Number = 12,
1366     Pages = {6443-6453},
1367     Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
1368     Volume = 29,
1369     Year = 1984}
1370    
1371     @article{Sutton90,
1372     Author = {A.~P. Sutton and J. Chen},
1373     Date-Modified = {2006-02-15 10:33:48 -0500},
1374     Journal = {Phil. Mag. Lett.},
1375     Pages = {139-146},
1376     Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
1377     Volume = 61,
1378     Year = 1990}
1379    
1380     @article{Lu97,
1381     Author = {J. Lu and J.~A. Szpunar},
1382     Journal = {Phil. Mag. A},
1383     Pages = {1057-1066},
1384     Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
1385     Volume = {75},
1386     Year = {1997}}
1387    
1388     @article{Shlesinger99,
1389     Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
1390     Journal = {Am. J. Phys.},
1391     Pages = {1253-1259},
1392     Title = {Above, below, and beyond Brownian motion},
1393     Volume = 67,
1394     Year = 1999}
1395    
1396     @article{Klafter96,
1397     Author = {J. Klafter and M. Shlesinger and G. Zumofen},
1398     Journal = {Physics Today},
1399     Pages = {33-39},
1400     Title = {Beyond Brownian Motion},
1401     Volume = 49,
1402     Year = 1996}
1403    
1404     @article{Blumen83,
1405     Author = {A. Blumen and J. Klafter and G. Zumofen},
1406     Journal = {Phys. Rev. B},
1407     Pages = {3429-3435},
1408     Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
1409     Volume = 27,
1410     Year = 1983}
1411    
1412     @article{Klafter94,
1413     Author = {J. Klafter and G. Zumofen},
1414     Journal = jpc,
1415     Pages = {7366-7370},
1416     Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
1417     Volume = 98,
1418     Year = 1994}
1419    
1420     @article{Dzugutov92,
1421     Author = {M. Dzugutov},
1422     Journal = pra,
1423     Pages = {R2984-R2987},
1424     Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
1425     Volume = 46,
1426     Year = 1992}
1427    
1428     @article{Moore94,
1429     Author = {P. Moore and T. Keyes},
1430     Journal = jcp,
1431     Pages = 6709,
1432     Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
1433     Volume = 100,
1434     Year = 1994}
1435    
1436     @article{Seeley89,
1437     Author = {G. Seeley and T. Keyes},
1438     Journal = jcp,
1439     Pages = {5581-5586},
1440     Title = {Normal-mode analysis of liquid-state dynamics},
1441     Volume = 91,
1442     Year = 1989}
1443    
1444     @article{Madan90,
1445     Author = {B. Madan and T. Keyes and G. Seeley},
1446     Journal = jcp,
1447     Pages = {7565-7569},
1448     Title = {Diffusion in supercooled liquids via normal mode analysis},
1449     Volume = 92,
1450     Year = 1990}
1451    
1452     @article{Madan91,
1453     Author = {B. Madan and T. Keyes and G. Seeley},
1454     Journal = jcp,
1455     Pages = {6762-6769},
1456     Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
1457     Volume = 94,
1458     Year = 1991}
1459    
1460     @article{Buchner92,
1461     Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
1462     Journal = jcp,
1463     Pages = {8522-8535},
1464     Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
1465     Volume = 97,
1466     Year = 1992}
1467    
1468     @article{Wan94,
1469     Author = {Yi. Wan and R.~M. Stratt},
1470     Journal = jcp,
1471     Pages = {5123-5138},
1472     Title = {Liquid theory for the instantaneous normal modes of a liquid},
1473     Volume = 100,
1474     Year = 1994}
1475    
1476     @article{Stratt95,
1477     Author = {R.~M. Stratt},
1478     Journal = {Acc. Chem. Res.},
1479     Pages = {201-207},
1480     Title = {The instantaneous normal modes of liquids},
1481     Volume = 28,
1482     Year = 1995}
1483    
1484     @article{Nitzan95,
1485     Author = {G.~V. Vijayadamodar and A. Nitzan},
1486     Journal = jcp,
1487     Pages = {2169-2177},
1488     Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
1489     Volume = 103,
1490     Year = 1995}
1491    
1492     @article{Ribeiro98,
1493     Author = {M.~C.~C. Ribeiro and P.~A. Madden},
1494     Journal = jcp,
1495     Pages = {3256-3263},
1496     Title = {Unstable Modes in Ionic Melts},
1497     Volume = 108,
1498     Year = 1998}
1499    
1500     @article{Keyes98,
1501     Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
1502     Date-Modified = {2006-02-15 10:22:13 -0500},
1503     Journal = jcp,
1504     Pages = {4693-4694},
1505     Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
1506     Volume = 109,
1507     Year = 1998}
1508    
1509     @article{Alemany98,
1510     Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
1511     Journal = jcp,
1512     Pages = {5175-5176},
1513     Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
1514     Volume = 109,
1515     Year = 1998}
1516    
1517     @article{Belonoshko00,
1518     Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
1519     Journal = prb,
1520     Pages = {3838-3844},
1521     Title = {Quasi ab initio molecular dynamic study of Cu melting},
1522     Volume = 61,
1523     Year = 2000}
1524    
1525     @article{Banhart92,
1526     Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1527     Journal = prb,
1528     Pages = {9968-9975},
1529     Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1530     Volume = 46,
1531     Year = 1992}
1532    
1533     @article{Wendt78,
1534     Author = {H. Wendt and F.~F. Abraham},
1535     Journal = prl,
1536     Pages = 1244,
1537     Volume = 41,
1538     Year = 1978}
1539    
1540     @article{Lewis91,
1541     Author = {L.~J. Lewis},
1542     Journal = prb,
1543     Pages = {4245-4254},
1544     Title = {Atomic dynamics through the glass transition},
1545     Volume = 44,
1546     Year = 1991}
1547    
1548     @article{Liu92,
1549     Author = {R.~S. Liu and D.~W. Qi and S. Wang},
1550     Journal = prb,
