ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/oopseDocs/oopseDoc.bib
Revision: 3395
Committed: Fri May 16 14:25:26 2008 UTC (16 years, 1 month ago) by gezelter
File size: 60429 byte(s)
Log Message:
OOPSE docs for version 4

File Contents

# User Rev Content
1 gezelter 3395 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3    
4    
5     %% Created for Dan Gezelter at 2008-05-16 10:19:07 -0400
6    
7    
8     %% Saved with string encoding Western (ASCII)
9    
10    
11     @string{acp = {Adv. Chem. Phys.}}
12    
13     @string{bj = {Biophys. J.}}
14    
15     @string{cp = {Chem. Phys.}}
16    
17     @string{cpc = {Comp. Phys. Comm.}}
18    
19     @string{cpl = {Chem. Phys. Lett.}}
20    
21     @string{jacs = {J. Am. Chem. Soc.}}
22    
23     @string{jcc = {J. Comp. Chem.}}
24    
25     @string{jcp = {J. Chem. Phys.}}
26    
27     @string{jml = {J. Mol. Liq.}}
28    
29     @string{jpc = {J. Phys. Chem.}}
30    
31     @string{jpca = {J. Phys. Chem. A}}
32    
33     @string{jpcb = {J. Phys. Chem. B}}
34    
35     @string{mp = {Mol. Phys.}}
36    
37     @string{pnas = {Proc. Natl. Acad. Sci. USA}}
38    
39     @string{pra = {Phys. Rev. A}}
40    
41     @string{prb = {Phys. Rev. B}}
42    
43     @string{pre = {Phys. Rev. E}}
44    
45     @string{prl = {Phys. Rev. Lett.}}
46    
47     @string{rmp = {Rev. Mod. Phys.}}
48    
49    
50     @article{Fennell06,
51     Author = {C.~J. Fennell and J.~D. Gezelter},
52     Date-Added = {2008-05-16 10:19:01 -0400},
53     Date-Modified = {2008-05-16 10:19:01 -0400},
54     Doi = {10.1063/1.2206581},
55     Journal = jcp,
56     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_PairwiseSummationMethods_06.pdf},
57     Number = {23},
58     Pages = {234104(12)},
59     Rating = {5},
60     Read = {Yes},
61     Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
62     Volume = {124},
63     Year = {2006},
64     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}
65    
66     @article{Heyes81,
67     Author = {D.~M. Heyes},
68     Date-Added = {2008-05-16 10:18:50 -0400},
69     Date-Modified = {2008-05-16 10:18:50 -0400},
70     Journal = jcp,
71     Keywords = {Empty Keywords},
72     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
73     Number = {3},
74     Pages = {1924-1929},
75     Title = {Electrostatic potentials and fields in infinite point charge lattices},
76     Volume = {74},
77     Year = {1981}}
78    
79     @article{Jones56,
80     Author = {R.~E. Jones and D.~H. Templeton},
81     Date-Added = {2008-05-16 10:18:41 -0400},
82     Date-Modified = {2008-05-16 10:18:41 -0400},
83     Journal = jcp,
84     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
85     Number = {5},
86     Pages = {1062-1063},
87     Title = {Optimum Atomic Shape for \uppercase{B}ertaut Series},
88     Volume = {25},
89     Year = {1956}}
90    
91     @book{Allen87,
92     Address = {New York},
93     Author = {M.~P. Allen and D.~J. Tildesley},
94     Date-Added = {2008-05-16 10:18:32 -0400},
95     Date-Modified = {2008-05-16 10:18:32 -0400},
96     Publisher = {Oxford University Press},
97     Title = {Computer Simulations of Liquids},
98     Year = 1987}
99    
100     @article{Wolf99,
101     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
102     Date-Added = {2008-05-16 10:18:22 -0400},
103     Date-Modified = {2008-05-16 10:18:22 -0400},
104     Journal = jcp,
105     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
106     Number = {17},
107     Pages = {8254-8282},
108     Rating = {0},
109     Read = {No},
110     Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
111     Volume = {110},
112     Year = {1999}}
113    
114     @book{Berne90,
115     Address = {Malabar, Florida},
116     Author = {B.~J. Berne and R. Pecora},
117     Publisher = {Robert E. Krieger Publishing Company, Inc.},
118     Title = {Dynamic Light Scattering},
119     Year = 1990}
120    
121     @article{Evans77,
122     Author = {D.~J. Evans},
123     Journal = {Mol. Phys.},
124     Pages = {317-325},
125     Title = {On the representation of orientation space},
126     Volume = 34,
127     Year = 1977}
128    
129     @article{Tuckerman92,
130     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
131     Journal = jcp,
132     Pages = {1990-2001},
133     Title = {Reversible multiple time scale molecular dynamics},
134     Volume = 97,
135     Year = 1992}
136    
137     @book{Hansen86,
138     Address = {London},
139     Author = {J.~P. Hansen and I.~R. McDonald},
140     Chapter = 7,
141     Pages = {199-206},
142     Publisher = {Academic Press},
143     Title = {Theory of Simple Liquids},
144     Year = 1986}
145    
146     @article{Angelani98,
147     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
148     Journal = prl,
149     Number = 21,
150     Pages = {4648-4651},
151     Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
152     Volume = 81,
153     Year = 1998}
154    
155     @article{Stillinger82,
