ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/mdRipple/mdripple.bib
Revision: 3174
Committed: Fri Jul 13 22:01:52 2007 UTC (16 years, 11 months ago) by xsun
File size: 82698 byte(s)
Log Message:
adding the image files and write the introduction section in tex file

File Contents

# User Rev Content
1 xsun 3147 @string{jcp = "J. Chem. Phys."}
2     @string{cpl = "Chem. Phys. Lett."}
3     @string{jpc = "J. Phys. Chem."}
4     @string{jpcA = "J. Phys. Chem. A"}
5     @string{jpcB = "J. Phys. Chem. B"}
6     @string{cp = "Chem. Phys."}
7     @string{acp = "Adv. Chem. Phys."}
8     @string{pra = "Phys. Rev. A"}
9     @string{prb = "Phys. Rev. B"}
10     @string{pre = "Phys. Rev. E"}
11     @string{prl = "Phys. Rev. Lett."}
12     @string{rmp = "Rev. Mod. Phys."}
13     @string{jml = "J. Mol. Liq."}
14     @string{mp = "Mol. Phys."}
15     @string{pnas = "Proc. Natl. Acad. Sci. USA"}
16     @string{jacs = "J. Am. Chem. Soc."}
17     @string{jcc = "J. Comp. Chem."}
18     @string{cpc = "Comp. Phys. Comm."}
19     @string{bj = "Biophys. J."}
20    
21     @article{Ayton95,
22     author = {G. Ayton and M.~J.~P. Gingras and G.~N. Patey},
23     title = {Orientational Ordering in Spatially Disordered Dipolar System},
24     journal = prl,
25     volume = 75,
26     number = 12,
27     pages = {2360-2363},
28     year = 1995}
29    
30     @article{Ayton97,
31     author = "G. Ayton and M. J. P. Gingras and G. N. Patey",
32     title = "Ferroelectric and dipolar glass phases of noncrystalline systems",
33     journal = pre,
34     volume = 56,
35     number = 1,
36     pages = "562-570",
37     year = 1997}
38    
39     @article{Katsaras00,
40     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",
41     title = "Clarification of the ripple phase of lecithin bilayer using fully hydrated, aligned samples",
42     journal = pre,
43     volume = 61,
44     number = 5,
45     pages = "5668-5677",
46     year = 2000}
47    
48     @article{Lubensky93,
49     author = "T. C. Lubensky and F. C. MacKintosh",
50     title = "Theory of ``Ripple'' Phases of Lipid Bilayers",
51     journal = prl,
52     volume = 71,
53     number = 10,
54     pages = "1565-1568",
55     year = 1993}
56    
57     @article{Sun96,
58     author = "W. J. Sun and S. Tristram-Nagle and R. M. Suter and J. F. Nagle",
59     title = "Structure of the Ripple Phase in Lecithin Bilayers",
60     journal = pnas,
61     volume = 93,
62     pages = "7008-7012",
63     year = 1996}
64    
65     @article{Kaasgaard03,
66     author = "Thomas Kaasgaard and Chad Leidy and John H. Crowe and Ole G. Mouritsen and Kent J\o rgensen",
67     title = "Temperature-Controlled Structure and Kinetics of Ripple Phases in One- and Two-Component Supported Lipid Bilayers",
68     journal = bj,
69     volume = 85,
70     number = 1,
71     pages = "350-360",
72     year = 2003}
73    
74     @article{Tao91,
75     author = "R. Tao and J. M. Sun",
76     title = "Three-Dimensional Structure of Induced Electrorheological Solid",
77     journal = prl,
78     volume = 67,
79     number = 3,
80     pages = "398-401",
81     year = 1991}
82    
83     @article{Weis92,
84     author = "J. J. Weis and D. Levesque and G. J. Zarragoicoechea",
85     title = "Orientational Order in Simple Dipolar Liquid-Crystal Models",
86     journal = prl,
87     volume = 69,
88     number = 6,
89     pages = "913-916",
90     year = 1992}
91    
92     @article{Wei92,
93     author = "Dongqing Wei and G. N. Patey",
94     title = "Orientational Order in Simple Dipolar Liquids: Computer Simulation of a Ferroeletric Nematic Phase",
95     journal = prl,
96     volume = 68,
97     number = 13,
98     pages = "2043-2045",
99     year = 1992}
100    
101     @article{Pandit03,
102     author = "Sagar A. Pandit and David Bostick and Max L. Berkowitz",
103     title = "An algorithm to describe molecular scale rugged surfaces and its application to the study of a water/lipid bilayer interface",
104     journal = jcp,
105     volume = 119,
106     number = 4,
107     pages = "2199-2205",
108     year = 2003}
109    
110     @article{Luttinger46,
111     author = "J. M. Luttinger and L. Tisza",
112     title = "Theory of Dipole Interaction in Crystals",
113     journal = "Physical Review",
114     volume = 70,
115     number = 11,
116     pages = "954-964",
117     year = 1946}
118    
119     @article{Heimburg00,
120     author = "Thomas Heimburg",
121     title = "A Model for the Lipid Pretransition: Coupling of Ripple Formation with the Chain-Melting Transition",
122     journal = bj,
123     volume = 78,
124     pages = "1154-1165",
125     year = 2000}
126    
127     @article{Goldstein88,
128     author = "Raymond E. Goldstein and Stanislas Leibler",
129     title = "Model for Lamellar Phases of Interacting Lipid Membranes",
130     journal = prl,
131     volume = 61,
132     number = 19,
133     pages = "2213-2216",
134     year = 1988}
135    
136     @article{McCullough90,
137     author = "W. Scott McCullough and H. L. Scott",
138     title = "Statistical-Mechanial Theory of the Ripple Phase of Lipid Bilayers",
139     journal = prl,
140     volume = 65,
141     number = 7,
142     pages = "931-934",
143     year = 1990}
144    
145     @article{Banerjee02,
146     author = "Srilekha Banerjee",
147     title = "Exploring the Ripple Phase of Biomembranes",
148     journal = "Physica A",
149     volume = 308,
150     pages = "89-100",
151     year = 2002}
152    
153     @article{Sengupta03,
154     author = "Kheya Sengupta and V. A. Raghunathan and John Katsaras",
155     title = "Structure of the Ripple Phase of Phospholipid Multibilayers",
156     journal = pre,
157     volume = 68,
158     number = 031710,
159     pages = "1-12",
160     year = 2003}
161    
162     @article{Mason01,
163     author = "P. C. Mason and J. F. Nagle and R. M. Epand and J. Katsaras",
164     title = "Anomalous Swelling in Phospholipid bilayers is not coupled to the formation of a ripple phase",
165     journal = pre,
166     volume = 63,
167     number = 030902,
168     pages = "1-4",
169     year = 2001}
170    
171     @article{Tieleman96,
172     author = "D. P. Tieleman and H. J. C. Berendsen",
173     title = "Molecular Dynamics Simulations of a Fully Hydrated Dipalmitoylphosphatidylcholine Bilayer with Different Macroscopic Boundary Conditions and Parameters",
174     journal = jcp,
175     volume = 105,
176     number = 11,
177     pages = "4871-4880",
178     year = 1996}
179    
180     @article{Kubica02,
181     author = "Krystian Kubica",
182     title = "Computer Simulation studies on significance of Lipid Polar Head Oreintation",
183     journal = "Computers and Chemistry",
184     volume = 26,
185     pages = "351-356",
186     year = 2002}
187    
188     @article{Leidy02,
189     author = "Chad Leidy and Thomas Kaasgaard and John H. Crowe and Ole G. Mouritsen and Kent J\o gensen",
190     title = "Ripples and the Formation of Anisotropic Lipid Domains: Imaging Two-Component Supported Double Bilayers by Atomic Force Microscopy",
191     journal = bj,
192     volume = 83,
193     pages = "2625-2633",
194     year = 2002}
195    
196     @article{Misbah98,
197     author = "C. Misbah and J. Duplat and B. Houchmandzadeh",
198     title = "Transition to Ripple Phases in Hydrated Amphiphiles",
199     journal = prl,
200     volume = 80,
201     number = 20,
202     pages = "4598-4601",
203     year = 1998}
204    
205    
206    
207     @Book{Cevc87,
208     author = {Gregor Cevc and Derek Marsh},
209     title = {Phospholipid Bilayers},
210     publisher = {Wiley-Interscience},
211     year = 1980,
212     address = {New York}
213     }
214    
215     @article{Copeland80,
216     author = "B. R. Copeland and H. M. McConnell",
217     title = "The Rippled Structure in Bilayer Membranes of Phosphatidylcholine and Binary Mixture of Phosphatidylcholine and Cholesterol",
218     journal = "Biochim. Biophys. Acta.",
219     volume = 599,
220     pages = "95-109",
221     year = 1980}
222    
223     @article{Meyer96,
224     author = "H. W. Meyer",
225     title = "Pretansition-Ripples in Bilayers of Dipalmitoylphosphatidylcholine: Undulation or Periodic Segments? A Freeze-Fracture Study",
226     journal = "Biochim. Biophys. Acta.",
227     volume = 1302,
228     pages = "221-245",
229     year = 1996}
230    
231    
232    
233     @Article{Carlson87,
234     author = {J.~M. Carlson and J.~P. Sethna},
235     title = {Theory of ripple phase in hydrated phospholipid bilayers},
236     journal = pra,
237     year = 1987,
238     volume = 36,
239     number = 7,
240     pages = 3359
241     }
242    
243     @Article{Marder84,
244     author = {M. Marder and H.~L. Frisch and J.~S. Langer and H.~M. McConnell},
245     title = {Theory of the intermediate rippled phase of phospholipid bilayers},
246     journal = pnas,
247     year = 1984,
248     volume = 81,
249     pages = {6559-6561}
250     }
251    
252     @Article{Bannerjee02,
253     author = {S. Bannerjee},
254     title = {Exploring the ripple phase of biomembranes},
255     journal = {Physica A},
256     year = 2002,
257     volume = 308,
258     pages = {89-100}
259     }
260    
261     @Article{deVries05,
262     author = {A.~H. de~Vries and S. Yefimov and A.~E. Mark and S.~J. Marrink},
263     title = {Molecular structure of the lecithin ripple phase},
264     journal = pnas,
265     year = 2005,
266     volume = 102,
267     number = 15,
268     pages = {5392-5396}
269     }
270    
271     @Article{Ayton02,
272     author = {G. Ayton and G.~A. Voth},
273     title = {Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers},
274     journal = {Biophys. J.},
275     year = 2002,
276     volume = 83,
277     pages = {3357-3370}
278     }
279    
280     @Article{Brannigan04b,
281     author = {G. Brannigan and A.~C. Tamboli and F.~L.~H. Brown},
282     title = {The role of molecular shape in bilayer elasticity and phase behavior},
283     journal = jcp,
284     year = 2004,
285     key = 121,
286     volume = 7,
287     pages = {3259-3271}
288     }
289    
290     @Article{Brannigan04a,
291     author = {G. Brannigan and F.~L.~H. Brown},
292     title = {Solvent-free simulations of fluid membrane bilayers},
293     journal = jcp,
294     year = 2004,
295     volume = 120,
296     number = 2,
297     pages = {1059-1071}
298     }
299    
300     @Book{Safran94,
301     author = {S.~A. Safran},
302     title = {Statistical Thermodynamics of Surfaces, Interfaces, and Membranes},
303     publisher = {Addison-Wesley},
304     year = 1994,
305     address = {Reading, MA}
306     }
307    
308     @Article{Tlusty00,
309     author = {T. Tlusty and S.~A. Safran},
310     title = {Defect-Induced Phase Separation in Dipolar Fluids},
311     journal = {Science},
312     year = 2000,
313     volume = 290,
314     pages = {1328-1331}
315     }
316    
317     @Article{Teixeira00,
318     author = {P~I~C Teixeira and J~M Tavares and M~M Telo da Gama},
319     title = {The effect of dipolar forces on the structure and thermodynamics of classical fluids},
320     journal = {J. Phys.: Condens. Matter},
321     year = 2000,
322     volume = 12,
323     pages = {R411-R434}
324     }
325    
326     @Article{Duncan06,
327     author = {Peter D. Duncan and Philip J. Camp},
328     title = {Aggregation Kinetics and the Nature of Phase Separation in Two-Dimensional Dipolar Fluids},
329     journal = prl,
330     year = 2006,
331     volume = 97,
332     pages = 107202
333     }
334    
335     @Article{Tavares02,
