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Revision: 759
Committed: Wed Sep 10 22:42:57 2003 UTC (20 years, 9 months ago) by chrisfen
File size: 52084 byte(s)
Log Message:
Adjustments to the introduction.  Minor additions to the methods section.

Chris

File Contents

# User Rev Content
1 chrisfen 743 @string{jcp = "J. Chem. Phys."}
2     @string{cpl = "Chem. Phys. Lett."}
3     @string{jpc = "J. Phys. Chem."}
4     @string{jpcA = "J. Phys. Chem. A"}
5     @string{jpcB = "J. Phys. Chem. B"}
6     @string{cp = "Chem. Phys."}
7     @string{acp = "Adv. Chem. Phys."}
8     @string{pra = "Phys. Rev. A"}
9     @string{prb = "Phys. Rev. B"}
10     @string{pre = "Phys. Rev. E"}
11     @string{prl = "Phys. Rev. Lett."}
12     @string{rmp = "Rev. Mod. Phys."}
13     @string{jml = "J. Mol. Liq."}
14     @string{mp = "Mol. Phys."}
15     @string{pnas = "Proc. Natl. Acad. Sci. USA"}
16     @string{jacs = "J. Am. Chem. Soc."}
17     @string{jcc = "J. Comput. Chem."}
18    
19     @Book{Berne90,
20     author = {B.~J. Berne and R. Pecora},
21     title = {Dynamic Light Scattering},
22     publisher = {Robert E. Krieger Publishing Company, Inc.},
23     year = 1990,
24     address = {Malabar, Florida}
25     }
26    
27     @Article{Evans77,
28     author = {D.~J. Evans},
29     title = {On the representation of orientation space},
30     journal = {Mol. Phys.},
31     year = 1977,
32     volume = 34,
33     pages = {317-325}
34     }
35    
36     @Article{Tuckerman92,
37     author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
38     title = {Reversible multiple time scale molecular dynamics},
39     journal = jcp,
40     year = 1992,
41     volume = 97,
42     pages = {1990-2001}
43     }
44    
45     @Book{Hansen86,
46     author = {J.~P. Hansen and I.~R. McDonald},
47     title = {Theory of Simple Liquids},
48     chapter = 7,
49     publisher = {Academic Press},
50     year = 1986,
51     address = {London},
52     pages = {199-206}
53     }
54    
55     @Article{Angelani98,
56     author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
57     title = {Connected Network of Minima as a Model Glass: Long
58     Time Dynamics},
59     journal = prl,
60     year = 1998,
61     volume = 81,
62     number = 21,
63     pages = {4648-4651}
64     }
65    
66     @Article{Stillinger82,
67     author = {F.~H. Stillinger and T.~A. Weber},
68     title = {Hidden structure in liquids},
69     journal = pra,
70     year = 1982,
71     volume = 25,
72     number = 2,
73     pages = {978-989}
74     }
75    
76     @Article{Stillinger83,
77     author = {F.~H. Stillinger and T.~A. Weber},
78     title = {Dynamics of structural transitions in liquids},
79     journal = pra,
80     year = 1983,
81     volume = 28,
82     number = 4,
83     pages = {2408-2416}
84     }
85    
86     @Article{Weber84,
87     author = {T.~A. Weber and F.~H. Stillinger},
88     title = {The effect of density on the inherent structure in
89     liquids},
90     journal = jcp,
91     year = 1984,
92     volume = 80,
93     number = 6,
94     pages = {2742-2746}
95     }
96    
97     @Article{Stillinger85,
98     author = {F.~H. Stillinger and T.~A. Weber},
99     title = {Inherent structure theory of liquids in the
100     hard-sphere limit},
101     journal = jcp,
102     year = 1985,
103     volume = 83,
104     number = 9,
105     pages = {4767-4775}
106     }
107    
108     @Article{Stillinger98,
109     author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
110     title = {Signatures of distinct dynamical regimes in the
111     energy landscape of a glass-forming liquid},
112     journal = {Nature},
113     year = 1998,
114     volume = 393,
115     pages = {554-557}
116     }
117    
118    
119     @Article{Parkhurst75a,
120     author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
121     title = {Dense liquids. I. The effect of density and
122     temperature on viscosity of tetramethylsilane and
123     benzene-$\mbox{D}_6$},
124     journal = jcp,
125     year = 1975,