1551     Pages = {451-453},
1552     Title = {Subpeaks of structure factors for rapidly quenched metals},
1553     Volume = 45,
1554     Year = 1992}
1555    
1556     @article{Anheuser94,
1557     Author = {K. Anheuser and J.P. Northover},
1558     Journal = {Brit. Num. J.},
1559     Pages = 22,
1560     Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
1561     Volume = 64,
1562     Year = 1994}
1563    
1564     @article{Pense92,
1565     Author = {A. W. Pense},
1566     Journal = {Mat. Char.},
1567     Pages = 213,
1568     Title = {The Decline and Fall of the Roman Denarius},
1569     Volume = 29,
1570     Year = 1992}
1571    
1572     @article{Ngai81,
1573     Author = {K.~L. Ngai and F.-S. Liu},
1574     Journal = prb,
1575     Pages = {1049-1065},
1576     Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1577     Volume = 24,
1578     Year = 1981}
1579    
1580     @unpublished{Truhlar00,
1581     Author = {D.~G. Truhlar and A. Kohen},
1582     Date-Modified = {2006-02-15 16:35:52 -0500},
1583     Note = {private correspondence},
1584     Year = {2000}}
1585    
1586     @article{Truhlar78,
1587     Author = {Donald G. Truhlar},
1588     Journal = {J. Chem. Ed.},
1589     Pages = 309,
1590     Title = {Interpretation of the Activation Energy},
1591     Volume = 55,
1592     Year = 1978}
1593    
1594     @book{Tolman27,
1595     Address = {New York},
1596     Author = {R. C. Tolman},
1597     Pages = {260-270},
1598     Publisher = {Chemical Catalog Co.},
1599     Title = {Statistical Mechanics with Applications to Physics and Chemistry},
1600     Year = 1927}
1601    
1602     @article{Tolman20,
1603     Author = {R. C. Tolman},
1604     Journal = jacs,
1605     Pages = 2506,
1606     Title = {Statistical Mechanics Applied to Chemical Kinetics},
1607     Volume = 42,
1608     Year = 1920}
1609    
1610     @article{Ediger96,
1611     Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
1612     Date-Modified = {2006-02-15 10:16:35 -0500},
1613     Journal = jpc,
1614     Pages = 13200,
1615     Title = {Supercooled Liquids and Glasses},
1616     Volume = 100,
1617     Year = 1996}
1618    
1619     @inbook{Blumen86,
1620     Address = {Amsterdam},
1621     Author = {A. Blumen and J. Klafter and G. Zumofen},
1622     Chapter = {Reactions in Disordered Media Modelled by Fractals},
1623     Editor = {Luciano Peitronero and E. Tosatti},
1624     Pages = 399,
1625     Publisher = {North-Holland},
1626     Series = {International Symposium on Fractals in Physics},
1627     Title = {Fractals in Physics},
1628     Year = 1986}
1629    
1630     @article{Shlesinger84,
1631     Author = {M.~F. Shlesinger and E.~W. Montroll},
1632     Journal = {Proc. Natl. Acad. Sci. USA},
1633     Pages = {1280-1283},
1634     Title = {On the Williams-Watts function of dielectric relaxation},
1635     Volume = 81,
1636     Year = 1984}
1637    
1638     @article{Klafter86,
1639     Author = {J. Klafter and M.~F. Shlesinger},
1640     Journal = {Proc. Natl. Acad. Sci. USA},
1641     Pages = {848-851},
1642     Title = {On the relationship among three theories of relaxation in disordered systems},
1643     Volume = 83,
1644     Year = 1986}
1645    
1646     @article{Li01,
1647     Author = {Z. Li and M. Lieberman and W. Hill},
1648     Date-Modified = {2006-02-15 10:25:36 -0500},
1649     Journal = {Langmuir},
1650     Pages = {4887-4894},
1651     Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
1652     Volume = 17,
1653     Year = 2001}
1654    
1655     @article{Evans93,
1656     Author = {J.~W. Evans},
1657     Date-Modified = {2006-02-15 10:17:03 -0500},
1658     Journal = rmp,
1659     Pages = {1281-1329},
1660     Title = {Random and Cooperative Sequential Adsorption},
1661     Volume = 65,
1662     Year = 1993}
1663    
1664     @article{Dwyer1977,
1665     Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1666     Journal = {Surf. Sci.},
1667     Pages = 617,
1668     Volume = 64,
1669     Year = 1977}
1670    
1671     @article{Macritche78,
1672     Author = {F. MacRitche},
1673     Date-Modified = {2006-02-15 10:27:37 -0500},
1674     Journal = {Adv. Protein Chem.},
1675     Pages = 283,
1676     Volume = 32,
1677     Year = 1978}
1678    
1679     @article{Feder80,
1680     Author = {J. Feder},
1681     Date-Modified = {2006-02-15 10:17:21 -0500},
1682     Journal = {J. Theor. Biol.},
1683     Pages = 237,
1684     Volume = 87,
1685     Year = 1980}
1686    
1687     @article{Ramsden93,
1688     Author = {J.~J. Ramsden},
1689     Date-Modified = {2006-02-15 10:31:03 -0500},
1690     Journal = prl,
1691     Pages = 295,
1692     Volume = 71,
1693     Year = 1993}
1694    
1695     @article{Egelhoff89,
1696     Author = {W.~F. Egelhoff and I. Jacob},
1697     Date-Modified = {2006-02-15 10:16:54 -0500},
1698     Journal = prl,
1699     Pages = 921,
1700     Volume = 62,
1701     Year = 1989}
1702    
1703     @article{Viot92a,
1704     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1705     Date-Modified = {2006-02-15 10:12:51 -0500},
1706     Journal = jpc,
1707     Pages = {5212-5218},
1708     Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1709     Volume = 97,
1710     Year = 1992}
1711    
1712     @article{Viot92b,
1713     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1714     Date-Modified = {2006-02-15 10:12:57 -0500},
1715     Journal = {Physica A},
1716     Pages = {248-252},
1717     Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
1718     Volume = 191,
1719     Year = 1992}
1720    
1721     @article{Dobson1987,
1722     Author = {B.~W. Dobson},
1723     Journal = prb,
1724     Pages = 1068,
1725     Volume = 36,
1726     Year = 1987}
1727    
1728     @article{Boyer95,
1729     Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1730     Date-Modified = {2006-02-15 10:15:52 -0500},
1731     Journal = jcp,
1732     Pages = 1607,