156     Author = {F.~H. Stillinger and T.~A. Weber},
157     Journal = pra,
158     Number = 2,
159     Pages = {978-989},
160     Title = {Hidden structure in liquids},
161     Volume = 25,
162     Year = 1982}
163    
164     @article{Stillinger83,
165     Author = {F.~H. Stillinger and T.~A. Weber},
166     Journal = pra,
167     Number = 4,
168     Pages = {2408-2416},
169     Title = {Dynamics of structural transitions in liquids},
170     Volume = 28,
171     Year = 1983}
172    
173     @article{Weber84,
174     Author = {T.~A. Weber and F.~H. Stillinger},
175     Journal = jcp,
176     Number = 6,
177     Pages = {2742-2746},
178     Title = {The effect of density on the inherent structure in liquids},
179     Volume = 80,
180     Year = 1984}
181    
182     @article{Stillinger85,
183     Author = {F.~H. Stillinger and T.~A. Weber},
184     Journal = jcp,
185     Number = 9,
186     Pages = {4767-4775},
187     Title = {Inherent structure theory of liquids in the hard-sphere limit},
188     Volume = 83,
189     Year = 1985}
190    
191     @article{Stillinger98,
192     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
193     Journal = {Nature},
194     Pages = {554-557},
195     Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
196     Volume = 393,
197     Year = 1998}
198    
199     @article{Parkhurst75a,
200     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
201     Journal = jcp,
202     Number = 6,
203     Pages = {2698-2704},
204     Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
205     Volume = 63,
206     Year = 1975}
207    
208     @article{Parkhurst75b,
209     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
210     Journal = jcp,
211     Number = 6,
212     Pages = {2705-2709},
213     Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene },
214     Volume = 63,
215     Year = 1975}
216    
217     @article{Forester97,
218     Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
219     Journal = {J. Chem. Soc. - Faraday Transactions},
220     Pages = {613-619},
221     Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
222     Volume = 93,
223     Year = 1997}
224    
225     @article{Tieleman98,
226     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
227     Journal = bj,
228     Pages = {2786-2801},
229     Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
230     Volume = 74,
231     Year = 1998}
232    
233     @article{Cascales98,
234     Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
235     Journal = {J. Phys. Chem. B},
236     Pages = {625-631},
237     Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
238     Volume = 102,
239     Year = 1998}
240    
241     @article{Bassolino95,
242     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
243     Journal = {J. Am. Chem. Soc.},
244     Pages = {4118-4129},
245     Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
246     Volume = 117,
247     Year = 1995}
248    
249     @article{Alper95,
250     Author = {H.~E. Alper and T.~R. Stouch},
251     Journal = {J. Phys. Chem.},
252     Pages = {5724-5731},
253     Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
254     Volume = 99,
255     Year = 1995}
256    
257     @article{Sok92,
258     Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
259     Journal = {J. Chem. Phys.},
260     Pages = {4699-4704},
261     Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
262     Volume = 96,
263     Year = 1992}
264    
265     @article{Rabani99,
266     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
267     Journal = prl,
268     Pages = {3649},
269     Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
270     Volume = 82,
271     Year = {1999}}
272    
273     @article{Rabani97,
274     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
275     Journal = {J. Chem. Phys.},
276     Pages = {6867-6876},
277     Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
278     Volume = 107,
279     Year = 1997}
280    
281     @article{Gezelter99,
282     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
283     Journal = jcp,
284     Pages = 3444,
285     Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
286     Volume = 110,
287     Year = 1999}
288    
289     @article{Gezelter98a,
290     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
291     Journal = jcp,
292     Pages = 4695,
293     Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
294     Volume = 109,
295     Year = 1998}
296    
297     @article{Gezelter97,
298     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
299     Journal = jcp,
300     Pages = 4618,
301     Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
302     Volume = 107,
303     Year = 1997}
304    
305     @article{Zwanzig83,
306     Author = {R. Zwanzig},
307     Journal = jcp,
308     Pages = {4507-4508},
309     Title = {On the relation between self-diffusion and viscosity of liquids},
310     Volume = 79,
311     Year = 1983}
312    
313     @article{Zwanzig88,