126     volume = 63,
127     number = 6,
128     pages = {2698-2704}
129     }
130    
131     @Article{Parkhurst75b,
132     author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
133     title = {Dense liquids. II. The effect of density and
134     temperature on viscosity of tetramethylsilane and
135     benzene },
136     journal = jcp,
137     year = 1975,
138     volume = 63,
139     number = 6,
140     pages = {2705-2709}
141     }
142    
143     @Article{Forester97,
144     author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
145     title = {Antibiotic activity of valinomycin - Molecular
146     dynamics simulations involving the water/membrane
147     interface},
148     journal = {J. Chem. Soc. - Faraday Transactions},
149     year = 1997,
150     volume = 93,
151     pages = {613-619}
152     }
153    
154     @Article{Tieleman98,
155     author = {D.~P. Tieleman and H.~J.~C. Berendsen},
156     title = {A molecular dynamics study of the pores formed by
157     Escherichia coli OmpF porin in a fully hydrated
158     palmitoyloleoylphosphatidylcholine bilayer},
159     journal = {Biophys. J.},
160     year = 1998,
161     volume = 74,
162     pages = {2786-2801}
163     }
164    
165     @Article{Cascales98,
166     author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
167     title = {Anaesthetic mechanism on a model biological
168     membrane: A molecular dynamics simulation study},
169     journal = {J. Phys. Chem. B},
170     year = 1998,
171     volume = 102,
172     pages = {625-631}
173     }
174    
175     @Article{Bassolino95,
176     author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
177     title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID
178     BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
179     journal = {J. Am. Chem. Soc.},
180     year = 1995,
181     volume = 117,
182     pages = {4118-4129}
183     }
184    
185     @Article{Alper95,
186     author = {H.~E. Alper and T.~R. Stouch},
187     title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN
188     BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
189     journal = {J. Phys. Chem.},
190     year = 1995,
191     volume = 99,
192     pages = {5724-5731}
193     }
194    
195     @Article{Sok92,
196     author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren},
197     title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF
198     SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
199     journal = {J. Chem. Phys.},
200     year = 1992,
201     volume = 96,
202     pages = {4699-4704}
203     }
204    
205     @Article{Rabani99,
206     author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
207     title = {Direct Observation of Stretched-Exponential
208     Relaxation in Low-Temperature Lennard-Jones Systems
209     Using the Cage Correlation Function},
210     journal = prl,
211     year = {1999},
212     volume = 82,
213     pages = {3649}
214     }
215    
216     @Article{Rabani97,
217     author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
218     title = {Calculating the hopping rate for self-diffusion on
219     rough potential energy surfaces: Cage correlations},
220     journal = {J. Chem. Phys.},
221     year = 1997,
222     volume = 107,
223     pages = {6867-6876}
224     }
225    
226     @Article{Gezelter99,
227     author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
228     title = {Methods for calculating the hopping rate for
229     orientational and spatial diffusion in a molecular
230     liquid: $\mbox{CS}_{2}$},
231     journal = jcp,
232     year = 1999,
233     volume = 110,
234     pages = 3444
235     }
236    
237     @Article{Gezelter98a,
238     author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
239     title = {Response to 'Comment on a Critique of the
240     Instantaneous Normal Mode (INM) Approach to
241     Diffusion'},
242     journal = jcp,
243     year = 1998,
244     volume = 109,
245     pages = 4695
246     }
247    
248     @Article{Gezelter97,