336     author = {J.~M. Tavares and J.~J. Weis and M.~M. Telo da Gama},
337     title = {Quasi-two-dimensional dipolar fluid at low densities: Monte Carlo simulations and theory},
338     journal = pre,
339     year = 2002,
340     volume = 65,
341     pages = 061201
342     }
343    
344     @Article{Duncan04,
345     author = {Peter D. Duncan and Philip J. Camp},
346     title = {Structure and dynamics in monolayer of dipolar spheres},
347     journal = jcp,
348     year = 2004,
349     volume = 121,
350     number = 22,
351     pages = {11322-11331}
352     }
353    
354     @Article{Holm05,
355     author = {C. Holm and J.-J. Weis},
356     title = {The structure of ferrofluids: A status report},
357     journal = {Curr. Opin. Colloid Interface Sci.},
358     year = 2005,
359     volume = 10,
360     pages = {133-140}
361     }
362    
363     @Article{Jiang04,
364     author = {F.~Y. Jiang and Y. Bouret and J.~T. Kindt},
365     title = {Molecular Dynamics Simulations of the Lipid Bilayer Edge},
366     journal = {Biophys. J.},
367     year = 2004,
368     volume = 87,
369     pages = {182-192}
370     }
371    
372     @Article{deJoannis06,
373     author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt},
374     title = {Coarse-Grained Model Simulations of Mixed-Lipid Systems: Composition and Line Tension of a Stabilized Bilayer Edge},
375     journal = {Langmuir},
376     year = 2006,
377     volume = 22,
378     pages = {998-1005}
379     }
380    
381     @Article{Marland1979,
382     author = {L.~G. Marland and D.~D. Betts},
383     title = {Frustration Effect in Quantum Spin Systems},
384     journal = prl,
385     year = 1979,
386     volume = 43,
387     number = 21,
388     pages = {1618-1621}
389     }
390    
391     @Article{Toulouse1977,
392     author = {G. Toulouse},
393     title = {Theory of Frustration Effect in Spin-Glasses. I.},
394     journal = {Commun. Phys.},
395     year = 1977,
396     volume = 2,
397     number = 4,
398     pages = {115-119}
399     }
400    
401     @Article{Seifert97,
402     author = {Udo Seifert},
403     title = {Configurations of fluid membranes and vesicles},
404     journal = {Adv. Phys.},
405     year = 1997,
406     volume = 46,
407     number = 1,
408     pages = {13-137}
409     }
410    
411     @article{Brodka04,
412     Author = {A. Br\'{o}dka},
413     Date-Added = {2006-04-26 09:41:52 -0400},
414     Date-Modified = {2006-04-26 09:43:52 -0400},
415     Doi = {10.1016/j.cplett.2004.10.086},
416     Journal = {Chem. Phys. Lett.},
417     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf},
418     Pages = {62-67},
419     Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
420     Volume = {400},
421     Year = {2004}}
422    
423     @article{deJoannis02,
424     Author = {J. {de Joannis} and A. Arnold and C. Holm},
425     Date-Added = {2006-04-26 09:40:15 -0400},
426     Date-Modified = {2006-04-26 09:45:19 -0400},
427     Doi = {10.1063/1.1491954},
428     Journal = {J. Chem. Phys.},
429     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf},
430     Number = {6},
431     Pages = {2503-2512},
432     Title = {Electrostatics in periodic slab geometries. II},
433     Volume = {117},
434     Year = {2002}}
435    
436     @article{Kawata01,
437     Author = {M. Kawata and M. Mikami},
438     Date-Added = {2006-04-26 09:38:01 -0400},
439     Date-Modified = {2006-04-26 09:40:11 -0400},
440     Journal = {Chem. Phys. Lett.},
441     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf},
442     Pages = {157-164},
443     Title = {Rapid calculation of two-dimensional Ewald summation},
444     Volume = {340},
445     Year = {2001}}
446    
447     @article{Arnold02,
448     Author = {A. Arnold and J. {de Joannis} and C. Holm},
449     Date-Added = {2006-04-26 09:36:09 -0400},
450     Date-Modified = {2006-04-26 09:37:52 -0400},
451     Doi = {10.1063/1.1491955},
452     Journal = {J. Chem. Phys.},
453     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf},
454     Number = {6},
455     Pages = {2496-2502},
456     Title = {Electrostatics in periodic slab geometries. I},
457     Volume = {117},
458     Year = {2002}}
459    
460     @article{Kolafa92,
461     Author = {J. Kolafa and J.~W. Perram},
462     Date-Added = {2006-03-21 09:41:58 -0500},
463     Date-Modified = {2006-03-21 09:42:47 -0500},
464     Journal = {Mol. Simul.},
465     Pages = {351-368},
466     Title = {Cutoff Errors in the Ewald. Summation Formulae for Point Charge Systems},
467     Volume = {9},
468     Year = {1992}}
469    
470     @article{Karasawa89,
471     Author = {N. Karasawa and W.~A. {Goddard III}},
472     Date-Added = {2006-03-21 09:11:44 -0500},
473     Date-Modified = {2006-03-21 09:13:00 -0500},
474     Journal = {J. Phys. Chem.},
475     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf},
476     Pages = {7320-7327},
477     Title = {Acceleration of Convergence for Lattice Sums},
478     Volume = {93},
479     Year = {1989}}
480    
481     @article{Rhee89,
482     Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
483     Date-Added = {2006-03-18 20:48:07 -0500},
484     Date-Modified = {2006-03-18 20:51:09 -0500},
485     Journal = {Phys. Rev. B},
486     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
487     Number = {1},
488     Pages = {36-42},
489     Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
490     Volume = {40},
491     Year = {1989}}
492    
493     @article{Hunenberger99a,
494     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
495     Date-Added = {2006-03-18 20:14:24 -0500},
496     Date-Modified = {2006-03-18 20:16:01 -0500},
497     Journal = {J. Chem. Phys.},
498     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
499     Number = {4},
500     Pages = {1856-1872},
501     Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
502     Volume = {110},
503     Year = {1999}}
504    
505     @article{Roberts95,
506     Author = {J.~E. Roberts and J. Schnitker},
507     Date-Added = {2006-03-18 20:12:23 -0500},
508     Date-Modified = {2006-03-18 20:13:36 -0500},
509     Journal = {J. Phys. Chem.},
510     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
511     Pages = {1322-1331},
512     Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
513     Volume = {99},
514     Year = {1995}}
515    
516     @article{Roberts94,
517     Author = {J.~E. Roberts and J. Schnitker},
518     Date-Added = {2006-03-18 20:10:37 -0500},
519     Date-Modified = {2006-03-18 20:12:19 -0500},
520     Journal = {J. Chem. Phys.},
521     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
522     Number = {6},
523     Pages = {5024-5031},
524     Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
525     Volume = {101},
526     Year = {1994}}
527    
528     @article{Yeh99,
529     Author = {I.-C. Yeh and M.~L. Berkowitz},
530     Date-Added = {2006-03-18 19:24:27 -0500},
531     Date-Modified = {2006-03-18 19:26:08 -0500},
532     Journal = {J. Chem. Phys.},
533     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
534     Number = {7},
535     Pages = {3155-3162},
536     Title = {Ewald summation for systems with slab geometry},
537     Volume = {111},
538     Year = {1999}}
539    
540     @article{Parry76,
541     Author = {D.~E. Parry},
542     Date-Added = {2006-03-18 19:11:01 -0500},
543     Date-Modified = {2006-03-18 19:14:01 -0500},
544     Journal = {Surf. Sci.},
545     Pages = {195},
546     Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
547     Volume = {54},
548     Year = {1976}}
549    
550     @article{Parry75,
551     Author = {D.~E. Parry},
552     Date-Added = {2006-03-18 19:08:40 -0500},
553     Date-Modified = {2006-03-18 19:16:14 -0500},
554     Journal = {Surf. Sci.},
555     Pages = {433-440},
556     Title = {The electrostatic potential in the surface region of an ionic crystal},
557     Volume = {49},
558     Year = {1975}}
559    
560     @article{deLeeuw79,
561     Author = {S.~W. {de Leeuw} and J.~W. Perram},
562     Date-Added = {2006-03-18 19:05:18 -0500},
563     Date-Modified = {2006-03-18 19:07:48 -0500},
564     Journal = {Mol. Phys.},
565     Pages = {1313-1327},
566     Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
567     Volume = {37},
568     Year = {1979}}
569    
570     @article{Heyes77,
571     Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
572     Date-Added = {2006-03-18 19:02:16 -0500},
573     Date-Modified = {2006-03-18 19:04:48 -0500},
574     Journal = {J. Chem. Soc., Faraday Trans. II},
575     Number = {7},
576     Pages = {1485-1496},
577     Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
578     Volume = {73},
579     Year = {1977}}
580    
581     @article{Spohr97,
582     Author = {E. Spohr},
583     Date-Added = {2006-03-18 18:51:02 -0500},
584     Date-Modified = {2006-03-18 18:52:21 -0500},
585     Journal = {J. Chem. Phys.},
586     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
587     Number = {16},
588     Pages = {6342-6348},
589     Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
590     Volume = {107},
591     Year = {1997}}
592    
593     @article{Weber00,
594     Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
595     Date-Added = {2006-03-16 09:49:22 -0500},
596     Date-Modified = {2006-03-16 09:51:17 -0500},
597     Doi = {10.1021/jp9937757},
598     Journal = {J. Phys. Chem. B},
599     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
600     Number = {15},
601     Pages = {3668-3675},
602     Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
603     Volume = {104},
604     Year = {2000}}
605    
606     @article{Hunenberger99b,
607     Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
608     Date-Added = {2006-03-16 09:45:10 -0500},
609     Date-Modified = {2006-03-18 20:16:16 -0500},
610     Journal = {Biophys. Chem.},
611     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
612     Pages = {69-88},
613     Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
614     Volume = {78},
615     Year = {1999}}
616    
617     @article{Petersen95,
618     Author = {H.~G. Petersen},
619     Date-Added = {2006-03-16 08:43:02 -0500},
620     Date-Modified = {2006-03-16 08:44:32 -0500},
621     Journal = {J. Chem. Phys.},
622     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
623     Month = {September},
624     Number = {9},
625     Pages = {3668-3679},
626     Title = {Accuracy and efficiency of the particle mesh Ewald method},
627     Volume = {103},
628     Year = {1995}}
629    
630     @article{Luty95,
631     Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
632     Date-Added = {2006-03-16 08:39:13 -0500},
633     Date-Modified = {2006-03-16 08:41:15 -0500},
634     Journal = {J. Chem. Phys.},
635     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
636     Number = {8},
637     Pages = {3014-3021},
638     Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
639     Volume = {103},
640     Year = {1995}}
641    
642     @article{Barker73,
643     Author = {J.~A. Barker and R.~O. Watts},
644     Date-Added = {2006-03-15 18:58:17 -0500},
645     Date-Modified = {2006-03-18 11:36:56 -0500},
646     Journal = {Mol. Phys.},
647     Pages = {789-792},
648     Title = {Monte Carlo studies of the dielectric properties of water-like models},
649     Volume = {26},
650     Year = {1973}}
651    
652     @article{Adams79,
653     Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
654     Date-Added = {2006-03-15 17:46:36 -0500},
655     Date-Modified = {2006-03-15 17:48:04 -0500},
656     Journal = {Mol. Phys.},
657     Number = {2},
658     Pages = {387-400},