1733     Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
1734     Volume = 103,
1735     Year = 1995}
1736    
1737     @article{Viot92c,
1738     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1739     Date-Modified = {2006-02-15 10:13:03 -0500},
1740     Journal = {Physica A},
1741     Pages = {248-252},
1742     Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
1743     Volume = 191,
1744     Year = 1992}
1745    
1746     @article{Ricci94,
1747     Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
1748     Date-Modified = {2006-02-15 10:31:32 -0500},
1749     Journal = jcp,
1750     Pages = 9164,
1751     Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1752     Volume = 101,
1753     Year = 1994}
1754    
1755     @article{Semmler98,
1756     Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1757     Date-Modified = {2006-02-15 10:14:46 -0500},
1758     Journal = {Langmuir},
1759     Pages = {5127-5132},
1760     Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
1761     Volume = 14,
1762     Year = 1998}
1763    
1764     @article{Solomon86,
1765     Author = {H. Solomon and H. Weiner},
1766     Date-Modified = {2006-02-15 10:10:38 -0500},
1767     Journal = {Comm. Statistics A},
1768     Pages = {2571-2607},
1769     Title = {A REVIEW OF THE PACKING PROBLEM},
1770     Volume = 15,
1771     Year = 1986}
1772    
1773     @article{Bonnier93,
1774     Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
1775     Date-Modified = {2006-02-15 10:08:35 -0500},
1776     Journal = {Physica A},
1777     Pages = {1-10},
1778     Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
1779     Volume = 198,
1780     Year = 1993}
1781    
1782     @book{Frenkel96,
1783     Address = {New York},
1784     Author = {D. Frenkel and B. Smit},
1785     Date-Modified = {2006-02-15 10:18:08 -0500},
1786     Publisher = {Academic Press},
1787     Title = {Understanding Molecular Simulation : From Algorithms to Applications},
1788     Year = 1996}
1789    
1790     @article{Dullweber1997,
1791     Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
1792     Journal = jcp,
1793     Number = 15,
1794     Pages = {5840-5851},
1795     Title = {Symplectic splitting methods for rigid body molecular dynamics},
1796     Volume = 107,
1797     Year = 1997}
1798    
1799     @article{Martin98,
1800     Author = {M. Martin and J.~I. Siepmann},
1801     Date-Modified = {2006-02-15 10:15:05 -0500},
1802     Journal = jpcB,
1803     Pages = {2569-2577},
1804     Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
1805     Volume = 102,
1806     Year = 1998}
1807    
1808     @article{Marrink01a,
1809     Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
1810     Date-Modified = {2006-02-15 10:28:09 -0500},
1811     Journal = jacs,
1812     Pages = {8638-8639},
1813     Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
1814     Volume = 123,
1815     Year = 2001}
1816    
1817     @article{Liu96b,
1818     Author = {Y. Liu and T. Ichiye},
1819     Date-Modified = {2006-02-15 10:27:07 -0500},
1820     Journal = jpc,
1821     Pages = {2723-2730},
1822     Title = {Soft sticky dipole potential for liquid water: a new model},
1823     Volume = 100,
1824     Year = 1996}
1825    
1826     @article{Liu96a,
1827     Author = {Y. Liu and T. Ichiye},
1828     Date-Modified = {2006-02-15 10:27:01 -0500},
1829     Journal = {Chem. Phys. Lett.},
1830     Pages = {334-340},
1831     Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1832     Volume = 256,
1833     Year = 1996}
1834    
1835     @article{Chandra99,
1836     Author = {A. Chandra and T. Ichiye},
1837     Date-Modified = {2006-02-15 10:09:36 -0500},
1838     Journal = {J. Chem. Phys.},
1839     Number = 6,
1840     Pages = {2701-2709},
1841     Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1842     Volume = 111,
1843     Year = 1999}
1844    
1845     @book{Allen87,
1846     Address = {New York},
1847     Author = {M.~P. Allen and D.~J. Tildesley},
1848     Date-Modified = {2006-02-15 10:08:08 -0500},
1849     Publisher = {Oxford University Press},
1850     Title = {Computer Simulations of Liquids},
1851     Year = 1987}
1852    
1853     @book{Leach01,
1854     Address = {Harlow, England},
1855     Author = {A.~R. Leach},
1856     Date-Modified = {2006-02-15 10:25:19 -0500},
1857     Edition = {2nd},
1858     Publisher = {Pearson Educated Limited},
1859     Title = {Molecular Modeling: Principles and Applications},
1860     Year = 2001}
1861    
1862     @article{Katsaras00,
1863     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},
1864     Date-Modified = {2006-02-15 10:21:52 -0500},
1865     Journal = {Physical Review E},
1866     Number = 5,
1867     Pages = {5668-5677},
1868     Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
1869     Volume = 61,
1870     Year = 2000}
1871    
1872     @article{Sengupta00,
1873     Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
1874     Date-Modified = {2006-02-15 10:32:00 -0500},
1875     Journal = {Europhysics Letters},
1876     Number = 6,
1877     Pages = {722-728},
1878     Title = {Novel structural Features of the ripple phase of phospholipids},
1879     Volume = 49,
1880     Year = 2000}
1881    
1882     @article{Venable00,
1883     Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1884     Date-Modified = {2006-02-15 10:11:19 -0500},
1885     Journal = jcp,
1886     Number = 10,
1887     Pages = {4822-4832},
1888     Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1889     Volume = 112,
1890     Year = 2000}
1891    
1892     @article{Lindahl00,
1893     Author = {E. Lindahl and O. Edholm},
1894     Date-Modified = {2006-02-15 10:26:05 -0500},
1895     Journal = {Biophysical Journal},
1896     Month = {July},
1897     Pages = {426-433},
1898     Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1899     Volume = 79,
1900     Year = 2000}
1901    