249     author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
250     title = {Can imaginary instantaneous normal mode frequencies
251     predict barriers to self-diffusion?},
252     journal = jcp,
253     year = 1997,
254     volume = 107,
255     pages = 4618
256     }
257    
258     @Article{Zwanzig83,
259     author = {R. Zwanzig},
260     title = {On the relation between self-diffusion and viscosity
261     of liquids},
262     journal = jcp,
263     year = 1983,
264     volume = 79,
265     pages = {4507-4508}
266     }
267    
268     @Article{Zwanzig88,
269     author = {R. Zwanzig},
270     title = {Diffusion in rough potential},
271     journal = {Proc. Natl. Acad. Sci. USA},
272     year = 1988,
273     volume = 85,
274     pages = 2029
275     }
276    
277     @Article{Stillinger95,
278     author = {F.~H. Stillinger},
279     title = {A Topographic View of Supercooled Liquids and Glass
280     Formation},
281     journal = {Science},
282     year = 1995,
283     volume = 267,
284     pages = {1935-1939}
285     }
286    
287     @InCollection{Angell85,
288     author = {C.~A. Angell},
289     title = {unknown},
290     booktitle = {Relaxations in Complex Systems},
291     publisher = {National Technical Information Service,
292     U.S. Department of Commerce},
293     year = 1985,
294     editor = {K.~Ngai and G.~B. Wright},
295     address = {Springfield, VA},
296     pages = 1
297     }
298    
299     @Article{Bembenek96,
300     author = {S.~D. Bembenek and B.~B. Laird},
301     title = {The role of localization in glasses and supercooled liquids},
302     journal = jcp,
303     year = 1996,
304     volume = 104,
305     pages = 5199
306     }
307    
308     @Article{Sun97,
309     author = {X. Sun and W.~H. Miller},
310     title = {Semiclassical initial value representation for
311     electronically nonadiabatic molecular dynamics},
312     journal = jcp,
313     year = 1997,
314     volume = 106,
315     pages = 6346
316     }
317    
318     @Article{Spath96,
319     author = {B.~W. Spath and W.~H. Miller},
320     title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION
321     PROBABILITIES},
322     journal = jcp,
323     year = 1996,
324     volume = 104,
325     pages = 95
326     }
327    
328     @Book{Warshel91,
329     author = {Arieh Warshel},
330     title = {Computer modeling of chemical reactions in enzymes
331     and solutions},
332     publisher = {Wiley},
333     year = 1991,
334     address = {New York}
335     }
336    
337     @Article{Vuilleumier97,
338     author = {Rodolphe Vuilleumier and Daniel Borgis},
339     title = {Molecular Dynamics of an excess proton in water
340     using a non-additive valence bond force field},
341     journal = jpc,
342     year = 1997,
343     volume = {in press}
344     }
345    
346     @Article{Kob95a,
347     author = {W. Kob and H.~C. Andersen},
348     title = {Testing mode-coupling theory for a supercooled
349     binary Lennard-Jones mixtures: The van Hove
350     corraltion function},
351     journal = pre,
352     year = 1995,
353     volume = 51,
354     pages = {4626-4641}
355     }
356    
357     @Article{Kob95b,
358     author = {W. Kob and H.~C. Andersen},
359     title = {Testing mode-coupling theory for a supercooled
360     binary Lennard-Jones mixtures. II. Intermediate
361     scattering function and dynamic susceptibility},
362     journal = pre,
363     year = 1995,
364     volume = 52,
365     pages = {4134-4153}
366     }
367    
368     @InProceedings{Gotze89,
369     author = "W. G{\"{o}}tze",
370     title = "Aspects of Structural Glass Transitions",
371     editor = "J.~P. Hansen and D. Levesque and J. Zinn-Justin",
372     volume = "I",
373     pages = "287-503",
374     booktitle = "Liquids, Freezing and Glass Transitions",
375     year = 1989,
376     publisher = "North-Holland",
377     address = "Amsterdam"
378     }
379    
380     @Article{Sun97a,
381     author = "X. Sun and W.~H. Miller",
382     title = {Mixed semiclassical-classical approaches to the