659     Title = {The computer simulation of polar liquids},
660     Volume = {38},
661     Year = {1979}}
662    
663     @article{Rahman71,
664     Author = {A. Rahman and F.~H. Stillinger},
665     Date-Added = {2006-03-15 17:04:53 -0500},
666     Date-Modified = {2006-03-15 17:07:29 -0500},
667     Journal = {J. Chem. Phys.},
668     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
669     Month = {October},
670     Number = {7},
671     Pages = {3336-3359},
672     Title = {Molecular Dynamics Study of Liquid Water},
673     Volume = {55},
674     Year = {1971}}
675    
676     @article{Andrea83,
677     Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
678     Date-Added = {2006-03-15 15:16:12 -0500},
679     Date-Modified = {2006-03-15 15:18:10 -0500},
680     Journal = {J. Chem. Phys.},
681     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
682     Number = {9},
683     Pages = {4576-4584},
684     Title = {The role of long ranged forces in determining the structure and properties of liquid water},
685     Volume = {79},
686     Year = {1983}}
687    
688     @article{Brush66,
689     Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
690     Date-Added = {2006-03-13 16:55:39 -0500},
691     Date-Modified = {2006-03-13 17:01:15 -0500},
692     Journal = {J. Chem. Phys.},
693     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
694     Month = {September},
695     Number = {6},
696     Pages = {2102-2118},
697     Title = {Monte Carlo Study of a One-Component Plasma. I},
698     Volume = {45},
699     Year = {1966}}
700    
701     @article{Ewald21,
702     Author = {P.~P. Ewald},
703     Date-Added = {2006-03-13 13:32:04 -0500},
704     Date-Modified = {2006-03-16 22:39:27 -0500},
705     Journal = {Ann. Physik},
706     Pages = {253-287},
707     Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
708     Volume = {64},
709     Year = {1921}}
710    
711     @article{Jones56,
712     Author = {R.~E. Jones and D.~H. Templeton},
713     Date-Added = {2006-03-13 13:25:58 -0500},
714     Date-Modified = {2006-03-13 13:27:15 -0500},
715     Journal = {J. Chem. Phys.},
716     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
717     Number = {5},
718     Pages = {1062-1063},
719     Title = {Optimum Atomic Shape for Bertaut Series},
720     Volume = {25},
721     Year = {1956}}
722    
723     @article{Heyes81,
724     Author = {D.~M. Heyes},
725     Date-Added = {2006-03-13 13:12:45 -0500},
726     Date-Modified = {2006-03-13 13:14:27 -0500},
727     Journal = {J. Chem. Phys.},
728     Keywords = {Empty Keywords},
729     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
730     Number = {3},
731     Pages = {1924-1929},
732     Title = {Electrostatic potentials and fields in infinite point charge lattices},
733     Volume = {74},
734     Year = {1981}}
735    
736     @article{Steinbach94,
737     Author = {P.~J. Steinbach and B.~R. Brooks},
738     Date-Added = {2006-03-12 19:26:45 -0500},
739     Date-Modified = {2006-03-12 19:29:43 -0500},
740     Doi = {10.1002/jcc.540150702},
741     Journal = {J. Comput. Chem.},
742     Number = {7},
743     Pages = {667-683},
744     Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
745     Volume = {15},
746     Year = {1994}}
747    
748     @article{deLeeuw80,
749     Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
750     Date-Added = {2006-03-07 10:26:31 -0500},
751     Date-Modified = {2006-03-07 10:30:11 -0500},
752     Journal = {Proc. R. Soc. London Ser. A},
753     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/deLeeuw_EwaldSum_80.pdf},
754     Number = {1752},
755     Pages = {27-56},
756     Title = {Simulation of Electostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants},
757     Volume = {373},
758     Year = {1980}}
759    
760     @article{Essmann95,
761     Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen},
762     Date-Added = {2006-03-05 12:25:25 -0500},
763     Date-Modified = {2006-03-23 13:47:48 -0500},
764     Journal = {J. Chem. Phys.},
765     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf},
766     Number = {19},
767     Pages = {8577-8593},
768     Title = {A smooth particle mesh Ewald method},
769     Volume = {103},
770     Year = {1995}}
771    
772     @article{Kast03,
773     Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling},
774     Date-Added = {2006-02-18 16:47:26 -0500},
775     Date-Modified = {2006-02-18 16:51:25 -0500},
776     Journal = {Chem. Phys. Lett.},
777     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf},
778     Pages = {398-404},
779     Title = {Integral equation theory for correcting truncation errors in molecular simulations},
780     Volume = {367},
781     Year = {2003}}
782    
783     @article{Tobias01,
784     Author = {D.~J. Tobias},
785     Date-Added = {2006-02-15 11:28:58 -0500},
786     Date-Modified = {2006-02-15 11:32:16 -0500},
787     Journal = {Curr. Opin. Struct. Biol.},
788     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Tobias_ElectrostaticsCalculations_01.pdf},
789     Pages = {253-261},
790     Title = {Electrostatics calculations: recent methodological advances and applications to membranes},
791     Volume = {11},
792     Year = {2001}}
793    
794     @article{Zahn02,
795     Author = {D. Zahn and B. Schilling and S.~M. Kast},
796     Date-Added = {2006-02-15 09:21:27 -0500},
797     Date-Modified = {2006-02-15 09:24:07 -0500},
798     Journal = {J. Phys. Chem. B},
799     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf},
800     Number = {41},
801     Pages = {10725-10732},
802     Title = {Enhancement of the Wolf Damped Coulomb Potential: Static, Dynamic, and Dielectric Properties of Liquid Water from Molecular Simulation},
803     Volume = {106},
804     Year = {2002}}
805    
806     @article{Wolf99,
807     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
808     Date-Added = {2006-02-15 09:09:39 -0500},
809     Date-Modified = {2006-02-15 09:25:30 -0500},
810     Journal = {J. Chem. Phys.},
811     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
812     Number = {17},
813     Pages = {8255-8282},
814     Rating = {0},
815     Read = {No},
816     Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise},
817     Volume = {110},
818     Year = {1999}}
819    
820     @book{Berne90,
821     Address = {Malabar, Florida},
822     Author = {B.~J. Berne and R. Pecora},
823     Publisher = {Robert E. Krieger Publishing Company, Inc.},
824     Title = {Dynamic Light Scattering},
825     Year = 1990}
826    
827     @article{Evans77,
828     Author = {D.~J. Evans},
829     Journal = {Mol. Phys.},
830     Pages = {317-325},
831     Title = {On the representation of orientation space},
832     Volume = 34,
833     Year = 1977}
834    
835     @article{Tuckerman92,
836     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
837     Journal = jcp,
838     Pages = {1990-2001},
839     Title = {Reversible multiple time scale molecular dynamics},
840     Volume = 97,
841     Year = 1992}
842    
843     @book{Hansen86,
844     Address = {London},
845     Author = {J.~P. Hansen and I.~R. McDonald},
846     Chapter = 7,
847     Pages = {199-206},
848     Publisher = {Academic Press},
849     Title = {Theory of Simple Liquids},
850     Year = 1986}
851    
852     @article{Angelani98,
853     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
854     Journal = prl,
855     Number = 21,
856     Pages = {4648-4651},
857     Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
858     Volume = 81,
859     Year = 1998}
860    
861     @article{Stillinger82,
862     Author = {F.~H. Stillinger and T.~A. Weber},
863     Journal = pra,
864     Number = 2,
865     Pages = {978-989},
866     Title = {Hidden structure in liquids},
867     Volume = 25,
868     Year = 1982}
869    
870     @article{Stillinger83,
871     Author = {F.~H. Stillinger and T.~A. Weber},
872     Journal = pra,
873     Number = 4,
874     Pages = {2408-2416},
875     Title = {Dynamics of structural transitions in liquids},
876     Volume = 28,
877     Year = 1983}
878    
879     @article{Weber84,
880     Author = {T.~A. Weber and F.~H. Stillinger},
881     Journal = jcp,
882     Number = 6,
883     Pages = {2742-2746},
884     Title = {The effect of density on the inherent structure in liquids},
885     Volume = 80,
886     Year = 1984}
887    
888     @article{Stillinger85,
889     Author = {F.~H. Stillinger and T.~A. Weber},
890     Journal = jcp,
891     Number = 9,
892     Pages = {4767-4775},
893     Title = {Inherent structure theory of liquids in the hard-sphere limit},
894     Volume = 83,
895     Year = 1985}
896    
897     @article{Stillinger98,
898     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
899     Journal = {Nature},
900     Pages = {554-557},
901     Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
902     Volume = 393,
903     Year = 1998}
904    
905     @article{Parkhurst75a,
906     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
907     Journal = jcp,
908     Number = 6,
909     Pages = {2698-2704},
910     Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
911     Volume = 63,
912     Year = 1975}
913    
914     @article{Parkhurst75b,
915     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
916     Journal = jcp,
917     Number = 6,
918     Pages = {2705-2709},
919     Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
920     Volume = 63,
921     Year = 1975}
922    
923     @article{Forester97,
924     Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
925     Journal = {J. Chem. Soc. - Faraday Transactions},
926     Pages = {613-619},
927     Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
928     Volume = 93,
929     Year = 1997}
930    
931     @article{Tieleman98,
932     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
933     Journal = {Biophys. J.},
934     Pages = {2786-2801},
935     Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
936     Volume = 74,
937     Year = 1998}
938    
939     @article{Cascales98,
940     Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
941     Journal = {J. Phys. Chem. B},
942     Pages = {625-631},
943     Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
944     Volume = 102,
945     Year = 1998}
946    
947     @article{Bassolino95,
948     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
949     Journal = {J. Am. Chem. Soc.},
950     Pages = {4118-4129},
951     Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
952     Volume = 117,
953     Year = 1995}
954    
955     @article{Alper95,
956     Author = {H.~E. Alper and T.~R. Stouch},
957     Journal = {J. Phys. Chem.},
958     Pages = {5724-5731},
959     Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
960     Volume = 99,
961     Year = 1995}
962    
963     @article{Sok92,
964     Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
965     Journal = {J. Chem. Phys.},
966     Pages = {4699-4704},
967     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
968     Volume = 96,
969     Year = 1992}
970    
971     @article{Rabani99,
972     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
973     Journal = prl,
974     Pages = {3649},
975     Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
976     Volume = 82,
977     Year = {1999}}
978    
979     @article{Rabani97,
980     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
981     Journal = {J. Chem. Phys.},
982     Pages = {6867-6876},
983     Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
984     Volume = 107,
985     Year = 1997}
986    