314     Author = {R. Zwanzig},
315     Journal = {Proc. Natl. Acad. Sci. USA},
316     Pages = 2029,
317     Title = {Diffusion in rough potential},
318     Volume = 85,
319     Year = 1988}
320    
321     @article{Stillinger95,
322     Author = {F.~H. Stillinger},
323     Journal = {Science},
324     Pages = {1935-1939},
325     Title = {A Topographic View of Supercooled Liquids and Glass Formation},
326     Volume = 267,
327     Year = 1995}
328    
329     @incollection{Angell85,
330     Address = {Springfield, VA},
331     Author = {C.~A. Angell},
332     Booktitle = {Relaxations in Complex Systems},
333     Editor = {K.~Ngai and G.~B. Wright},
334     Pages = 1,
335     Publisher = {National Technical Information Service, U.S. Department of Commerce},
336     Title = {unknown},
337     Year = 1985}
338    
339     @article{Bembenek96,
340     Author = {S.~D. Bembenek and B.~B. Laird},
341     Journal = jcp,
342     Pages = 5199,
343     Title = {The role of localization in glasses and supercooled liquids},
344     Volume = 104,
345     Year = 1996}
346    
347     @article{Sun97,
348     Author = {X. Sun and W.~H. Miller},
349     Journal = jcp,
350     Pages = 6346,
351     Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
352     Volume = 106,
353     Year = 1997}
354    
355     @article{Spath96,
356     Author = {B.~W. Spath and W.~H. Miller},
357     Journal = jcp,
358     Pages = 95,
359     Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
360     Volume = 104,
361     Year = 1996}
362    
363     @book{Warshel91,
364     Address = {New York},
365     Author = {Arieh Warshel},
366     Publisher = {Wiley},
367     Title = {Computer modeling of chemical reactions in enzymes and solutions},
368     Year = 1991}
369    
370     @article{Vuilleumier97,
371     Author = {Rodolphe Vuilleumier and Daniel Borgis},
372     Journal = jpc,
373     Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
374     Volume = {in press},
375     Year = 1997}
376    
377     @article{Kob95a,
378     Author = {W. Kob and H.~C. Andersen},
379     Journal = pre,
380     Pages = {4626-4641},
381     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
382     Volume = 51,
383     Year = 1995}
384    
385     @article{Kob95b,
386     Author = {W. Kob and H.~C. Andersen},
387     Journal = pre,
388     Pages = {4134-4153},
389     Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
390     Volume = 52,
391     Year = 1995}
392    
393     @inproceedings{Gotze89,
394     Address = {Amsterdam},
395     Author = {W. G{\"{o}}tze},
396     Booktitle = {Liquids, Freezing and Glass Transitions},
397     Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
398     Pages = {287-503},
399     Publisher = {North-Holland},
400     Title = {Aspects of Structural Glass Transitions},
401     Volume = {I},
402     Year = 1989}
403    
404     @article{Sun97a,
405     Author = {X. Sun and W.~H. Miller},
406     Journal = jcp,
407     Pages = 916,
408     Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
409     Year = 1997}
410    
411     @article{Keshavamurthy94,
412     Author = {S. Keshavamurthy and W.~H. Miller},
413     Journal = cpl,
414     Pages = 189,
415     Title = {ivr},
416     Volume = 218,
417     Year = 1994}
418    
419     @article{Billing75,
420     Author = {G.~D. Billing},
421     Journal = cpl,
422     Pages = 391,
423     Title = {ehrenfest},
424     Volume = 30,
425     Year = 1975}
426    
427     @article{Chang90,
428     Author = {Y.-T. Chang and W.~H. Miller},
429     Journal = jpc,
430     Pages = {5884-5888},
431     Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
432     Volume = 94,
433     Year = 1990}
434    
435     @article{Shor94,
436     Author = {P.W. Shor},
437     Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
438     Pages = {124-134},
439     Title = {Algorithms for quantum computation: discrete logarithms and factoring},
440     Year = 1994}
441    
442     @article{Feynman82,
443     Author = {R.~P. Feynman},
444     Journal = {Int. J. Theor. Phys.},
445     Pages = {467-488},
446     Title = {Simulating physics with computers},
447     Volume = 21,
448     Year = 1982}
449    
450     @article{Grover97,
451     Author = {L.~K. Grover},
452     Journal = prl,
453     Pages = {4709-4712},
454     Title = {Quantum computers can search arbitrarily large databases by a single query},
455     Volume = 79,
456     Year = 1997}
457    
458     @article{Chuang98,
459     Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
460     Journal = prl,
461     Pages = {3408-3411},
462     Title = {Experimental Implementation of Fast Quantum Searching},
463     Volume = 80,
464     Year = 1998}
465    
466     @article{Monroe95,
467     Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
468     Journal = prl,
469     Pages = 4714,
470     Title = {Demonstration of a fundamental quantum logic gate},
471     Volume = 75,
472     Year = 1995}
473    
474     @article{Lent93,