1902     @article{Saiz02,
1903     Author = {L. Saiz and M. Klein},
1904     Date-Modified = {2006-02-15 10:31:50 -0500},
1905     Journal = jcp,
1906     Number = 7,
1907     Pages = {3052-3057},
1908     Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
1909     Volume = 116,
1910     Year = 2002}
1911    
1912     @article{Stevens95,
1913     Author = {M.~J. Stevens and G.~S. Grest},
1914     Date-Modified = {2006-02-15 10:10:47 -0500},
1915     Journal = {Physical Review E},
1916     Number = 6,
1917     Pages = {5976-5983},
1918     Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
1919     Volume = 51,
1920     Year = 1995}
1921    
1922     @article{Darden93,
1923     Author = {T. Darden and D. York and L. Pedersen},
1924     Date-Modified = {2006-03-16 08:37:25 -0500},
1925     Journal = {J. Chem. Phys.},
1926     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
1927     Number = 12,
1928     Pages = {10089-10092},
1929     Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
1930     Volume = 98,
1931     Year = 1993}
1932    
1933     @article{Goetz98,
1934     Author = {R. Goetz and R. Lipowsky},
1935     Date-Modified = {2006-02-15 10:18:26 -0500},
1936     Journal = {J. Chem. Phys.},
1937     Number = 17,
1938     Pages = 7397,
1939     Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
1940     Volume = 108,
1941     Year = 1998}
1942    
1943     @article{Marrink01b,
1944     Author = {S.~J. Marrink and A.~E. Mark},
1945     Date-Modified = {2006-02-15 10:28:01 -0500},
1946     Journal = {Journal of Physical Chemistry B},
1947     Pages = {6122-6127},
1948     Title = {Effect of undulations on surface tension in simulated bilayers},
1949     Volume = 105,
1950     Year = 2001}
1951    
1952     @article{Metropolis49,
1953     Author = {N. Metropolis and S. Ulam},
1954     Date-Modified = {2006-02-15 10:29:03 -0500},
1955     Journal = {J. Am. Stat. Ass.},
1956     Pages = {335-341},
1957     Title = {The $\mbox{Monte Carlo}$ Method},
1958     Volume = 44,
1959     Year = 1949}
1960    
1961     @article{Metropolis53,
1962     Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1963     Date-Modified = {2006-03-09 10:44:24 -0500},
1964     Journal = {J. Chem. Phys.},
1965     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
1966     Pages = {1087-1092},
1967     Title = {Equation of State Calculations by Fast Computing Machines},
1968     Volume = 21,
1969     Year = 1953}
1970    
1971     @article{Born12,
1972     Author = {M. Born and Th. Von~Karman},
1973     Date-Modified = {2006-02-15 10:08:50 -0500},
1974     Journal = {Physik Z.},
1975     Number = {297-309},
1976     Title = {Uber Schwingungen in Raumgittern},
1977     Volume = 13,
1978     Year = 1912}
1979    
1980     @book{Chandler87,
1981     Author = {David Chandler},
1982     Date-Modified = {2006-02-15 10:09:20 -0500},
1983     Publisher = {Oxford University Press},
1984     Title = {Introduction to Modern Statistical Mechanics},
1985     Year = 1987}
1986    
1987     @article{Pearlman95,
1988     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},
1989     Date-Modified = {2006-02-15 10:30:13 -0500},
1990     Journal = {Computer Physics Communications},
1991     Pages = {1-41},
1992     Title = {{\sc 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},
1993     Volume = 91,
1994     Year = 1995}
1995    
1996     @book{Goldstein01,
1997     Address = {San Francisco},
1998     Author = {H. Goldstein and C. Poole and J. Safko},
1999     Edition = {3rd},
2000     Publisher = {Addison Wesley},
2001     Title = {Classical Mechanics},
2002     Year = 2001}
2003    
2004     @article{Bratko85,
2005     Author = {D. Bratko and L. Blum and A. Luzar},
2006     Journal = jcp,
2007     Number = 12,
2008     Pages = {6367-6370},
2009     Title = {A simple model for the intermolecular potential of water},
2010     Volume = 83,
2011     Year = 1985}
2012    
2013     @article{Bratko95,
2014     Author = {L. Blum and F. Vericat and D. Bratko},
2015     Journal = jcp,
2016     Number = 3,
2017     Pages = {1461-1462},
2018     Title = {Towards an analytical model of water: The octupolar model},
2019     Volume = 102,
2020     Year = 1995}
2021    
2022     @article{Tan03,
2023     Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
2024     Journal = cpl,
2025     Pages = {646-652},
2026     Title = {A temperature of maximum density in soft sticky dipole water},
2027     Volume = 376,
2028     Year = 2003}
2029    
2030     @article{Soper86,
2031     Author = {A.~K. Soper and M.~G. Phillips},
2032     Journal = cp,
2033     Number = 1,
2034     Pages = {47-60},
2035     Title = {A new determination of the structure of water at 298K},
2036     Volume = 107,
2037     Year = 1986}
2038    
2039     @article{Plimpton95,
2040     Author = {S. Plimpton},
2041     Date-Modified = {2006-02-15 10:30:31 -0500},
2042     Journal = {J. Comp. Phys.},
2043     Pages = {1-19},
2044     Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
2045     Volume = 117,
2046     Year = 1995}
2047    
2048     @article{Tartaglino02,
2049     Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
2050     Date-Modified = {2006-02-15 10:34:04 -0500},
2051     Journal = prb,
2052     Pages = 241406,
2053     Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
2054     Volume = 65,
2055     Year = 2002}
2056    
2057     @article{Ercolessi88,
2058     Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
2059     Journal = {Philosophical Magazine A},
2060     Pages = {213-226},
2061     Title = {Simulation of Gold in the Glue Model.},
2062     Volume = 58,
2063     Year = 1988}
2064    
2065     @article{Finnis84,
2066     Author = {M.~W Finnis and J.~E. Sinclair},
2067     Journal = {Phil. Mag. A},
2068     Pages = {45-55},
2069     Title = {A Simple Empirical N-Body Potential for Transition-Metals},
2070     Volume = 50,