987     @article{Gezelter99,
988     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
989     Journal = jcp,
990     Pages = 3444,
991     Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
992     Volume = 110,
993     Year = 1999}
994    
995     @article{Gezelter98,
996     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
997     Date-Modified = {2006-02-15 10:18:42 -0500},
998     Journal = jcp,
999     Pages = 4695,
1000     Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
1001     Volume = 109,
1002     Year = 1998}
1003    
1004     @article{Gezelter97,
1005     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
1006     Journal = jcp,
1007     Pages = 4618,
1008     Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
1009     Volume = 107,
1010     Year = 1997}
1011    
1012     @article{Zwanzig83,
1013     Author = {R. Zwanzig},
1014     Journal = jcp,
1015     Pages = {4507-4508},
1016     Title = {On the relation between self-diffusion and viscosity of liquids},
1017     Volume = 79,
1018     Year = 1983}
1019    
1020     @article{Zwanzig88,
1021     Author = {R. Zwanzig},
1022     Journal = {Proc. Natl. Acad. Sci. USA},
1023     Pages = 2029,
1024     Title = {Diffusion in rough potential},
1025     Volume = 85,
1026     Year = 1988}
1027    
1028     @article{Stillinger95,
1029     Author = {F.~H. Stillinger},
1030     Journal = {Science},
1031     Pages = {1935-1939},
1032     Title = {A Topographic View of Supercooled Liquids and Glass Formation},
1033     Volume = 267,
1034     Year = 1995}
1035    
1036     @incollection{Angell85,
1037     Address = {Springfield, VA},
1038     Author = {C.~A. Angell},
1039     Booktitle = {Relaxations in Complex Systems},
1040     Editor = {K.~Ngai and G.~B. Wright},
1041     Pages = 1,
1042     Publisher = {National Technical Information Service, U.S. Department of Commerce},
1043     Title = {unknown},
1044     Year = 1985}
1045    
1046     @article{Bembenek96,
1047     Author = {S.~D. Bembenek and B.~B. Laird},
1048     Journal = jcp,
1049     Pages = 5199,
1050     Title = {The role of localization in glasses and supercooled liquids},
1051     Volume = 104,
1052     Year = 1996}
1053    
1054     @article{Sun97a,
1055     Author = {X. Sun and W.~H. Miller},
1056     Date-Modified = {2006-02-15 10:33:35 -0500},
1057     Journal = jcp,
1058     Pages = 6346,
1059     Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
1060     Volume = 106,
1061     Year = 1997}
1062    
1063     @article{Spath96,
1064     Author = {B.~W. Spath and W.~H. Miller},
1065     Journal = jcp,
1066     Pages = 95,
1067     Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
1068     Volume = 104,
1069     Year = 1996}
1070    
1071     @book{Warshel91,
1072     Address = {New York},
1073     Author = {Arieh Warshel},
1074     Publisher = {Wiley},
1075     Title = {Computer modeling of chemical reactions in enzymes and solutions},
1076     Year = 1991}
1077    
1078     @article{Vuilleumier97,
1079     Author = {Rodolphe Vuilleumier and Daniel Borgis},
1080     Journal = jpc,
1081     Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
1082     Volume = {in press},
1083     Year = 1997}
1084    
1085     @article{Kob95a,
1086     Author = {W. Kob and H.~C. Andersen},
1087     Journal = pre,
1088     Pages = {4626-4641},
1089     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
1090     Volume = 51,
1091     Year = 1995}
1092    
1093     @article{Kob95b,
1094     Author = {W. Kob and H.~C. Andersen},
1095     Journal = pre,
1096     Pages = {4134-4153},
1097     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
1098     Volume = 52,
1099     Year = 1995}
1100    
1101     @inproceedings{Gotze89,
1102     Address = {Amsterdam},
1103     Author = {W. G{\"{o}}tze},
1104     Booktitle = {Liquids, Freezing and Glass Transitions},
1105     Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
1106     Pages = {287-503},
1107     Publisher = {North-Holland},
1108     Title = {Aspects of Structural Glass Transitions},
1109     Volume = {I},
1110     Year = 1989}
1111    
1112     @article{Sun97b,
1113     Author = {X. Sun and W.~H. Miller},
1114     Date-Modified = {2006-02-15 10:33:29 -0500},
1115     Journal = jcp,
1116     Pages = 916,
1117     Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
1118     Year = 1997}
1119    
1120     @article{Keshavamurthy94,
1121     Author = {S. Keshavamurthy and W.~H. Miller},
1122     Journal = cpl,
1123     Pages = 189,
1124     Title = {ivr},
1125     Volume = 218,
1126     Year = 1994}
1127    
1128     @article{Billing75,
1129     Author = {G.~D. Billing},
1130     Journal = cpl,
1131     Pages = 391,
1132     Title = {ehrenfest},
1133     Volume = 30,
1134     Year = 1975}
1135    
1136     @article{Chang90,
1137     Author = {Y.-T. Chang and W.~H. Miller},
1138     Journal = jpc,
1139     Pages = {5884-5888},
1140     Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
1141     Volume = 94,
1142     Year = 1990}
1143    
1144     @article{Shor94,
1145     Author = {P.W. Shor},
1146     Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
1147     Pages = {124-134},
1148     Title = {Algorithms for quantum computation: discrete logarithms and factoring},
1149     Year = 1994}
1150    
1151     @article{Feynman82,
1152     Author = {R.~P. Feynman},
1153     Journal = {Int. J. Theor. Phys.},
1154     Pages = {467-488},
1155     Title = {Simulating physics with computers},
1156     Volume = 21,
1157     Year = 1982}
1158    
1159     @article{Grover97,
1160     Author = {L.~K. Grover},
1161     Journal = prl,
1162     Pages = {4709-4712},
1163     Title = {Quantum computers can search arbitrarily large databases by a single query},
1164     Volume = 79,
1165     Year = 1997}
1166    
1167     @article{Chuang98,
1168     Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
1169     Journal = prl,
1170     Pages = {3408-3411},
1171     Title = {Experimental Implementation of Fast Quantum Searching},
1172     Volume = 80,
1173     Year = 1998}
1174    
1175     @article{Monroe95,
1176     Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
1177     Journal = prl,
1178     Pages = 4714,
1179     Title = {Demonstration of a fundamental quantum logic gate},
1180     Volume = 75,
1181     Year = 1995}
1182    
1183     @article{Lent93,
1184     Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
1185     Journal = {Nanotechnology},
1186     Pages = {49-57},
1187     Title = {Quantum Cellular Automata},
1188     Volume = 4,
1189     Year = 1993}
1190    
1191     @article{Barenco95,
1192     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},
1193     Journal = {Phys. Rev. A},
1194     Pages = {3457-3467},
1195     Title = {elementary gates for quantum computation},
1196     Volume = 52,
1197     Year = 1995}
1198    
1199     @article{Reinot97,
1200     Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
1201     Date-Modified = {2006-02-15 10:31:21 -0500},
1202     Journal = jcp,
1203     Pages = {457-466},
1204     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},
1205     Volume = 106,
1206     Year = 1997}
1207    
1208     @article{Laflamme96,
1209     Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
1210     Journal = prl,
1211     Pages = 77,
1212     Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
1213     Volume = 98,
1214     Year = 1996}
1215    
1216     @article{Shor95,
1217     Author = {P.~W. Shor},
1218     Journal = {Phys. Rev. A},
1219     Pages = {2493-2496},
1220     Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
1221     Volume = 52,
1222     Year = 1995}
1223    
1224     @article{Calderbank96,
1225     Author = {A.~R. Calderbank and P.~W. Shor},
1226     Journal = {Phys. Rev. A},
1227     Pages = {1098-1105},
1228     Title = {Good quantum error-correcting codes exist},
1229     Volume = 54,
1230     Year = 1996}
1231    
1232     @article{Steane96,
1233     Author = {A.~M. Steane},
1234     Journal = prl,
1235     Pages = {793-797},
1236     Title = {Error correcting codes in quantum theory},
1237     Volume = 77,
1238     Year = 1996}
1239    
1240     @article{Gezelter95,
1241     Author = {J.~D. Gezelter and W.~H. Miller},
1242     Journal = jcp,
1243     Pages = {7868-7876},
1244     Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
1245     Volume = 103,
1246     Year = 1995}
1247    
1248     @article{Chakrabarti92,
1249     Author = {A.~C. Chakrabarti and D.~W. Deamer},
1250     Journal = {Biochimica et Biophysica Acta},
1251     Pages = {171-177},
1252     Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
1253     Volume = 1111,
1254     Year = 1992}
1255    
1256     @article{Paula96,
1257     Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
1258     Journal = {Biophys. J.},
1259     Pages = {339-348},
1260     Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
1261     Volume = 70,
1262     Year = 1996}
1263    
1264     @article{Little96,
1265     Author = {H.~J. Little},
1266     Journal = {Pharmacology \& Therapeutics},
1267     Pages = {37-58},
1268     Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
1269     Volume = 69,
1270     Year = 1996}
1271    
1272     @article{McKinnon92,
1273     Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
1274     Journal = jpc,
1275     Pages = {10497-10506},
1276     Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
1277     Volume = 96,
1278     Year = 1992}
1279    
1280     @article{Venable93,
1281     Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
1282     Journal = {Science},
1283     Pages = {223-226},
1284     Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
1285     Volume = 262,
1286     Year = 1993}
1287    
1288     @article{Essmann99,
1289     Author = {U. Essmann and M.~L. Berkowitz},
1290     Journal = {Biophys. J.},
1291     Pages = {2081-2089},
1292     Title = {Dynamical properties of phospholipid bilayers from computer simulation},
1293     Volume = 76,
1294     Year = 1999}
1295    
1296     @article{Tu98,
1297     Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
1298     Journal = {Biophys. J.},
1299     Pages = {2123-2134},
1300     Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
1301     Volume = 75,
1302     Year = 1998}
1303    
1304     @article{Pomes96,
1305     Author = {R. Pomes and B. Roux},
1306     Journal = {Biophys. J.},
1307     Pages = {19-39},
1308     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},
1309     Volume = 71,
1310     Year = 1996}
1311    
1312     @article{Duwez60,
1313     Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
1314     Journal = {J. Appl. Phys.},
1315     Pages = {1136-1137},
1316     Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
1317     Volume = 31,
1318     Year = 1960}
1319    
1320     @article{Peker93,
1321     Author = {A. Peker and W.~L. Johnson},
1322     Journal = {Appl. Phys. Lett.},
1323     Pages = {2342-2344},
1324     Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
1325     Volume = 63,
1326     Year = 1993}
1327    
1328     @article{ChoiYim97,
1329     Author = {H. Choi-Yim and W.~L. Johnson},
1330     Journal = {Appl. Phys. Lett.},
1331     Pages = {3808-3810},
1332     Title = {Bulk metallic glass matrix composites},
1333     Volume = 71,
1334     Year = 1997}
1335    
1336     @article{Heller93,
1337     Author = {H. Heller and M. Schaefer and K. Schulten},
1338     Journal = jpc,
1339     Pages = {8343-8360},
1340     Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
1341     Volume = 97,
1342     Year = 1993}
1343    