475     Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
476     Journal = {Nanotechnology},
477     Pages = {49-57},
478     Title = {Quantum Cellular Automata},
479     Volume = 4,
480     Year = 1993}
481    
482     @article{Barenco95,
483     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},
484     Journal = {Phys. Rev. A},
485     Pages = {3457-3467},
486     Title = {elementary gates for quantum computation},
487     Volume = 52,
488     Year = 1995}
489    
490     @article{Small97,
491     Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
492     Journal = jcp,
493     Pages = {457-466},
494     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},
495     Volume = 106,
496     Year = 1997}
497    
498     @article{Laflamme96,
499     Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
500     Journal = prl,
501     Pages = 77,
502     Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
503     Volume = 98,
504     Year = 1996}
505    
506     @article{Shor95,
507     Author = {P.~W. Shor},
508     Journal = {Phys. Rev. A},
509     Pages = {2493-2496},
510     Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
511     Volume = 52,
512     Year = 1995}
513    
514     @article{Calderbank96,
515     Author = {A.~R. Calderbank and P.~W. Shor},
516     Journal = {Phys. Rev. A},
517     Pages = {1098-1105},
518     Title = {Good quantum error-correcting codes exist},
519     Volume = 54,
520     Year = 1996}
521    
522     @article{Steane96,
523     Author = {A.~M. Steane},
524     Journal = prl,
525     Pages = {793-797},
526     Title = {Error correcting codes in quantum theory},
527     Volume = 77,
528     Year = 1996}
529    
530     @article{Gezelter95,
531     Author = {J.~D. Gezelter and W.~H. Miller},
532     Journal = jcp,
533     Pages = {7868-7876},
534     Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
535     Volume = 103,
536     Year = 1995}
537    
538     @article{Chakrabarti92,
539     Author = {A.~C. Chakrabarti and D.~W. Deamer},
540     Journal = {Biochimica et Biophysica Acta},
541     Pages = {171-177},
542     Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
543     Volume = 1111,
544     Year = 1992}
545    
546     @article{Paula96,
547     Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
548     Journal = bj,
549     Pages = {339-348},
550     Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
551     Volume = 70,
552     Year = 1996}
553    
554     @article{Little96,
555     Author = {H.~J. Little},
556     Journal = {Pharmacology \& Therapeutics},
557     Pages = {37-58},
558     Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
559     Volume = 69,
560     Year = 1996}
561    
562     @article{McKinnon92,
563     Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
564     Journal = jpc,
565     Pages = {10497-10506},
566     Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
567     Volume = 96,
568     Year = 1992}
569    
570     @article{Venable93,
571     Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
572     Journal = {Science},
573     Pages = {223-226},
574     Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
575     Volume = 262,
576     Year = 1993}
577    
578     @article{Essmann99,
579     Author = {U. Essmann and M.~L. Berkowitz},
580     Journal = bj,
581     Pages = {2081-2089},
582     Title = {Dynamical properties of phospholipid bilayers from computer simulation},
583     Volume = 76,
584     Year = 1999}
585    
586     @article{Tu98,
587     Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
588     Journal = bj,
589     Pages = {2123-2134},
590     Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
591     Volume = 75,
592     Year = 1998}
593    
594     @article{Pomes96,
595     Author = {R. Pomes and B. Roux},
596     Journal = bj,
597     Pages = {19-39},
598     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},
599     Volume = 71,
600     Year = 1996}
601    
602     @article{Duwez60,
603     Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
604     Journal = {J. Appl. Phys.},
605     Pages = {1136-1137},
606     Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
607     Volume = 31,
608     Year = 1960}
609    
610     @article{Peker93,
611     Author = {A. Peker and W.~L. Johnson},
612     Journal = {Appl. Phys. Lett.},
613     Pages = {2342-2344},
614     Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
615     Volume = 63,
616     Year = 1993}
617    
618     @article{ChoiYim97,
619     Author = {H. Choi-Yim and W.~L. Johnson},
620     Journal = {Appl. Phys. Lett.},
621     Pages = {3808-3810},
622     Title = {Bulk metallic glass matrix composites},
623     Volume = 71,
624     Year = 1997}
625    
626     @article{Sun96,
627     Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
628     Journal = {J. Mater. Res.},
629     Pages = {2738-2743},
630     Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
631     Volume = 11,
632     Year = 1996}