2071     Year = 1984}
2072    
2073     @article{Foiles86,
2074     Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
2075     Date-Modified = {2006-02-15 10:17:44 -0500},
2076     Journal = prb,
2077     Number = 12,
2078     Pages = 7983,
2079     Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2080     Volume = 33,
2081     Year = 1986}
2082    
2083     @article{Daw93,
2084     Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
2085     Date-Modified = {2006-02-15 10:16:13 -0500},
2086     Journal = {Mat. Sci. Rep.},
2087     Pages = {251-310},
2088     Title = {The embededd-atom method},
2089     Volume = 9,
2090     Year = 1993}
2091    
2092     @article{Johnson89,
2093     Author = {R.~A. Johnson},
2094     Date-Modified = {2006-02-15 10:21:36 -0500},
2095     Journal = prb,
2096     Number = 17,
2097     Pages = 12554,
2098     Title = {Alloy models with the embedded-atom method},
2099     Volume = 39,
2100     Year = 1989}
2101    
2102     @article{Kol97,
2103     Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
2104     Date-Modified = {2006-02-15 10:24:53 -0500},
2105     Journal = jcp,
2106     Number = 7,
2107     Pages = {2580-2588},
2108     Title = {A symplectic method for rigid-body molecular simulation},
2109     Volume = 107,
2110     Year = 1997}
2111    
2112     @article{Hoover85,
2113     Author = {W.~G. Hoover},
2114     Date-Modified = {2006-02-15 10:21:18 -0500},
2115     Journal = pra,
2116     Pages = 1695,
2117     Title = {Canonical dynamics: Equilibrium phase-space distributions},
2118     Volume = 31,
2119     Year = 1985}
2120    
2121     @article{Roux91,
2122     Author = {B. Roux and M. Karplus},
2123     Journal = jpc,
2124     Number = 15,
2125     Pages = {4856-4868},
2126     Title = {Ion transport in a Gramicidin-like channel: dynamics and mobility},
2127     Volume = 95,
2128     Year = 1991}
2129    
2130     @article{Marrink94,
2131     Author = {S.~J Marrink and H.~J.~C. Berendsen},
2132     Journal = jpc,
2133     Number = 15,
2134     Pages = {4155-4168},
2135     Title = {Simulation of water transport through a lipid membrane},
2136     Volume = 98,
2137     Year = 1994}
2138    
2139     @article{Daw89,
2140     Author = {Murray~S. Daw},
2141     Journal = {Physical Review B},
2142     Pages = {7441-7452},
2143     Title = {Model of metallic cohesion: The embedded-atom method},
2144     Volume = 39,
2145     Year = 1989}
2146    
2147     @inbook{Voter95b,
2148     Author = {A.~F. Voter},
2149     Chapter = 4,
2150     Date-Modified = {2006-02-15 10:35:07 -0500},
2151     Editor = {J.~H. Westbrook and R.~L. Fleischer},
2152     Pages = 77,
2153     Publisher = {John Wiley and Sons Ltd},
2154     Title = {Intermetallic Compounds: Principles and Practice},
2155     Volume = 1,
2156     Year = 1995}
2157    
2158     @article{Marrink02,
2159     Author = {S.~J. Marrink and D.~P. Teileman},
2160     Date-Modified = {2006-02-15 10:28:20 -0500},
2161     Journal = {Biophysical Journal},
2162     Pages = {2386-2392},
2163     Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
2164     Volume = 83,
2165     Year = 2002}
2166    
2167     @article{Sum03,
2168     Author = {A.~K. Sum and J.~J. de~Pablo},
2169     Date-Modified = {2006-02-15 10:11:01 -0500},
2170     Journal = {Biophysical Journal},
2171     Pages = {3636-3645},
2172     Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2173     Volume = 85,
2174     Year = 2003}
2175    
2176     @article{Gomez03,
2177     Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
2178     Date-Modified = {2006-02-15 10:17:14 -0500},
2179     Journal = {Eur. Biophys. J.},
2180     Pages = {217-227},
2181     Title = {Setting up and optimization of membrane protein simulations},
2182     Volume = 31,
2183     Year = 2002}
2184    
2185     @article{Smondyrev99,
2186     Author = {A.~M. Smondyrev and M.~L. Berkowitz},
2187     Date-Modified = {2006-02-15 10:10:29 -0500},
2188     Journal = {Biophysical Journal},
2189     Pages = {2472-2478},
2190     Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
2191     Volume = 76,
2192     Year = 1999}
2193    
2194     @article{Nina02,
2195     Author = {M. Nina and T. Simonson},
2196     Date-Modified = {2006-02-15 10:29:27 -0500},
2197     Journal = {J. Phys. Chem. B},
2198     Pages = {3696-3705},
2199     Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
2200     Volume = 106,
2201     Year = 2002}
2202    
2203     @article{Norberg00,
2204     Author = {J. Norberg and L. Nilsson},
2205     Date-Modified = {2006-02-15 10:29:36 -0500},
2206     Journal = {Biophysical Journal},
2207     Pages = {1537-1553},
2208     Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2209     Volume = 79,
2210     Year = 2000}
2211    
2212     @article{Patra03,
2213     Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2214     Date-Modified = {2006-02-15 10:29:58 -0500},
2215     Journal = {Biophysical Journal},
2216     Pages = {3636-3645},
2217     Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
2218     Volume = 84,
2219     Year = 2003}
2220    
2221     @article{Marrink04,
2222     Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
2223     Date-Modified = {2006-02-15 10:28:28 -0500},
2224     Journal = {J. Phys. Chem. B},
2225     Pages = {750-760},
2226     Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
2227     Volume = 108,
2228     Year = 2004}
2229    
2230     @article{Andersen83,
2231     Author = {H.~C. Andersen},
2232     Date-Modified = {2006-02-15 10:08:20 -0500},
2233     Journal = {Journal of Computational Physics},
2234     Pages = {24-34},
2235     Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
2236     Volume = 52,
2237     Year = 1983}
2238    
2239     @article{Hura00,
2240     Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
2241     Date-Modified = {2006-02-15 10:21:28 -0500},