383     dynamics of complex molecular systems},
384     journal = jcp,
385     year = 1997,
386     pages = 916
387     }
388    
389     @Article{Keshavamurthy94,
390     author = "S. Keshavamurthy and W.~H. Miller",
391     title = "ivr",
392     journal = cpl,
393     year = 1994,
394     volume = 218,
395     pages = 189
396     }
397    
398     @Article{Billing75,
399     author = "G.~D. Billing",
400     title = "ehrenfest",
401     journal = cpl,
402     year = 1975,
403     volume = 30,
404     pages = 391
405     }
406    
407     @Article{Chang90,
408     author = {Y.-T. Chang and W.~H. Miller},
409     title = {An Empirical Valence Bond Model for Constructing
410     Global Potential Energy Surfaces for Chemical
411     Reactions of Polyatomic Molecular Systems},
412     journal = jpc,
413     year = 1990,
414     volume = 94,
415     pages = {5884-5888}
416     }
417    
418     @Article{Shor94,
419     author = {P.W. Shor},
420     title = {Algorithms for quantum computation: discrete
421     logarithms and factoring},
422     journal = {Proceedings of the 35th Annual Symposium
423     on Foundations of Computer Science},
424     year = 1994,
425     pages = {124-134}
426     }
427    
428     @Article{Feynman82,
429     author = {R.~P. Feynman},
430     title = {Simulating physics with computers},
431     journal = {Int. J. Theor. Phys.},
432     year = 1982,
433     volume = 21,
434     pages = {467-488}
435     }
436    
437     @Article{Grover97,
438     author = {L.~K. Grover},
439     title = {Quantum computers can search arbitrarily large
440     databases by a single query},
441     journal = prl,
442     year = 1997,
443     volume = 79,
444     pages = {4709-4712}
445     }
446    
447     @Article{Chuang98,
448     author = {I. Chuang and N. Gershenfeld and M. Kubinec},
449     title = {Experimental Implementation of Fast Quantum Searching},
450     journal = prl,
451     year = 1998,
452     volume = 80,
453     pages = {3408-3411}
454     }
455    
456     @Article{Monroe95,
457     author = "C. Monroe and D.~M. Meekhof and B.~E. King and
458     W.~M. Itano and D.~J. Wineland",
459     title = {Demonstration of a fundamental quantum logic gate},
460     journal = prl,
461     year = 1995,
462     volume = 75,
463     pages = 4714
464     }
465    
466     @Article{Lent93,
467     author = "C.~S. Lent and P.~D. Tougaw and W.~Porod and
468     G.~H. Bernstein",
469     title = {Quantum Cellular Automata},
470     journal = {Nanotechnology},
471     year = 1993,
472     volume = 4,
473     pages = {49-57}
474     }
475    
476     @Article{Barenco95,
477     author = "A. Barenco and C.~H. Bennett and R. Cleve and
478     D.~P. DiVincenzo and N. Margolus and P. Shor and
479     T. Sleator and J.~A. Smolin and H. Weinfurter",
480     title = {elementary gates for quantum computation},
481     journal = {Phys. Rev. A},
482     year = 1995,
483     volume = 52,
484     pages = {3457-3467}
485     }
486    
487     @Article{Small97,
488     author = {T. Reinot and J.~M. Hayes and G.~J. Small},
489     title = {Electronic dephasing and electron-phonon coupling of
490     aluminum phthalocyanine tetrasulphonate in
491     hyperquenched and annealed glassy films of ethanol
492     and methanol over a broad temperature range},
493     journal = jcp,
494     year = 1997,
495     volume = 106,
496     pages = {457-466}
497     }
498    
499     @Article{Laflamme96,
500     author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
501     title = {A perfect quantum error correcting code: 5 bit code
502     correcting a general 1 qubit error to encode 1 qubit
503     of information},
504     journal = prl,
505     year = 1996,
506     volume = 98,
507     pages = 77
508     }
509    
510     @Article{Shor95,
511     author = {P.~W. Shor},
512     title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
513     journal = {Phys. Rev. A},
514     year = 1995,
515     volume = 52,
516     pages = {2493-2496}
517     }
518    
519     @Article{Calderbank96,