633    
634     @article{Heller93,
635     Author = {H. Heller and M. Schaefer and K. Schulten},
636     Journal = jpc,
637     Pages = {8343-8360},
638     Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
639     Volume = 97,
640     Year = 1993}
641    
642     @article{Kushick76,
643     Author = {J. Kushick and B.~J. Berne},
644     Journal = jcp,
645     Pages = {1362-1367},
646     Title = {Computer Simulation of anisotropic molecular fluids},
647     Volume = 64,
648     Year = 1976}
649    
650     @article{Berardi96,
651     Author = {R. Berardi and S. Orlandi and C Zannoni},
652     Journal = cpl,
653     Pages = {357-362},
654     Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
655     Volume = 261,
656     Year = 1996}
657    
658     @article{Berardi99,
659     Author = {R. Berardi and S. Orlandi and C. Zannoni},
660     Journal = {Int. J. Mod. Phys. C},
661     Pages = {477-484},
662     Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
663     Volume = 10,
664     Year = 1999}
665    
666     @article{Pasterny2000,
667     Author = {K. Pasterny and E. Gwozdz and A. Brodka},
668     Journal = {J. Mol. Liq.},
669     Pages = {173-184},
670     Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
671     Volume = 85,
672     Year = 2000}
673    
674     @article{Jorgensen83,
675     Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
676     Journal = jcp,
677     Pages = {926-935},
678     Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
679     Volume = 79,
680     Year = 1983}
681    
682     @article{Berardi98,
683     Author = {R. Berardi and C. Fava and C. Zannoni},
684     Journal = cpl,
685     Pages = {8-14},
686     Title = {A Gay-Berne potential for dissimilar biaxial particles},
687     Volume = 297,
688     Year = 1998}
689    
690     @article{Luckhurst90,
691     Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
692     Journal = {Liquid Crystals},
693     Pages = {451-464},
694     Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the Gay-Berne model mesogen},
695     Volume = 8,
696     Year = 1990}
697    
698     @article{Gay81,
699     Author = {J.~G. Gay and B.~J. Berne},
700     Journal = jcp,
701     Pages = {3316-3319},
702     Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
703     Volume = 74,
704     Year = 1981}
705    
706     @article{Berne72,
707     Author = {B.~J. Berne and P. Pechukas},
708     Journal = jcp,
709     Pages = {4213-4216},
710     Title = {Gaussian Model Potentials for Molecular Interactions},
711     Volume = 56,
712     Year = 1972}
713    
714     @article{Perram96,
715     Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
716     Journal = pre,
717     Pages = {6565-6572},
718     Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
719     Volume = 54,
720     Year = 1996}
721    
722     @article{Cornell95,
723     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},
724     Journal = jacs,
725     Pages = {5179-5197},
726     Title = {A second generation force field for the simulation of proteins and nucleic acids},
727     Volume = 117,
728     Year = 1995}
729    
730     @article{Brooks83,
731     Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
732     Journal = jcc,
733     Pages = {187-217},
734     Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
735     Volume = 4,
736     Year = 1983}
737    
738     @incollection{MacKerell98,
739     Address = {New York},
740     Author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and M. Karplus},
741     Booktitle = {The Encyclopedia of Computational Chemistry},
742     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
743     Pages = {271-277},
744     Publisher = {John Wiley \& Sons},
745     Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
746     Volume = 1,
747     Year = 1998}
748    
749     @incollection{Jorgensen98,
750     Address = {New York},
751     Author = {W.~L. Jorgensen},
752     Booktitle = {The Encyclopedia of Computational Chemistry},
753     Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
754     Pages = {1986-1989},
755     Publisher = {John Wiley \& Sons},
756     Title = {OPLS Force Fields},
757     Volume = 3,
758     Year = 1998}
759    
760     @article{Rabani2000,
761     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
762     Journal = prl,
763     Pages = 467,
764     Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
765     Volume = 85,
766     Year = 2000}
767    
768     @book{Cevc87,
769     Address = {New York},
770     Author = {G. Cevc and D. Marsh},
771     Publisher = {John Wiley \& Sons},
772     Title = {Phospholipid Bilayers},
773     Year = 1987}
774    
775     @article{Janiak79,
776     Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
777     Journal = {J. Biol. Chem.},
778     Pages = {6068-6078},
779     Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
780     Volume = 254,
781     Year = 1979}
782    
783     @book{Tobias90,
784     Address = {Tucson},