2242     Journal = {J. Chem. Phys.},
2243     Pages = {9140-9148},
2244     Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
2245     Volume = 113,
2246     Year = 2000}
2247    
2248     @article{Ryckaert77,
2249     Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
2250     Date-Modified = {2006-02-15 10:31:44 -0500},
2251     Journal = {Journal of Computational Physics},
2252     Pages = {327-341},
2253     Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
2254     Volume = 23,
2255     Year = 1977}
2256    
2257     @inbook{Fowles99,
2258     Author = {G.~R. Fowles and G.~L. Cassiday},
2259     Chapter = 10,
2260     Date-Modified = {2006-02-15 10:18:00 -0500},
2261     Edition = {6th},
2262     Publisher = {Saunders College Publishing},
2263     Title = {Analytical Mechanics},
2264     Year = 1999}
2265    
2266     @article{Petrache00,
2267     Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2268     Date-Modified = {2006-02-15 10:30:24 -0500},
2269     Journal = {Biophysical Journal},
2270     Pages = {3172-3192},
2271     Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2272     Volume = 79,
2273     Year = 2000}
2274    
2275     @article{Egberts88,
2276     Author = {E. Egberts and H.~J.~C. Berendsen},
2277     Date-Modified = {2006-02-15 10:16:43 -0500},
2278     Journal = {J. Chem. Phys.},
2279     Pages = {3718-3732},
2280     Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
2281     Volume = 89,
2282     Year = 1988}
2283    
2284     @article{Holz00,
2285     Author = {M. Holz and S.~R. Heil and A. Sacco},
2286     Journal = {Phys. Chem. Chem. Phys.},
2287     Pages = {4740-4742},
2288     Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
2289     Volume = 2,
2290     Year = 2000}
2291    
2292     @incollection{Zannoni94,
2293     Author = {C. Zannoni},
2294     Booktitle = {The Molecular Dynamics of Liquid Crstals},
2295     Chapter = 6,
2296     Date-Modified = {2006-02-15 10:12:36 -0500},
2297     Editor = {G.~R. Luckhurst and C.~A. Veracini},
2298     Pages = {139-169},
2299     Publisher = {Kluwer Academic Publishers},
2300     Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
2301     Year = 1994}
2302    
2303     @article{Melchionna93,
2304     Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
2305     Date-Modified = {2006-02-15 10:28:54 -0500},
2306     Journal = {Molecular Physics},
2307     Pages = {533-544},
2308     Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
2309     Volume = 78,
2310     Year = 1993}
2311    
2312     @article{Fennell04,
2313     Author = {C.~J. Fennell and J.~D. Gezelter},
2314     Date-Modified = {2006-02-15 09:08:04 -0500},
2315     Journal = jcp,
2316     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
2317     Number = 19,
2318     Pages = {9175-9184},
2319     Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
2320     Volume = 120,
2321     Year = 2004}
2322    
2323     @article{Klein01,
2324     Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
2325     Date-Modified = {2006-02-15 10:27:22 -0500},
2326     Journal = {J. Phys. Chem. B},
2327     Pages = {4464-4470},
2328     Title = {A Coarse Grain Model for Phospholipid Simulations},
2329     Volume = 105,
2330     Year = 2001}
2331    
2332     @article{Marrink03,
2333     Author = {S.~J. Marrink and A.~E. Mark},
2334     Date-Modified = {2006-03-16 09:54:52 -0500},
2335     Journal = {J. Am. Chem. Soc.},
2336     Pages = {15233-15242},
2337     Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2338     Volume = 125,
2339     Year = 2003}
2340    
2341     @article{Fletcher64,
2342     Author = {R. Fletcher and C.~M. Reeves},
2343     Date-Modified = {2006-02-15 10:17:34 -0500},
2344     Journal = {Comput. J.},
2345     Number = 2,
2346     Pages = {149-154},
2347     Title = {Function minimization by conjugate gradients},
2348     Volume = 7,
2349     Year = 1964}
2350    
2351     @article{Polak69,
2352     Author = {E. Polak and G. Ribiere},
2353     Date-Modified = {2006-02-15 10:14:00 -0500},
2354     Journal = {Rev. Fr. Inform. Rech. Oper.},
2355     Pages = {35-43},
2356     Title = {Note sur la convergence de methodes de directions conjugees},
2357     Volume = {16-R1},
2358     Year = 1969}
2359    
2360     @article{Voter87,
2361     Author = {A.~F. Voter and S.~P. Chen},
2362     Date-Modified = {2006-02-15 10:35:19 -0500},
2363     Journal = {Mat. Res. Soc. Symp. Proc.},
2364     Pages = {175},
2365     Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
2366     Volume = {82},
2367     Year = {1987}}
2368    
2369     @article{Hendrickson95,
2370     Author = {Bruce Hendrickson and Steve Plimpton},
2371     Date-Modified = {2006-02-15 10:19:11 -0500},
2372     Journal = {Journal of Parallel and Distributed Computing},
2373     Pages = {15-25},
2374     Title = {Parallel Many-body Simulations without All-to-All Communication},
2375     Volume = {27},
2376     Year = {1995}}
2377    
2378     @inproceedings{Paradyn93,
2379     Address = {Pittsburgh, PA},
2380     Author = {S.~J. Plimpton and B.~A. Hendrickson},
2381     Booktitle = {Materials Theory and Modelling},
2382     Date-Modified = {2006-02-15 10:30:42 -0500},
2383     Editor = {J. Broughton and P. Bristowe and J. Newsam},
2384     Pages = 37,
2385     Publisher = {Materials Research Society},
2386     Series = {MRS Proceedings},
2387     Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
2388     Volume = 291,
2389     Year = 1993}
2390    
2391     @article{Voter95a,
2392     Author = {A.~F. Voter},
2393     Date-Modified = {2006-02-15 10:35:27 -0500},
2394     Journal = {Intermetallic Compounds: Principles and Practice},
2395     Pages = {77},
2396     Title = {The Embedded-Atom Method},
2397     Volume = {1},
2398     Year = {1995}}
2399    
2400     @article{Heller90,
2401     Author = {H. Heller and H. Grubmuller and K. Schulten},