1344     @article{Kushick76,
1345     Author = {J. Kushick and B.~J. Berne},
1346     Journal = jcp,
1347     Pages = {1362-1367},
1348     Title = {Computer Simulation of anisotropic molecular fluids},
1349     Volume = 64,
1350     Year = 1976}
1351    
1352     @article{Berardi96,
1353     Author = {R. Berardi and S. Orlandi and C Zannoni},
1354     Journal = cpl,
1355     Pages = {357-362},
1356     Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
1357     Volume = 261,
1358     Year = 1996}
1359    
1360     @article{Berardi99,
1361     Author = {R. Berardi and S. Orlandi and C. Zannoni},
1362     Journal = {Int. J. Mod. Phys. C},
1363     Pages = {477-484},
1364     Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
1365     Volume = 10,
1366     Year = 1999}
1367    
1368     @article{Pasterny00,
1369     Author = {K. Pasterny and E. Gwozdz and A. Brodka},
1370     Date-Modified = {2006-02-15 10:29:47 -0500},
1371     Journal = {J. Mol. Liq.},
1372     Pages = {173-184},
1373     Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
1374     Volume = 85,
1375     Year = 2000}
1376    
1377     @article{Jorgensen83,
1378     Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
1379     Journal = jcp,
1380     Pages = {926-935},
1381     Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
1382     Volume = 79,
1383     Year = 1983}
1384    
1385     @article{Berardi98,
1386     Author = {R. Berardi and C. Fava and C. Zannoni},
1387     Journal = cpl,
1388     Pages = {8-14},
1389     Title = {A Gay-Berne potential for dissimilar biaxial particles},
1390     Volume = 297,
1391     Year = 1998}
1392    
1393     @article{Luckhurst90,
1394     Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
1395     Journal = {Liquid Crystals},
1396     Pages = {451-464},
1397     Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the Gay-Berne model mesogen},
1398     Volume = 8,
1399     Year = 1990}
1400    
1401     @article{Gay81,
1402     Author = {J.~G. Gay and B.~J. Berne},
1403     Journal = jcp,
1404     Pages = {3316-3319},
1405     Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
1406     Volume = 74,
1407     Year = 1981}
1408    
1409     @article{Berne72,
1410     Author = {B.~J. Berne and P. Pechukas},
1411     Journal = jcp,
1412     Pages = {4213-4216},
1413     Title = {Gaussian Model Potentials for Molecular Interactions},
1414     Volume = 56,
1415     Year = 1972}
1416    
1417     @article{Perram96,
1418     Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
1419     Journal = pre,
1420     Pages = {6565-6572},
1421     Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
1422     Volume = 54,
1423     Year = 1996}
1424    
1425     @article{Cornell95,
1426     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},
1427     Journal = jacs,
1428     Pages = {5179-5197},
1429     Title = {A second generation force field for the simulation of proteins and nucleic acids},
1430     Volume = 117,
1431     Year = 1995}
1432    
1433     @article{Brooks83,
1434     Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
1435     Journal = {J. Comp. Chem.},
1436     Pages = {187-217},
1437     Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
1438     Volume = 4,
1439     Year = 1983}
1440    
1441     @incollection{MacKerell98,
1442     Address = {New York},
1443     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},
1444     Booktitle = {The Encyclopedia of Computational Chemistry},
1445     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1446     Pages = {271-277},
1447     Publisher = {John Wiley \& Sons},
1448     Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
1449     Volume = 1,
1450     Year = 1998}
1451    
1452     @incollection{Jorgensen98a,
1453     Address = {New York},
1454     Author = {W.~L. Jorgensen},
1455     Booktitle = {The Encyclopedia of Computational Chemistry},
1456     Date-Modified = {2006-02-15 10:21:45 -0500},
1457     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
1458     Pages = {1986-1989},
1459     Publisher = {John Wiley \& Sons},
1460     Title = {OPLS Force Fields},
1461     Volume = 3,
1462     Year = 1998}
1463    
1464     @article{Rabani00,
1465     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
1466     Date-Modified = {2006-02-15 10:30:55 -0500},
1467     Journal = prl,
1468     Pages = 467,
1469     Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
1470     Volume = 85,
1471     Year = 2000}
1472    
1473    
1474     @article{Janiak79,
1475     Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
1476     Journal = {J. Biol. Chem.},
1477     Pages = {6068-6078},
1478     Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
1479     Volume = 254,
1480     Year = 1979}
1481    
1482     @book{Tobias90,
1483     Address = {Tucson},
1484     Author = {Sheila Tobias},
1485     Publisher = {Research Corp.},
1486     Title = {They're not Dumb. They're Different: Stalking the Second Tier},
1487     Year = 1990}
1488    
1489     @article{Mazur92,
1490     Author = {E. Mazur},
1491     Journal = {Optics and Photonics News},
1492     Pages = 38,
1493     Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing?},
1494     Volume = 3,
1495     Year = 1992}
1496    
1497     @book{Mazur97,
1498     Address = {New Jersey},
1499     Author = {Eric Mazur},
1500     Publisher = {Prentice Hall},
1501     Title = {Peer Instruction: A User's Manual},
1502     Year = 1997}
1503    
1504     @article{Wigner55,
1505     Author = {E.~P. Wigner},
1506     Journal = {Annals of Mathematics},
1507     Pages = {548-564},
1508     Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
1509     Volume = 62,
1510     Year = 1955}
1511    
1512     @article{Gaukel98,
1513     Author = {C. Gaukel and H.~R. Schober},
1514     Journal = {Solid State Comm.},
1515     Pages = {1-5},
1516     Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
1517     Volume = 107,
1518     Year = 1998}
1519    
1520     @article{Qi99,
1521     Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
1522     Journal = prb,
1523     Number = 5,
1524     Pages = {3527-3533},
1525     Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
1526     Volume = 59,
1527     Year = 1999}
1528    
1529     @article{Khorunzhy97,
1530     Author = {A. Khorunzhy and G.~J. Rodgers},
1531     Journal = {J. Math. Phys.},
1532     Pages = {3300-3320},
1533     Title = {Eigenvalue distribution of large dilute random matrices},
1534     Volume = 38,
1535     Year = 1997}
1536    
1537     @article{Rodgers88,
1538     Author = {G.~J. Rodgers and A. Bray},
1539     Journal = {Phys. Rev. B},
1540     Pages = 355703562,
1541     Title = {Density of States of a Sparse Random Matrix},
1542     Volume = 37,
1543     Year = 1988}
1544    
1545     @article{Rodgers90,
1546     Author = {G.~J. Rodgers and C. {De Dominicis}},
1547     Journal = {J. Phys. A: Math. Gen.},
1548     Pages = {1567-1573},
1549     Title = {Density of states of sparse random matrices},
1550     Volume = 23,
1551     Year = 1990}
1552    
1553     @inproceedings{Barker80,
1554     Author = {J.~A. Barker},
1555     Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
1556     Editor = {D. Ceperley},
1557     Pages = {45-6},
1558     Series = {NRCC Workshop Proceedings},
1559     Title = {Reaction field method for polar fluids},
1560     Volume = 9,
1561     Year = 1980}
1562    
1563     @article{Smith82,
1564     Author = {W. Smith},
1565     Journal = {CCP5 Quarterly},
1566     Pages = {13-25},
1567     Title = {Point multipoles in the Ewald summation},
1568     Volume = 4,
1569     Year = 1982}
1570    
1571     @article{Daw84,
1572     Author = {M.~S. Daw and M.~I. Baskes},
1573     Journal = prb,
1574     Number = 12,
1575     Pages = {6443-6453},
1576     Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
1577     Volume = 29,
1578     Year = 1984}
1579    
1580     @article{Sutton90,
1581     Author = {A.~P. Sutton and J. Chen},
1582     Date-Modified = {2006-02-15 10:33:48 -0500},
1583     Journal = {Phil. Mag. Lett.},
1584     Pages = {139-146},
1585     Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
1586     Volume = 61,
1587     Year = 1990}
1588    
1589     @article{Lu97,
1590     Author = {J. Lu and J.~A. Szpunar},
1591     Journal = {Phil. Mag. A},
1592     Pages = {1057-1066},
1593     Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
1594     Volume = {75},
1595     Year = {1997}}
1596    
1597     @article{Shlesinger99,
1598     Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
1599     Journal = {Am. J. Phys.},
1600     Pages = {1253-1259},
1601     Title = {Above, below, and beyond Brownian motion},
1602     Volume = 67,
1603     Year = 1999}
1604    
1605     @article{Klafter96,
1606     Author = {J. Klafter and M. Shlesinger and G. Zumofen},
1607     Journal = {Physics Today},
1608     Pages = {33-39},
1609     Title = {Beyond Brownian Motion},
1610     Volume = 49,
1611     Year = 1996}
1612    
1613     @article{Blumen83,
1614     Author = {A. Blumen and J. Klafter and G. Zumofen},
1615     Journal = {Phys. Rev. B},
1616     Pages = {3429-3435},
1617     Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
1618     Volume = 27,
1619     Year = 1983}
1620    
1621     @article{Klafter94,
1622     Author = {J. Klafter and G. Zumofen},
1623     Journal = jpc,
1624     Pages = {7366-7370},
1625     Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
1626     Volume = 98,
1627     Year = 1994}
1628    
1629     @article{Dzugutov92,
1630     Author = {M. Dzugutov},
1631     Journal = pra,
1632     Pages = {R2984-R2987},
1633     Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
1634     Volume = 46,
1635     Year = 1992}
1636    
1637     @article{Moore94,
1638     Author = {P. Moore and T. Keyes},
1639     Journal = jcp,
1640     Pages = 6709,
1641     Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
1642     Volume = 100,
1643     Year = 1994}
1644    
1645     @article{Seeley89,
1646     Author = {G. Seeley and T. Keyes},
1647     Journal = jcp,
1648     Pages = {5581-5586},
1649     Title = {Normal-mode analysis of liquid-state dynamics},
1650     Volume = 91,
1651     Year = 1989}
1652    
1653     @article{Madan90,
1654     Author = {B. Madan and T. Keyes and G. Seeley},
1655     Journal = jcp,
1656     Pages = {7565-7569},
1657     Title = {Diffusion in supercooled liquids via normal mode analysis},
1658     Volume = 92,
1659     Year = 1990}
1660    
1661     @article{Madan91,
1662     Author = {B. Madan and T. Keyes and G. Seeley},
1663     Journal = jcp,
1664     Pages = {6762-6769},
1665     Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
1666     Volume = 94,
1667     Year = 1991}
1668    
1669     @article{Buchner92,
1670     Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
1671     Journal = jcp,
1672     Pages = {8522-8535},
1673     Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
1674     Volume = 97,
1675     Year = 1992}
1676    
1677     @article{Wan94,
1678     Author = {Yi. Wan and R.~M. Stratt},
1679     Journal = jcp,
1680     Pages = {5123-5138},
1681     Title = {Liquid theory for the instantaneous normal modes of a liquid},
1682     Volume = 100,
1683     Year = 1994}
1684    
1685     @article{Stratt95,
1686     Author = {R.~M. Stratt},
1687     Journal = {Acc. Chem. Res.},
1688     Pages = {201-207},
1689     Title = {The instantaneous normal modes of liquids},
1690     Volume = 28,
1691     Year = 1995}
1692    
1693     @article{Nitzan95,
1694     Author = {G.~V. Vijayadamodar and A. Nitzan},
1695     Journal = jcp,