785     Author = {Sheila Tobias},
786     Publisher = {Research Corp.},
787     Title = {They're not Dumb. They're Different: Stalking the Second Tier},
788     Year = 1990}
789    
790     @article{Mazur92,
791     Author = {E. Mazur},
792     Journal = {Optics and Photonics News},
793     Pages = 38,
794     Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing? },
795     Volume = 3,
796     Year = 1992}
797    
798     @book{Mazur97,
799     Address = {New Jersey},
800     Author = {Eric Mazur},
801     Publisher = {Prentice Hall},
802     Title = {Peer Instruction: A User's Manual},
803     Year = 1997}
804    
805     @article{Wigner55,
806     Author = {E.~P. Wigner},
807     Journal = {Annals of Mathematics},
808     Pages = {548-564},
809     Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
810     Volume = 62,
811     Year = 1955}
812    
813     @article{Gaukel98,
814     Author = {C. Gaukel and H.~R. Schober},
815     Journal = {Solid State Comm.},
816     Pages = {1-5},
817     Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
818     Volume = 107,
819     Year = 1998}
820    
821     @article{Qi99,
822     Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
823     Journal = prb,
824     Number = 5,
825     Pages = {3527-3533},
826     Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
827     Volume = 59,
828     Year = 1999}
829    
830     @article{Khorunzhy97,
831     Author = {A. Khorunzhy and G.~J. Rodgers},
832     Journal = {J. Math. Phys.},
833     Pages = {3300-3320},
834     Title = {Eigenvalue distribution of large dilute random matrices},
835     Volume = 38,
836     Year = 1997}
837    
838     @article{Rodgers88,
839     Author = {G.~J. Rodgers and A. Bray},
840     Journal = {Phys. Rev. B},
841     Pages = 355703562,
842     Title = {Density of States of a Sparse Random Matrix},
843     Volume = 37,
844     Year = 1988}
845    
846     @article{Rodgers90,
847     Author = {G.~J. Rodgers and C. {De Dominicis}},
848     Journal = {J. Phys. A: Math. Gen.},
849     Pages = {1567-1573},
850     Title = {Density of states of sparse random matrices},
851     Volume = 23,
852     Year = 1990}
853    
854     @inproceedings{Barker80,
855     Author = {J.~A. Barker},
856     Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
857     Editor = {D. Ceperley},
858     Pages = {45-6},
859     Series = {NRCC Workshop Proceedings},
860     Title = {Reaction field method for polar fluids},
861     Volume = 9,
862     Year = 1980}
863    
864     @article{Smith82,
865     Author = {W. Smith},
866     Journal = {CCP5 Quarterly},
867     Pages = {13-25},
868     Title = {Point multipoles in the Ewald summation},
869     Volume = 4,
870     Year = 1982}
871    
872     @article{Daw84,
873     Author = {M.~S. Daw and M.~I. Baskes},
874     Journal = prb,
875     Number = 12,
876     Pages = {6443-6453},
877     Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
878     Volume = 29,
879     Year = 1984}
880    
881     @article{Chen90,
882     Author = {A.~P. Sutton and J. Chen},
883     Journal = {Phil. Mag. Lett.},
884     Pages = {139-146},
885     Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
886     Volume = 61,
887     Year = 1990}
888    
889     @article{Lu97,
890     Author = {J. Lu and J.~A. Szpunar},
891     Journal = {Phil. Mag. A},
892     Pages = {1057-1066},
893     Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
894     Volume = {75},
895     Year = {1997}}
896    
897     @article{Shlesinger99,
898     Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
899     Journal = {Am. J. Phys.},
900     Pages = {1253-1259},
901     Title = {Above, below, and beyond Brownian motion},
902     Volume = 67,
903     Year = 1999}
904    
905     @article{Klafter96,
906     Author = {J. Klafter and M. Shlesinger and G. Zumofen},
907     Journal = {Physics Today},
908     Pages = {33-39},
909     Title = {Beyond Brownian Motion},
910     Volume = 49,
911     Year = 1996}
912    
913     @article{Blumen83,
914     Author = {A. Blumen and J. Klafter and G. Zumofen},
915     Journal = {Phys. Rev. B},
916     Pages = {3429-3435},
917     Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
918     Volume = 27,
919     Year = 1983}
920    
921     @article{Klafter94,
922     Author = {J. Klafter and G. Zumofen},
923     Journal = jpc,
924     Pages = {7366-7370},
925     Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
926     Volume = 98,
927     Year = 1994}
928    
929     @article{Dzugutov92,
930     Author = {M. Dzugutov},
931     Journal = pra,
932     Pages = {R2984-R2987},
933     Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
934     Volume = 46,
935     Year = 1992}
936    
937     @article{Moore94,
938     Author = {P. Moore and T. Keyes},
939     Journal = jcp,
940     Pages = 6709,
941     Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
942     Volume = 100,
943     Year = 1994}
944    
945     @article{Seeley89,
946     Author = {G. Seeley and T. Keyes},