2402     Date-Modified = {2006-02-15 10:19:02 -0500},
2403     Journal = {Molecular Simulation},
2404     Pages = {133},
2405     Title = {Molecular dynamics simulation on a parallel computer},
2406     Volume = {5},
2407     Year = {1990}}
2408    
2409     @book{Fox88,
2410     Address = {Englewood Cliffs, NJ},
2411     Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
2412     Publisher = {Prentice-Hall},
2413     Title = {Solving Promblems on Concurrent Processors},
2414     Volume = {I},
2415     Year = 1988}
2416    
2417     @article{Berendsen95,
2418     Author = {H.~J.~C. Berendsen and D. van~der~Spoel and R. van~Drunen},
2419     Date-Modified = {2006-02-15 10:20:47 -0500},
2420     Journal = {Comp. Phys. Comm.},
2421     Pages = {43-56},
2422     Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
2423     Volume = 91,
2424     Year = 1995}
2425    
2426     @article{Lindahl01,
2427     Author = {E. Lindahl and B. Hess and D. van~der~Spoel},
2428     Date-Modified = {2006-02-15 10:25:51 -0500},
2429     Journal = {J. Mol. Mod.},
2430     Pages = {306-317},
2431     Title = {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
2432     Volume = 7,
2433     Year = 2001}
2434    
2435     @article{Smith96,
2436     Author = {W. Smith and T. Forester},
2437     Date-Modified = {2006-02-15 10:10:14 -0500},
2438     Journal = {J. Molec. Graphics.},
2439     Number = 3,
2440     Pages = {136-141},
2441     Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package},
2442     Volume = 14,
2443     Year = 1996}
2444    
2445     @article{Ponder87,
2446     Author = {J.~W. Ponder and F.~M. Richards},
2447     Date-Modified = {2006-02-15 10:13:45 -0500},
2448     Journal = {J. Comp. Chem.},
2449     Number = 7,
2450     Pages = {1016-1024},
2451     Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
2452     Volume = 8,
2453     Year = 1987}
2454    
2455     @article{Berendsen87,
2456     Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
2457     Journal = jpc,
2458     Pages = {6269-6271},
2459     Title = {The Missing Term in Effective Pair Potentials},
2460     Volume = 91,
2461     Year = 1987}
2462    
2463     @incollection{Berendsen81,
2464     Address = {Dordrecht},
2465     Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
2466     Booktitle = {Intermolecular Forces},
2467     Editor = {B. Pullman},
2468     Pages = 331,
2469     Publisher = {Reidel},
2470     Title = {Simple Point Charge Water},
2471     Year = 1981}
2472    
2473     @article{Mahoney00,
2474     Author = {M.~W. Mahoney and W.~L. Jorgensen},
2475     Journal = jcp,
2476     Number = 20,
2477     Pages = {8910-8922},
2478     Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
2479     Volume = 112,
2480     Year = 2000}
2481    
2482     @article{Meineke05,
2483     Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter},
2484     Date-Modified = {2006-03-05 12:37:31 -0500},
2485     Journal = {J. Comp. Chem.},
2486     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf},
2487     Pages = {252-271},
2488     Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2489     Volume = 26,
2490     Year = 2005}
2491    
2492     @article{Baez95a,
2493     Author = {L.~A. B\`{a}ez and P. Clancy},
2494     Journal = mp,
2495     Number = 3,
2496     Pages = {385-396},
2497     Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
2498     Volume = 86,
2499     Year = 1995}
2500    
2501     @article{Baez95b,
2502     Author = {L.~A. B\`{a}ez and P. Clancy},
2503     Journal = jcp,
2504     Number = 22,
2505     Pages = {9744-9755},
2506     Title = {Phase equilibria in extended simple point charge ice-water systems},
2507     Volume = 103,
2508     Year = 1995}
2509    
2510     @article{Davidson84,
2511     Author = {E.~R. Davidson and K. Morokuma},
2512     Journal = jcp,
2513     Number = 8,
2514     Pages = {3741-3742},
2515     Title = {A proposed antiferroelectric structure for proton ordered ice Ih},
2516     Volume = 81,
2517     Year = 1984}
2518    
2519     @article{Sanz04,
2520     Author = {E. Sanz and C. Vega and J.~L.~F. Abascal and L.~G. MacDowell},
2521     Journal = prl,
2522     Number = 25,
2523     Pages = 255701,
2524     Title = {Phase Diagram of Water from Computer Simulation},
2525     Volume = 92,
2526     Year = 2004}
2527    
2528     @article{Onsager36,
2529     Author = {L. Onsager},
2530     Journal = jacs,
2531     Pages = {1486-1493},
2532     Title = {Electric Moments of Molecules in Liquids},
2533     Volume = 58,
2534     Year = 1936}
2535    
2536     @article{Matsumoto02,
2537     Author = {M. Matsumoto and S. Saito and I. Ohimine},
2538     Journal = {Nature (London)},
2539     Pages = {409-413},
2540     Title = {Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing},
2541     Volume = 416,
2542     Year = 2002}
2543    
2544     @article{Yamada02,
2545     Author = {M. Yamada and S. Mossa and H.~E. Stanley and F. Sciortino},
2546     Journal = prl,
2547     Number = 19,
2548     Pages = 195701,
2549     Title = {Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water},
2550     Volume = 88,
2551     Year = 2002}
2552    
2553     @article{Wallqvist95,
2554     Author = {A. Wallqvist and B.~J. Berne},
2555     Journal = jpc,
2556     Pages = {2885-2892},
2557     Title = {Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area},
2558     Volume = 99,
2559     Year = 1995}
2560    
2561     @article{Vlot99,
2562     Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
2563     Journal = jcp,
2564     Number = 1,
2565     Pages = {55-61},
2566     Title = {Free energy calculations on systems of rigid molecules: An application to the TIP4P model of H$_2$O},
2567     Volume = 110,
2568     Year = 1999}
2569    
2570     @article{Gao00,
2571     Author = {G.~T. Gao and X.~C. Zeng and H. Tanaka},
2572     Journal = jcp,
2573     Number = 19,
2574     Pages = {8534-8538},