1696     Pages = {2169-2177},
1697     Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
1698     Volume = 103,
1699     Year = 1995}
1700    
1701     @article{Ribeiro98,
1702     Author = {M.~C.~C. Ribeiro and P.~A. Madden},
1703     Journal = jcp,
1704     Pages = {3256-3263},
1705     Title = {Unstable Modes in Ionic Melts},
1706     Volume = 108,
1707     Year = 1998}
1708    
1709     @article{Keyes98,
1710     Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
1711     Date-Modified = {2006-02-15 10:22:13 -0500},
1712     Journal = jcp,
1713     Pages = {4693-4694},
1714     Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
1715     Volume = 109,
1716     Year = 1998}
1717    
1718     @article{Alemany98,
1719     Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
1720     Journal = jcp,
1721     Pages = {5175-5176},
1722     Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
1723     Volume = 109,
1724     Year = 1998}
1725    
1726     @article{Belonoshko00,
1727     Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
1728     Journal = prb,
1729     Pages = {3838-3844},
1730     Title = {Quasi ab initio molecular dynamic study of Cu melting},
1731     Volume = 61,
1732     Year = 2000}
1733    
1734     @article{Banhart92,
1735     Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1736     Journal = prb,
1737     Pages = {9968-9975},
1738     Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1739     Volume = 46,
1740     Year = 1992}
1741    
1742     @article{Wendt78,
1743     Author = {H. Wendt and F.~F. Abraham},
1744     Journal = prl,
1745     Pages = 1244,
1746     Volume = 41,
1747     Year = 1978}
1748    
1749     @article{Lewis91,
1750     Author = {L.~J. Lewis},
1751     Journal = prb,
1752     Pages = {4245-4254},
1753     Title = {Atomic dynamics through the glass transition},
1754     Volume = 44,
1755     Year = 1991}
1756    
1757     @article{Liu92,
1758     Author = {R.~S. Liu and D.~W. Qi and S. Wang},
1759     Journal = prb,
1760     Pages = {451-453},
1761     Title = {Subpeaks of structure factors for rapidly quenched metals},
1762     Volume = 45,
1763     Year = 1992}
1764    
1765     @article{Anheuser94,
1766     Author = {K. Anheuser and J.P. Northover},
1767     Journal = {Brit. Num. J.},
1768     Pages = 22,
1769     Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
1770     Volume = 64,
1771     Year = 1994}
1772    
1773     @article{Pense92,
1774     Author = {A. W. Pense},
1775     Journal = {Mat. Char.},
1776     Pages = 213,
1777     Title = {The Decline and Fall of the Roman Denarius},
1778     Volume = 29,
1779     Year = 1992}
1780    
1781     @article{Ngai81,
1782     Author = {K.~L. Ngai and F.-S. Liu},
1783     Journal = prb,
1784     Pages = {1049-1065},
1785     Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1786     Volume = 24,
1787     Year = 1981}
1788    
1789     @unpublished{Truhlar00,
1790     Author = {D.~G. Truhlar and A. Kohen},
1791     Date-Modified = {2006-02-15 16:35:52 -0500},
1792     Note = {private correspondence},
1793     Year = {2000}}
1794    
1795     @article{Truhlar78,
1796     Author = {Donald G. Truhlar},
1797     Journal = {J. Chem. Ed.},
1798     Pages = 309,
1799     Title = {Interpretation of the Activation Energy},
1800     Volume = 55,
1801     Year = 1978}
1802    
1803     @book{Tolman27,
1804     Address = {New York},
1805     Author = {R. C. Tolman},
1806     Pages = {260-270},
1807     Publisher = {Chemical Catalog Co.},
1808     Title = {Statistical Mechanics with Applications to Physics and Chemistry},
1809     Year = 1927}
1810    
1811     @article{Tolman20,
1812     Author = {R. C. Tolman},
1813     Journal = jacs,
1814     Pages = 2506,
1815     Title = {Statistical Mechanics Applied to Chemical Kinetics},
1816     Volume = 42,
1817     Year = 1920}
1818    
1819     @article{Ediger96,
1820     Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
1821     Date-Modified = {2006-02-15 10:16:35 -0500},
1822     Journal = jpc,
1823     Pages = 13200,
1824     Title = {Supercooled Liquids and Glasses},
1825     Volume = 100,
1826     Year = 1996}
1827    
1828     @inbook{Blumen86,
1829     Address = {Amsterdam},
1830     Author = {A. Blumen and J. Klafter and G. Zumofen},
1831     Chapter = {Reactions in Disordered Media Modelled by Fractals},
1832     Editor = {Luciano Peitronero and E. Tosatti},
1833     Pages = 399,
1834     Publisher = {North-Holland},
1835     Series = {International Symposium on Fractals in Physics},
1836     Title = {Fractals in Physics},
1837     Year = 1986}
1838    
1839     @article{Shlesinger84,
1840     Author = {M.~F. Shlesinger and E.~W. Montroll},
1841     Journal = {Proc. Natl. Acad. Sci. USA},
1842     Pages = {1280-1283},
1843     Title = {On the Williams-Watts function of dielectric relaxation},
1844     Volume = 81,
1845     Year = 1984}
1846    
1847     @article{Klafter86,
1848     Author = {J. Klafter and M.~F. Shlesinger},
1849     Journal = {Proc. Natl. Acad. Sci. USA},
1850     Pages = {848-851},
1851     Title = {On the relationship among three theories of relaxation in disordered systems},
1852     Volume = 83,
1853     Year = 1986}
1854    
1855     @article{Li01,
1856     Author = {Z. Li and M. Lieberman and W. Hill},
1857     Date-Modified = {2006-02-15 10:25:36 -0500},
1858     Journal = {Langmuir},
1859     Pages = {4887-4894},
1860     Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
1861     Volume = 17,
1862     Year = 2001}
1863    
1864     @article{Evans93,
1865     Author = {J.~W. Evans},
1866     Date-Modified = {2006-02-15 10:17:03 -0500},
1867     Journal = rmp,
1868     Pages = {1281-1329},
1869     Title = {Random and Cooperative Sequential Adsorption},
1870     Volume = 65,
1871     Year = 1993}
1872    
1873     @article{Dwyer1977,
1874     Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1875     Journal = {Surf. Sci.},
1876     Pages = 617,
1877     Volume = 64,
1878     Year = 1977}
1879    
1880     @article{Macritche78,
1881     Author = {F. MacRitche},
1882     Date-Modified = {2006-02-15 10:27:37 -0500},
1883     Journal = {Adv. Protein Chem.},
1884     Pages = 283,
1885     Volume = 32,
1886     Year = 1978}
1887    
1888     @article{Feder80,
1889     Author = {J. Feder},
1890     Date-Modified = {2006-02-15 10:17:21 -0500},
1891     Journal = {J. Theor. Biol.},
1892     Pages = 237,
1893     Volume = 87,
1894     Year = 1980}
1895    
1896     @article{Ramsden93,
1897     Author = {J.~J. Ramsden},
1898     Date-Modified = {2006-02-15 10:31:03 -0500},
1899     Journal = prl,
1900     Pages = 295,
1901     Volume = 71,
1902     Year = 1993}
1903    
1904     @article{Egelhoff89,
1905     Author = {W.~F. Egelhoff and I. Jacob},
1906     Date-Modified = {2006-02-15 10:16:54 -0500},
1907     Journal = prl,
1908     Pages = 921,
1909     Volume = 62,
1910     Year = 1989}
1911    
1912     @article{Viot92a,
1913     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1914     Date-Modified = {2006-02-15 10:12:51 -0500},
1915     Journal = jpc,
1916     Pages = {5212-5218},
1917     Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1918     Volume = 97,
1919     Year = 1992}
1920    
1921     @article{Viot92b,
1922     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1923     Date-Modified = {2006-02-15 10:12:57 -0500},
1924     Journal = {Physica A},
1925     Pages = {248-252},
1926     Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
1927     Volume = 191,
1928     Year = 1992}
1929    
1930     @article{Dobson1987,
1931     Author = {B.~W. Dobson},
1932     Journal = prb,
1933     Pages = 1068,
1934     Volume = 36,
1935     Year = 1987}
1936    
1937     @article{Boyer95,
1938     Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1939     Date-Modified = {2006-02-15 10:15:52 -0500},
1940     Journal = jcp,
1941     Pages = 1607,
1942     Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
1943     Volume = 103,
1944     Year = 1995}
1945    
1946     @article{Viot92c,
1947     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1948     Date-Modified = {2006-02-15 10:13:03 -0500},
1949     Journal = {Physica A},
1950     Pages = {248-252},
1951     Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
1952     Volume = 191,
1953     Year = 1992}
1954    
1955     @article{Ricci94,
1956     Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
1957     Date-Modified = {2006-02-15 10:31:32 -0500},
1958     Journal = jcp,
1959     Pages = 9164,
1960     Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1961     Volume = 101,
1962     Year = 1994}
1963    
1964     @article{Semmler98,
1965     Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1966     Date-Modified = {2006-02-15 10:14:46 -0500},
1967     Journal = {Langmuir},
1968     Pages = {5127-5132},
1969     Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
1970     Volume = 14,
1971     Year = 1998}
1972    
1973     @article{Solomon86,
1974     Author = {H. Solomon and H. Weiner},
1975     Date-Modified = {2006-02-15 10:10:38 -0500},
1976     Journal = {Comm. Statistics A},
1977     Pages = {2571-2607},
1978     Title = {A REVIEW OF THE PACKING PROBLEM},
1979     Volume = 15,
1980     Year = 1986}
1981    
1982     @article{Bonnier93,
1983     Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
1984     Date-Modified = {2006-02-15 10:08:35 -0500},
1985     Journal = {Physica A},
1986     Pages = {1-10},
1987     Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
1988     Volume = 198,
1989     Year = 1993}
1990    
1991     @book{Frenkel96,
1992     Address = {New York},
1993     Author = {D. Frenkel and B. Smit},
1994     Date-Modified = {2006-02-15 10:18:08 -0500},
1995     Publisher = {Academic Press},
1996     Title = {Understanding Molecular Simulation : From Algorithms to Applications},
1997     Year = 1996}
1998    
1999     @article{Dullweber1997,
2000     Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
2001     Journal = jcp,
2002     Number = 15,
2003     Pages = {5840-5851},
2004     Title = {Symplectic splitting methods for rigid body molecular dynamics},
2005     Volume = 107,
2006     Year = 1997}
2007    
2008     @article{Martin98,
2009     Author = {M. Martin and J.~I. Siepmann},
2010     Date-Modified = {2006-02-15 10:15:05 -0500},
2011     Journal = jpcB,
2012     Pages = {2569-2577},
2013     Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
2014     Volume = 102,
2015     Year = 1998}
2016    
2017     @article{Marrink01a,
2018     Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
2019     Date-Modified = {2006-02-15 10:28:09 -0500},
2020     Journal = jacs,
2021     Pages = {8638-8639},
2022     Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
2023     Volume = 123,
2024     Year = 2001}
2025    
2026     @article{Liu96b,
2027     Author = {Y. Liu and T. Ichiye},
2028     Date-Modified = {2006-02-15 10:27:07 -0500},
2029     Journal = jpc,
2030     Pages = {2723-2730},
2031     Title = {Soft sticky dipole potential for liquid water: a new model},
2032     Volume = 100,
2033     Year = 1996}
2034    
2035     @article{Liu96a,
2036     Author = {Y. Liu and T. Ichiye},
2037     Date-Modified = {2006-02-15 10:27:01 -0500},
2038     Journal = {Chem. Phys. Lett.},
2039     Pages = {334-340},
2040     Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
2041     Volume = 256,
2042     Year = 1996}
2043    
2044     @article{Chandra99,
2045     Author = {A. Chandra and T. Ichiye},
2046     Date-Modified = {2006-02-15 10:09:36 -0500},
2047     Journal = {J. Chem. Phys.},