947     Journal = jcp,
948     Pages = {5581-5586},
949     Title = {Normal-mode analysis of liquid-state dynamics},
950     Volume = 91,
951     Year = 1989}
952    
953     @article{Madan90,
954     Author = {B. Madan and T. Keyes and G. Seeley},
955     Journal = jcp,
956     Pages = {7565-7569},
957     Title = {Diffusion in supercooled liquids via normal mode analysis},
958     Volume = 92,
959     Year = 1990}
960    
961     @article{Madan91,
962     Author = {B. Madan and T. Keyes and G. Seeley},
963     Journal = jcp,
964     Pages = {6762-6769},
965     Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
966     Volume = 94,
967     Year = 1991}
968    
969     @article{Buchner92,
970     Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
971     Journal = jcp,
972     Pages = {8522-8535},
973     Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
974     Volume = 97,
975     Year = 1992}
976    
977     @article{Wan94,
978     Author = {Yi. Wan and R.~M. Stratt},
979     Journal = jcp,
980     Pages = {5123-5138},
981     Title = {Liquid theory for the instantaneous normal modes of a liquid},
982     Volume = 100,
983     Year = 1994}
984    
985     @article{Stratt95,
986     Author = {R.~M. Stratt},
987     Journal = {Acc. Chem. Res.},
988     Pages = {201-207},
989     Title = {The instantaneous normal modes of liquids},
990     Volume = 28,
991     Year = 1995}
992    
993     @article{Nitzan95,
994     Author = {G.~V. Vijayadamodar and A. Nitzan},
995     Journal = jcp,
996     Pages = {2169-2177},
997     Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
998     Volume = 103,
999     Year = 1995}
1000    
1001     @article{Ribeiro98,
1002     Author = {M.~C.~C. Ribeiro and P.~A. Madden},
1003     Journal = jcp,
1004     Pages = {3256-3263},
1005     Title = {Unstable Modes in Ionic Melts},
1006     Volume = 108,
1007     Year = 1998}
1008    
1009     @article{Keyes98a,
1010     Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
1011     Journal = jcp,
1012     Pages = {4693-4694},
1013     Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
1014     Volume = 109,
1015     Year = 1998}
1016    
1017     @article{Alemany98,
1018     Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
1019     Journal = jcp,
1020     Pages = {5175-5176},
1021     Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
1022     Volume = 109,
1023     Year = 1998}
1024    
1025     @article{Belonoshko00,
1026     Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
1027     Journal = prb,
1028     Pages = {3838-3844},
1029     Title = {Quasi ab initio molecular dynamic study of Cu melting},
1030     Volume = 61,
1031     Year = 2000}
1032    
1033     @article{Banhart92,
1034     Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1035     Journal = prb,
1036     Pages = {9968-9975},
1037     Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1038     Volume = 46,
1039     Year = 1992}
1040    
1041     @article{Wendt78,
1042     Author = {H. Wendt and F.~F. Abraham},
1043     Journal = prl,
1044     Pages = 1244,
1045     Volume = 41,
1046     Year = 1978}
1047    
1048     @article{Lewis91,
1049     Author = {L.~J. Lewis},
1050     Journal = prb,
1051     Pages = {4245-4254},
1052     Title = {Atomic dynamics through the glass transition},
1053     Volume = 44,
1054     Year = 1991}
1055    
1056     @article{Liu92,
1057     Author = {R.~S. Liu and D.~W. Qi and S. Wang},
1058     Journal = prb,
1059     Pages = {451-453},
1060     Title = {Subpeaks of structure factors for rapidly quenched metals},
1061     Volume = 45,
1062     Year = 1992}
1063    
1064     @book{pliny,
1065     Author = {Pliny},
1066     Publisher = { },
1067     Title = {Hist. Nat.},
1068     Volume = {XXXVI},
1069     Year = { }}
1070    
1071     @article{Anheuser94,
1072     Author = {K. Anheuser and J.P. Northover},
1073     Journal = {Brit. Num. J.},
1074     Pages = 22,
1075     Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
1076     Volume = 64,
1077     Year = 1994}
1078    
1079     @article{Pense92,
1080     Author = {A. W. Pense},
1081     Journal = {Mat. Char.},
1082     Pages = 213,
1083     Title = {The Decline and Fall of the Roman Denarius},
1084     Volume = 29,
1085     Year = 1992}
1086    
1087     @article{Ngai81,
1088     Author = {K.~L. Ngai and F.-S. Liu},
1089     Journal = prb,
1090     Pages = {1049-1065},
1091     Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1092     Volume = 24,
1093     Year = 1981}
1094    
1095     @unpublished{Truhlar00,
1096     Author = {D.~G. Truhlar and A. Kohen},
1097     Note = {private correspondence}}
1098    
1099     @article{Truhlar78,
1100     Author = {Donald G. Truhlar},
1101     Journal = {J. Chem. Ed.},
1102     Pages = 309,
1103     Title = {Interpretation of the Activation Energy},
1104     Volume = 55,
1105     Year = 1978}
1106    
1107     @book{Tolman27,
1108     Address = {New York},
1109     Author = {R. C. Tolman},