2575     Title = {The melting temperature of proton-disordered hexagonal ice: A computer simulation of 4-site transferable intermolecular potential model of water},
2576     Volume = 112,
2577     Year = 2000}
2578    
2579     @article{Bizid87,
2580     Author = {A. Bizid and L. Bosio and A. Defrain and M. Oumezzine},
2581     Journal = jcp,
2582     Number = 4,
2583     Pages = {2225-2230},
2584     Title = {Structure of high-density amorphous water. I. X-ray diffraction study},
2585     Volume = 87,
2586     Year = 1987}
2587    
2588     @article{Quintana92,
2589     Author = {J. Quintana and A.~D.~J. Haymet},
2590     Journal = cpl,
2591     Number = 3,
2592     Pages = {273-277},
2593     Title = {The chemical potential of water: molecular dynamics computer simulation of the CF and SPC models},
2594     Volume = 189,
2595     Year = 1992}
2596    
2597     @article{Mezei92,
2598     Author = {M. Mezei},
2599     Journal = {J. Comput. Chem.},
2600     Pages = 651,
2601     Title = {Don't Remember},
2602     Volume = 13,
2603     Year = 1992}
2604    
2605     @article{Widom63,
2606     Author = {B. Widom},
2607     Journal = jcp,
2608     Pages = 2808,
2609     Title = {Particle insertion},
2610     Volume = 39,
2611     Year = 1963}
2612    
2613     @article{Clancy94,
2614     Author = {L.~A. B\'{a}ez and P. Clancy},
2615     Journal = jcp,
2616     Number = 11,
2617     Pages = {9837-9840},
2618     Title = {Existence of a density maximum in extended simple point charge water},
2619     Volume = 101,
2620     Year = 1994}
2621    
2622     @article{Jorgensen98b,
2623     Author = {W.~L. Jorgensen and C. Jenson},
2624     Journal = jcc,
2625     Number = 10,
2626     Pages = {1179-1186},
2627     Title = {Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum Density},
2628     Volume = 19,
2629     Year = 1998}
2630    
2631     @article{Mahoney01,
2632     Author = {M.~W. Mahoney and W.~L. Jorgensen},
2633     Journal = jcp,
2634     Number = 1,
2635     Pages = {363-366},
2636     Title = {Diffusion constant of the TIP5P model of liquid water},
2637     Volume = 114,
2638     Year = 2001}
2639    
2640     @article{Rahman75,
2641     Author = {A. Rahman and F.~H. Stillinger and H.~L. Lemberg},
2642     Journal = jcp,
2643     Number = 12,
2644     Pages = {5223-5230},
2645     Title = {Study of a central force model for liquid water by molecular dynamics},
2646     Volume = 63,
2647     Year = 1975}
2648    
2649     @article{Spoel98,
2650     Author = {D. {van der Spoel} and P.~J. {van Maaren} and H.~J.~C. Berendsen},
2651     Date-Modified = {2006-03-05 12:38:54 -0500},
2652     Journal = jcp,
2653     Number = 24,
2654     Pages = {10220-10230},
2655     Title = {A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field},
2656     Volume = 108,
2657     Year = 1998}
2658    
2659     @article{Gallagher03,
2660     Author = {K.~R. Gallagher and K.~A. Sharp},
2661     Journal = jacs,
2662     Pages = 9853,
2663     Title = {A New Angle on Heat Capacity Changes in Hydrophobic Solvation},
2664     Volume = 125,
2665     Year = 2003}
2666    
2667     @article{Frenkel84,
2668     Author = {D. Frenkel and A.~J.~C. Ladd},
2669     Journal = jcp,
2670     Number = 7,
2671     Pages = {3188-3193},
2672     Title = {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
2673     Volume = 81,
2674     Year = 1984}
2675    
2676     @article{Hermens88,
2677     Author = {J. Hermans and A. Pathiaseril and A. Anderson},
2678     Journal = jacs,
2679     Pages = {5982-5986},
2680     Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
2681     Volume = 110,
2682     Year = 1988}
2683    
2684     @article{Meijer90,
2685     Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
2686     Journal = jcp,
2687     Number = 12,
2688     Pages = {7570-7575},
2689     Title = {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
2690     Volume = 92,
2691     Year = 1990}
2692    
2693     @article{Li96,
2694     Author = {H. Li and R. Helling and C. Tang and N. Wingreen},
2695     Journal = {Science},
2696     Pages = {666-669},
2697     Title = {Emergence of Preferred Structures in a Simple Model of Protein Folding},
2698     Volume = 273,
2699     Year = 1996}
2700    
2701     @article{Stillinger74,
2702     Author = {F.~H. Stillinger and A. Rahman},
2703     Journal = jcp,
2704     Number = 4,
2705     Pages = {1545-1557},
2706     Title = {Improved simulation of liquid water by molecular dynamics},
2707     Volume = 60,
2708     Year = 1974}
2709    
2710     @article{Caldwell95,
2711     Author = {J.~W. Caldwell and P.~A. Kollman},
2712     Journal = jpc,
2713     Number = 16,
2714     Pages = {6208-6219},
2715     Title = {Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and $N$-Methylacetamide},
2716     Volume = 99,
2717     Year = 1995}
2718    
2719     @article{Urbic00,
2720     Author = {T. Urbi\v{c} and V. Vlachy and Y.~V. Kalyuzhnyi and N.~T. Southall and K.~A. Dill},
2721     Date-Modified = {2006-02-15 10:34:30 -0500},
2722     Journal = jcp,
2723     Number = 6,
2724     Pages = {2843-2848},
2725     Title = {A two-dimensional model of water: Therory and computer simulations},
2726     Volume = 112,
2727     Year = 2000}
2728    
2729     @article{Yang04,
2730     Author = {Jianjun Yang and Sheng Meng and L.~F. Xu and E.~G. Wang},
2731     Journal = prl,
2732     Number = 14,
2733     Pages = 146102,
2734     Title = {Ice Tessellation on a Hydroxylated Silica Surface},
2735     Volume = 92,
2736     Year = 2004}
2737    
2738     @Misc{EPAPSdeposit,
2739     note = {See EPAPS Document No. \_\_\_\_\_\_\_\_\_\_\_\_\_\_ for supporting information. This document may be retrieved via the EPAPS homepage ({\tt http://www.aip.org/pubservs/epaps.html}) or from {\tt ftp.aip.org} in the directory {\tt /epaps/}. See the EPAPS homepage for more information.}
2740     }
2741