2048     Number = 6,
2049     Pages = {2701-2709},
2050     Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
2051     Volume = 111,
2052     Year = 1999}
2053    
2054     @book{Allen87,
2055     Address = {New York},
2056     Author = {M.~P. Allen and D.~J. Tildesley},
2057     Date-Modified = {2006-02-15 10:08:08 -0500},
2058     Publisher = {Oxford University Press},
2059     Title = {Computer Simulations of Liquids},
2060     Year = 1987}
2061    
2062     @book{Leach01,
2063     Address = {Harlow, England},
2064     Author = {A.~R. Leach},
2065     Date-Modified = {2006-02-15 10:25:19 -0500},
2066     Edition = {2nd},
2067     Publisher = {Pearson Educated Limited},
2068     Title = {Molecular Modeling: Principles and Applications},
2069     Year = 2001}
2070    
2071    
2072     @article{Sengupta00,
2073     Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
2074     Date-Modified = {2006-02-15 10:32:00 -0500},
2075     Journal = {Europhysics Letters},
2076     Number = 6,
2077     Pages = {722-728},
2078     Title = {Novel structural Features of the ripple phase of phospholipids},
2079     Volume = 49,
2080     Year = 2000}
2081    
2082     @article{Venable00,
2083     Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
2084     Date-Modified = {2006-02-15 10:11:19 -0500},
2085     Journal = jcp,
2086     Number = 10,
2087     Pages = {4822-4832},
2088     Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
2089     Volume = 112,
2090     Year = 2000}
2091    
2092     @article{Lindahl00,
2093     Author = {E. Lindahl and O. Edholm},
2094     Date-Modified = {2006-02-15 10:26:05 -0500},
2095     Journal = {Biophysical Journal},
2096     Month = {July},
2097     Pages = {426-433},
2098     Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
2099     Volume = 79,
2100     Year = 2000}
2101    
2102     @article{Saiz02,
2103     Author = {L. Saiz and M. Klein},
2104     Date-Modified = {2006-02-15 10:31:50 -0500},
2105     Journal = jcp,
2106     Number = 7,
2107     Pages = {3052-3057},
2108     Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
2109     Volume = 116,
2110     Year = 2002}
2111    
2112     @article{Stevens95,
2113     Author = {M.~J. Stevens and G.~S. Grest},
2114     Date-Modified = {2006-02-15 10:10:47 -0500},
2115     Journal = {Physical Review E},
2116     Number = 6,
2117     Pages = {5976-5983},
2118     Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
2119     Volume = 51,
2120     Year = 1995}
2121    
2122     @article{Darden93,
2123     Author = {T. Darden and D. York and L. Pedersen},
2124     Date-Modified = {2006-03-16 08:37:25 -0500},
2125     Journal = {J. Chem. Phys.},
2126     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
2127     Number = 12,
2128     Pages = {10089-10092},
2129     Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
2130     Volume = 98,
2131     Year = 1993}
2132    
2133     @article{Goetz98,
2134     Author = {R. Goetz and R. Lipowsky},
2135     Date-Modified = {2006-02-15 10:18:26 -0500},
2136     Journal = {J. Chem. Phys.},
2137     Number = 17,
2138     Pages = 7397,
2139     Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
2140     Volume = 108,
2141     Year = 1998}
2142    
2143     @article{Marrink01b,
2144     Author = {S.~J. Marrink and A.~E. Mark},
2145     Date-Modified = {2006-02-15 10:28:01 -0500},
2146     Journal = {Journal of Physical Chemistry B},
2147     Pages = {6122-6127},
2148     Title = {Effect of undulations on surface tension in simulated bilayers},
2149     Volume = 105,
2150     Year = 2001}
2151    
2152     @article{Metropolis49,
2153     Author = {N. Metropolis and S. Ulam},
2154     Date-Modified = {2006-02-15 10:29:03 -0500},
2155     Journal = {J. Am. Stat. Ass.},
2156     Pages = {335-341},
2157     Title = {The $\mbox{Monte Carlo}$ Method},
2158     Volume = 44,
2159     Year = 1949}
2160    
2161     @article{Metropolis53,
2162     Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
2163     Date-Modified = {2006-03-09 10:44:24 -0500},
2164     Journal = {J. Chem. Phys.},
2165     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf},
2166     Pages = {1087-1092},
2167     Title = {Equation of State Calculations by Fast Computing Machines},
2168     Volume = 21,
2169     Year = 1953}
2170    
2171     @article{Born12,
2172     Author = {M. Born and Th. Von~Karman},
2173     Date-Modified = {2006-02-15 10:08:50 -0500},
2174     Journal = {Physik Z.},
2175     Number = {297-309},
2176     Title = {Uber Schwingungen in Raumgittern},
2177     Volume = 13,
2178     Year = 1912}
2179    
2180     @book{Chandler87,
2181     Author = {David Chandler},
2182     Date-Modified = {2006-02-15 10:09:20 -0500},
2183     Publisher = {Oxford University Press},
2184     Title = {Introduction to Modern Statistical Mechanics},
2185     Year = 1987}
2186    
2187     @article{Pearlman95,
2188     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},
2189     Date-Modified = {2006-02-15 10:30:13 -0500},
2190     Journal = {Computer Physics Communications},
2191     Pages = {1-41},
2192     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},
2193     Volume = 91,
2194     Year = 1995}
2195    
2196     @book{Goldstein01,
2197     Address = {San Francisco},
2198     Author = {H. Goldstein and C. Poole and J. Safko},
2199     Edition = {3rd},
2200     Publisher = {Addison Wesley},
2201     Title = {Classical Mechanics},
2202     Year = 2001}
2203    
2204     @article{Bratko85,
2205     Author = {D. Bratko and L. Blum and A. Luzar},
2206     Journal = jcp,
2207     Number = 12,
2208     Pages = {6367-6370},
2209     Title = {A simple model for the intermolecular potential of water},
2210     Volume = 83,
2211     Year = 1985}
2212    
2213     @article{Bratko95,
2214     Author = {L. Blum and F. Vericat and D. Bratko},
2215     Journal = jcp,
2216     Number = 3,
2217     Pages = {1461-1462},
2218     Title = {Towards an analytical model of water: The octupolar model},
2219     Volume = 102,
2220     Year = 1995}
2221    
2222     @article{Tan03,
2223     Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
2224     Journal = cpl,
2225     Pages = {646-652},
2226     Title = {A temperature of maximum density in soft sticky dipole water},
2227     Volume = 376,
2228     Year = 2003}
2229    
2230     @article{Soper86,
2231     Author = {A.~K. Soper and M.~G. Phillips},
2232     Journal = cp,
2233     Number = 1,
2234     Pages = {47-60},
2235     Title = {A new determination of the structure of water at 298K},
2236     Volume = 107,
2237     Year = 1986}
2238    
2239     @article{Plimpton95,
2240     Author = {S. Plimpton},
2241     Date-Modified = {2006-02-15 10:30:31 -0500},
2242     Journal = {J. Comp. Phys.},
2243     Pages = {1-19},
2244     Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
2245     Volume = 117,
2246     Year = 1995}
2247    
2248     @article{Tartaglino02,
2249     Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
2250     Date-Modified = {2006-02-15 10:34:04 -0500},
2251     Journal = prb,
2252     Pages = 241406,
2253     Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
2254     Volume = 65,
2255     Year = 2002}
2256    
2257     @article{Ercolessi88,
2258     Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
2259     Journal = {Philosophical Magazine A},
2260     Pages = {213-226},
2261     Title = {Simulation of Gold in the Glue Model.},
2262     Volume = 58,
2263     Year = 1988}
2264    
2265     @article{Finnis84,
2266     Author = {M.~W Finnis and J.~E. Sinclair},
2267     Journal = {Phil. Mag. A},
2268     Pages = {45-55},
2269     Title = {A Simple Empirical N-Body Potential for Transition-Metals},
2270     Volume = 50,
2271     Year = 1984}
2272    
2273     @article{Foiles86,
2274     Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
2275     Date-Modified = {2006-02-15 10:17:44 -0500},
2276     Journal = prb,
2277     Number = 12,
2278     Pages = 7983,
2279     Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2280     Volume = 33,
2281     Year = 1986}
2282    
2283     @article{Daw93,
2284     Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
2285     Date-Modified = {2006-02-15 10:16:13 -0500},
2286     Journal = {Mat. Sci. Rep.},
2287     Pages = {251-310},
2288     Title = {The embededd-atom method},
2289     Volume = 9,
2290     Year = 1993}
2291    
2292     @article{Johnson89,
2293     Author = {R.~A. Johnson},
2294     Date-Modified = {2006-02-15 10:21:36 -0500},
2295     Journal = prb,
2296     Number = 17,
2297     Pages = 12554,
2298     Title = {Alloy models with the embedded-atom method},
2299     Volume = 39,
2300     Year = 1989}
2301    
2302     @article{Kol97,
2303     Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
2304     Date-Modified = {2006-02-15 10:24:53 -0500},
2305     Journal = jcp,
2306     Number = 7,
2307     Pages = {2580-2588},
2308     Title = {A symplectic method for rigid-body molecular simulation},
2309     Volume = 107,
2310     Year = 1997}
2311    
2312     @article{Hoover85,
2313     Author = {W.~G. Hoover},
2314     Date-Modified = {2006-02-15 10:21:18 -0500},
2315     Journal = pra,
2316     Pages = 1695,
2317     Title = {Canonical dynamics: Equilibrium phase-space distributions},
2318     Volume = 31,
2319     Year = 1985}
2320    
2321     @article{Roux91,
2322     Author = {B. Roux and M. Karplus},
2323     Journal = jpc,
2324     Number = 15,
2325     Pages = {4856-4868},
2326     Title = {Ion transport in a Gramicidin-like channel: dynamics and mobility},
2327     Volume = 95,
2328     Year = 1991}
2329    
2330     @article{Marrink94,
2331     Author = {S.~J Marrink and H.~J.~C. Berendsen},
2332     Journal = jpc,
2333     Number = 15,
2334     Pages = {4155-4168},
2335     Title = {Simulation of water transport through a lipid membrane},
2336     Volume = 98,
2337     Year = 1994}
2338    
2339     @article{Daw89,
2340     Author = {Murray~S. Daw},
2341     Journal = {Physical Review B},
2342     Pages = {7441-7452},
2343     Title = {Model of metallic cohesion: The embedded-atom method},
2344     Volume = 39,
2345     Year = 1989}
2346    
2347     @inbook{Voter95b,
2348     Author = {A.~F. Voter},
2349     Chapter = 4,
2350     Date-Modified = {2006-02-15 10:35:07 -0500},
2351     Editor = {J.~H. Westbrook and R.~L. Fleischer},
2352     Pages = 77,
2353     Publisher = {John Wiley and Sons Ltd},
2354     Title = {Intermetallic Compounds: Principles and Practice},
2355     Volume = 1,
2356     Year = 1995}
2357    
2358     @article{Marrink02,
2359     Author = {S.~J. Marrink and D.~P. Teileman},
2360     Date-Modified = {2006-02-15 10:28:20 -0500},
2361     Journal = {Biophysical Journal},
2362     Pages = {2386-2392},
2363     Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
2364     Volume = 83,
2365     Year = 2002}
2366    
2367     @article{Sum03,
2368     Author = {A.~K. Sum and J.~J. de~Pablo},
2369     Date-Modified = {2006-02-15 10:11:01 -0500},
2370     Journal = {Biophysical Journal},
2371     Pages = {3636-3645},
2372     Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
2373     Volume = 85,
2374     Year = 2003}
2375    
2376     @article{Gomez03,
2377     Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
2378     Date-Modified = {2006-02-15 10:17:14 -0500},
2379     Journal = {Eur. Biophys. J.},
2380     Pages = {217-227},
2381     Title = {Setting up and optimization of membrane protein simulations},
2382     Volume = 31,
2383     Year = 2002}
2384    
2385     @article{Smondyrev99,