520     author = {A.~R. Calderbank and P.~W. Shor},
521     title = {Good quantum error-correcting codes exist},
522     journal = {Phys. Rev. A},
523     year = 1996,
524     volume = 54,
525     pages = {1098-1105}
526     }
527    
528     @Article{Steane96,
529     author = {A.~M. Steane},
530     title = {Error correcting codes in quantum theory},
531     journal = prl,
532     year = 1996,
533     volume = 77,
534     pages = {793-797}
535     }
536    
537     @Article{Gezelter95,
538     author = {J.~D. Gezelter and W.~H. Miller},
539     title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE
540     RATE OF KETENE ISOMERIZATION},
541     journal = jcp,
542     year = 1995,
543     volume = 103,
544     pages = {7868-7876}
545     }
546    
547     @Article{Chakrabarti92,
548     author = {A.~C. Chakrabarti and D.~W. Deamer},
549     title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
550     journal = {Biochimica et Biophysica Acta},
551     year = 1992,
552     volume = 1111,
553     pages = {171-177}
554     }
555    
556     @Article{Paula96,
557     author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and
558     T.~H. Haines and D.~W. Deamer},
559     title = {Permeation of protons, potassium ions, and small
560     polar molecules through phospholipid bilayers as a
561     function of membrane thickness},
562     journal = {Biophys. J.},
563     year = 1996,
564     volume = 70,
565     pages = {339-348}
566     }
567    
568     @Article{Little96,
569     author = {H.~J. Little},
570     title = {How has molecular pharmacology contributed to our
571     understanding of the mechanism(s) of general
572     anesthesia?},
573     journal = {Pharmacology \& Therapeutics},
574     year = 1996,
575     volume = 69,
576     pages = {37-58}
577     }
578    
579     @Article{McKinnon92,
580     author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
581     title = {Nonequilibrium Molecular Dynamics Simulation of
582     Oxygen Diffusion through Hexadecane Monolayers with
583     Varying Concentrations of Cholesterol},
584     journal = jpc,
585     year = 1992,
586     volume = 96,
587     pages = {10497-10506}
588     }
589    
590     @Article{Venable93,
591     author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and
592     R.~W. Pastor},
593     title = {Molecular Dynamics Simulations of a Lipid Bilayer
594     and of Hexadecane: An Investigation of Membrane Fluidity},
595     journal = {Science},
596     year = 1993,
597     volume = 262,
598     pages = {223-226}
599     }
600    
601     @Article{Essmann99,
602     author = {U. Essmann and M.~L. Berkowitz},
603     title = {Dynamical properties of phospholipid bilayers from
604     computer simulation},
605     journal = {Biophys. J.},
606     year = 1999,
607     volume = 76,
608     pages = {2081-2089}
609     }
610    
611     @Article{Tu98,
612     author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
613     title = {Effects of anesthetics on the structure of a
614     phospholipid bilayer: Molecular dynamics
615     investigation of halothane in the hydrated liquid
616     crystal phase of dipalmitoylphosphatidylcholine},
617     journal = {Biophys. J.},
618     year = 1998,
619     volume = 75,
620     pages = {2123-2134}
621     }
622    
623     @Article{Pomes96,
624     author = {R. Pomes and B. Roux},
625     title = {Structure and dynamics of a proton wire: A
626     theoretical study of H+ translocation along the
627     single-file water chain in the gramicidin a channel},
628     journal = {Biophys. J.},
629     year = 1996,
630     volume = 71,
631     pages = {19-39}
632     }
633    
634     @Article{Duwez60,
635     author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
636     title = {Continuous Series of Metastable Solid Solutions in
637     Silver-Copper Alloys},
638     journal = {J. Appl. Phys.},
639     year = 1960,
640     volume = 31,
641     pages = {1136-1137}
642     }
643    
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