2386     Author = {A.~M. Smondyrev and M.~L. Berkowitz},
2387     Date-Modified = {2006-02-15 10:10:29 -0500},
2388     Journal = {Biophysical Journal},
2389     Pages = {2472-2478},
2390     Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
2391     Volume = 76,
2392     Year = 1999}
2393    
2394     @article{Nina02,
2395     Author = {M. Nina and T. Simonson},
2396     Date-Modified = {2006-02-15 10:29:27 -0500},
2397     Journal = {J. Phys. Chem. B},
2398     Pages = {3696-3705},
2399     Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
2400     Volume = 106,
2401     Year = 2002}
2402    
2403     @article{Norberg00,
2404     Author = {J. Norberg and L. Nilsson},
2405     Date-Modified = {2006-02-15 10:29:36 -0500},
2406     Journal = {Biophysical Journal},
2407     Pages = {1537-1553},
2408     Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
2409     Volume = 79,
2410     Year = 2000}
2411    
2412     @article{Patra03,
2413     Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
2414     Date-Modified = {2006-02-15 10:29:58 -0500},
2415     Journal = {Biophysical Journal},
2416     Pages = {3636-3645},
2417     Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
2418     Volume = 84,
2419     Year = 2003}
2420    
2421     @article{Marrink04,
2422     Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
2423     Date-Modified = {2006-02-15 10:28:28 -0500},
2424     Journal = {J. Phys. Chem. B},
2425     Pages = {750-760},
2426     Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
2427     Volume = 108,
2428     Year = 2004}
2429    
2430     @article{Andersen83,
2431     Author = {H.~C. Andersen},
2432     Date-Modified = {2006-02-15 10:08:20 -0500},
2433     Journal = {Journal of Computational Physics},
2434     Pages = {24-34},
2435     Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
2436     Volume = 52,
2437     Year = 1983}
2438    
2439     @article{Hura00,
2440     Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
2441     Date-Modified = {2006-02-15 10:21:28 -0500},
2442     Journal = {J. Chem. Phys.},
2443     Pages = {9140-9148},
2444     Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
2445     Volume = 113,
2446     Year = 2000}
2447    
2448     @article{Ryckaert77,
2449     Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
2450     Date-Modified = {2006-02-15 10:31:44 -0500},
2451     Journal = {Journal of Computational Physics},
2452     Pages = {327-341},
2453     Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
2454     Volume = 23,
2455     Year = 1977}
2456    
2457     @inbook{Fowles99,
2458     Author = {G.~R. Fowles and G.~L. Cassiday},
2459     Chapter = 10,
2460     Date-Modified = {2006-02-15 10:18:00 -0500},
2461     Edition = {6th},
2462     Publisher = {Saunders College Publishing},
2463     Title = {Analytical Mechanics},
2464     Year = 1999}
2465    
2466     @article{Petrache00,
2467     Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2468     Date-Modified = {2006-02-15 10:30:24 -0500},
2469     Journal = {Biophysical Journal},
2470     Pages = {3172-3192},
2471     Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2472     Volume = 79,
2473     Year = 2000}
2474    
2475     @article{Egberts88,
2476     Author = {E. Egberts and H.~J.~C. Berendsen},
2477     Date-Modified = {2006-02-15 10:16:43 -0500},
2478     Journal = {J. Chem. Phys.},
2479     Pages = {3718-3732},
2480     Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
2481     Volume = 89,
2482     Year = 1988}
2483    
2484     @article{Holz00,
2485     Author = {M. Holz and S.~R. Heil and A. Sacco},
2486     Journal = {Phys. Chem. Chem. Phys.},
2487     Pages = {4740-4742},
2488     Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
2489     Volume = 2,
2490     Year = 2000}
2491    
2492     @incollection{Zannoni94,
2493     Author = {C. Zannoni},
2494     Booktitle = {The Molecular Dynamics of Liquid Crstals},
2495     Chapter = 6,
2496     Date-Modified = {2006-02-15 10:12:36 -0500},
2497     Editor = {G.~R. Luckhurst and C.~A. Veracini},
2498     Pages = {139-169},
2499     Publisher = {Kluwer Academic Publishers},
2500     Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
2501     Year = 1994}
2502    
2503     @article{Melchionna93,
2504     Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
2505     Date-Modified = {2006-02-15 10:28:54 -0500},
2506     Journal = {Molecular Physics},
2507     Pages = {533-544},
2508     Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
2509     Volume = 78,
2510     Year = 1993}
2511    
2512     @article{Fennell04,
2513     Author = {C.~J. Fennell and J.~D. Gezelter},
2514     Date-Modified = {2006-02-15 09:08:04 -0500},
2515     Journal = jcp,
2516     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_TempSSDs_04.pdf},
2517     Number = 19,
2518     Pages = {9175-9184},
2519     Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
2520     Volume = 120,
2521     Year = 2004}
2522    
2523     @article{Klein01,
2524     Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
2525     Date-Modified = {2006-02-15 10:27:22 -0500},
2526     Journal = {J. Phys. Chem. B},
2527     Pages = {4464-4470},
2528     Title = {A Coarse Grain Model for Phospholipid Simulations},
2529     Volume = 105,
2530     Year = 2001}
2531    
2532     @article{Marrink03,
2533     Author = {S.~J. Marrink and A.~E. Mark},
2534     Date-Modified = {2006-03-16 09:54:52 -0500},
2535     Journal = {J. Am. Chem. Soc.},
2536     Pages = {15233-15242},
2537     Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2538     Volume = 125,
2539     Year = 2003}
2540    
2541     @article{Onsager36,
2542     Author = {L. Onsager},
2543     Journal = jacs,
2544     Pages = {1486-1493},
2545     Title = {Electric Moments of Molecules in Liquids},
2546     Volume = 58,
2547     Year = 1936}
2548    
2549     @Article{Carraro1993,
2550     author = {Carlo Carraro and David R. Nelson},
2551     title = {Grain-boundary buckling and spin-glass models of disorder in membranes},
2552     journal = pre,
2553     year = 1993,
2554     volume = 48,
2555     number = 4,
2556     pages = {3082-3090}
2557     }
2558    
2559     @Article{Renard1966,
2560     author = {R\'emi Renard and Carl W. Garland},
2561     title = {Order-Disorder Phenomena. II. Elastic Constants of a Two-Dimensional Ising Model},
2562     journal = jcp,
2563     year = 1966,
2564     volume = 44,
2565     number = 3,
2566     pages = {1125-1129}
2567     }
2568    
2569     @Article{Zhu2005,
2570     author = {Xiaoliang Zhu and F. Tavazza and D.~P. Landau},
2571     title = {Critical behavior of an elastic Ising antiferromagnet at constant pressure},
2572     journal = prb,
2573     year = 2005,
2574     volume = 72,
2575     pages = 104102
2576     }
2577    
2578     @Article{Zhu2006,
2579     author = {Xiaoliang Zhu and D.~P. Landau},
2580     title = {Critical behavior of an elastic Ising model on a stacked triangular net at constant volume},
2581     journal = prb,
2582     year = 2006,
2583     volume = 73,
2584     pages = 064115
2585     }
2586    
2587     @Article{Jiang2006,
2588     author = {Ying Jiang and Thorsten Emig},
2589     title = {Ordering of geometrically frustrated classical and quantum triangular Ising magnets},
2590     journal = prb,
2591     year = 2006,
2592     volume = 73,
2593     pages = 104452
2594     }
2595    
2596     @Article{Raphael2000,
2597     author = {Robert M. Raphael and Aleksander S. Popel and William E. Brownell},
2598     title = {A Membrane Bending Model of Outer Hair Cell Electromotility},
2599     journal = bj,
2600     year = 2000,
2601     volume = 78,
2602     pages = {2844-2862}
2603     }
2604    
2605     @Article{Todorova2004,
2606     author = {L. Todorova and T. Angelov and Y. Marinov and A.~G. Petrov},
2607     title = {Evidence of flexoelectricity in polymer-dispersed liquid crystals},
2608     journal = {J. Mat. Sci. Mat. Elect.},
2609     year = 2004,
2610     volume = 14,
2611     pages = {817-818}
2612     }
2613    
2614     @Article{Petrov2006,
2615     author = {A.~G. Petrov},
2616     title = {Electricity and mechanics of biomembrane systems: Flexoelectricity in living membranes},
2617     journal = {Anal. Chim. Acta},
2618     year = 2006,
2619     pages = {70-83}
2620     }
2621    
2622     @Article{Seung1988,
2623     title = {Defects in flexible membranes with crystalline order},
2624     author = {Seung, H. S. and Nelson, David R.},
2625     journal = {Phys. Rev. A},
2626     volume = {38},
2627     number = {2},
2628     pages = {1005--1018},
2629     numpages = {13},
2630     year = {1988},
2631     month = {Jul},
2632     doi = {10.1103/PhysRevA.38.1005},
2633     publisher = {American Physical Society}
2634     }
2635    
2636     @Article{Mutz1991,
2637     title = {Wrinkling transition in partially polymerized vesicles},
2638     author = {Mutz, M. and Bensimon, D. and Brienne, M. J.},
2639     journal = {Phys. Rev. Lett.},
2640     volume = {67},
2641     number = {7},
2642     pages = {923--926},
2643     numpages = {3},
2644     year = {1991},
2645     month = {Aug},
2646     doi = {10.1103/PhysRevLett.67.923},
2647     publisher = {American Physical Society}
2648     }
2649    
2650     @article{Harden2006,
2651     author = {J. Harden and B. Mbanga and N. Eber and K. Fodor-Csorba and S. Sprunt and J. T. Gleeson and A. Jakli},
2652     collaboration = {},
2653     title = {Giant Flexoelectricity of Bent-Core Nematic Liquid Crystals},
2654     publisher = {APS},
2655     year = 2006,
2656     journal = {Physical Review Letters},
2657     volume = 97,
2658     number = 15,
2659     eid = 157802,
2660     numpages = 4,
2661     pages = 157802
2662     }
2663    
2664 xsun 3174 @Article{Lenz07,
2665 xsun 3147 author = {Olaf Lenz and Friederike Schmid},
2666     title = {Structure of Symmetric and Asymmetric "Ripple" Phases in Lipid Bilayers},
2667     journal = prl,
2668     year = 2007,
2669     volume = 98,
2670     number = 5,
2671     pages = 058104
2672     }
2673    
2674 xsun 3174 @article{Sun2007,
2675     Author = {Xiuquan Sun and J. Daniel Gezelter},
2676     Eid = {031602},
2677     Journal = pre,
2678     Keywords = {Lattice Theory; Membranes},
2679     Number = {3},
2680     Numpages = {7},
2681     Pages = {031602},
2682     Publisher = {Aps},
2683     Title = {Spontaneous Corrugation of Dipolar Membranes},
2684     Url = {Http://Link.Aps.Org/Abstract/Pre/V75/E031602},
2685     Volume = {75},
2686     Year = {2007}
2687     }
2688    
2689     @Article{Tsonchev04,
2690     author = {Stefan Tsonchev and George C. Schatz and Mark A. Ratner},
2691     title = {Electrostatically-Directed Self-Assembly of Cylindrical Peptide Amphiphile Nanostructures},
2692     journal = jpcB,
2693     year = 2004,
2694     volume = 108,
2695     pages = {8817-8822}
2696     }
2697    
2698     @Article{Cleaver96,
2699     author = {Douglas J. Cleaver and Christopher M. Care and Michael P. Allen and Maureen P. Neal},
2700     title = {Extension and generalization of the Gay-Berne potential},
2701     journal = pre,
2702     year = 1996,
2703     volume = 54,
2704     number = 1,
2705     pages = {559-567}
2706     }
2707    
2708     @article{Meineke05,
2709     Author = {M.~A. Meineke and C.~F. {Vardeman II} And T. Lin and C.~J. Fennell and J.~D. Gezelter},
2710     Date-Modified = {2007-06-24 09:16:17 -0400},
2711     Journal = jcc,
2712     Pages = {252-271},
2713     Title = {$\Mbox{OOPSE: A}$N Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics},
2714     Volume = 26,
2715     Year = 2005}
2716     }