1110     Pages = {260-270},
1111     Publisher = {Chemical Catalog Co.},
1112     Title = {Statistical Mechanics with Applications to Physics and Chemistry},
1113     Year = 1927}
1114    
1115     @article{Tolman20,
1116     Author = {R. C. Tolman},
1117     Journal = jacs,
1118     Pages = 2506,
1119     Title = {Statistical Mechanics Applied to Chemical Kinetics},
1120     Volume = 42,
1121     Year = 1920}
1122    
1123     @article{Nagel96,
1124     Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
1125     Journal = jpc,
1126     Pages = 13200,
1127     Title = {Supercooled Liquids and Glasses},
1128     Volume = 100,
1129     Year = 1996}
1130    
1131     @inbook{Blumen86,
1132     Address = {Amsterdam},
1133     Author = {A. Blumen and J. Klafter and G. Zumofen},
1134     Chapter = {Reactions in Disordered Media Modelled by Fractals},
1135     Editor = {Luciano Peitronero and E. Tosatti},
1136     Pages = 399,
1137     Publisher = {North-Holland},
1138     Series = {International Symposium on Fractals in Physics},
1139     Title = {Fractals in Physics},
1140     Year = 1986}
1141    
1142     @article{Shlesinger84,
1143     Author = {M.~F. Shlesinger and E.~W. Montroll},
1144     Journal = {Proc. Natl. Acad. Sci. USA},
1145     Pages = {1280-1283},
1146     Title = {On the Williams-Watts function of dielectric relaxation},
1147     Volume = 81,
1148     Year = 1984}
1149    
1150     @article{Klafter86,
1151     Author = {J. Klafter and M.~F. Shlesinger},
1152     Journal = {Proc. Natl. Acad. Sci. USA},
1153     Pages = {848-851},
1154     Title = {On the relationship among three theories of relaxation in disordered systems},
1155     Volume = 83,
1156     Year = 1986}
1157    
1158     @article{Li2001,
1159     Author = {Z. Li and M. Lieberman and W. Hill},
1160     Journal = {Langmuir},
1161     Pages = {4887-4894},
1162     Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
1163     Volume = 17,
1164     Year = 2001}
1165    
1166     @article{Evans1993,
1167     Author = {J.~W. Evans},
1168     Journal = rmp,
1169     Pages = {1281-1329},
1170     Title = {Random and Cooperative Sequential Adsorption},
1171     Volume = 65,
1172     Year = 1993}
1173    
1174     @article{Dwyer1977,
1175     Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
1176     Journal = {Surf. Sci.},
1177     Pages = 617,
1178     Volume = 64,
1179     Year = 1977}
1180    
1181     @article{Macritche1978,
1182     Author = {F. MacRitche},
1183     Journal = {Adv. Protein Chem.},
1184     Pages = 283,
1185     Volume = 32,
1186     Year = 1978}
1187    
1188     @article{Feder1980,
1189     Author = {J. Feder},
1190     Journal = {J. Theor. Biol.},
1191     Pages = 237,
1192     Volume = 87,
1193     Year = 1980}
1194    
1195     @article{Ramsden1993,
1196     Author = {J.~J. Ramsden},
1197     Journal = prl,
1198     Pages = 295,
1199     Volume = 71,
1200     Year = 1993}
1201    
1202     @article{Egelhoff1989,
1203     Author = {W.~F. Egelhoff and I. Jacob},
1204     Journal = prl,
1205     Pages = 921,
1206     Volume = 62,
1207     Year = 1989}
1208    
1209     @article{Viot1992a,
1210     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1211     Journal = jpc,
1212     Pages = {5212-5218},
1213     Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1214     Volume = 97,
1215     Year = 1992}
1216    
1217     @article{Viot1992b,
1218     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1219     Journal = {Physica A},
1220     Pages = {248-252},
1221     Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
1222     Volume = 191,
1223     Year = 1992}
1224    
1225     @article{Dobson1987,
1226     Author = {B.~W. Dobson},
1227     Journal = prb,
1228     Pages = 1068,
1229     Volume = 36,
1230     Year = 1987}
1231    
1232     @article{Boyer1995,
1233     Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1234     Journal = jcp,
1235     Pages = 1607,
1236     Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
1237     Volume = 103,
1238     Year = 1995}
1239    
1240     @article{Viot1992c,
1241     Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1242     Journal = {Physica A},
1243     Pages = {248-252},
1244     Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
1245     Volume = 191,
1246     Year = 1992}
1247    
1248     @article{Ricci1994,
1249     Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
1250     Journal = jcp,
1251     Pages = 9164,
1252     Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1253     Volume = 101,
1254     Year = 1994}
1255    
1256     @article{Semmler1998,
1257     Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1258     Journal = {Langmuir},
1259     Pages = {5127-5132},
1260     Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
1261     Volume = 14,
1262     Year = 1998}
1263    
1264     @article{Solomon1986,
1265     Author = {H. Solomon and H. Weiner},
1266     Journal = {Comm. Statistics A},
1267     Pages = {2571-2607},
1268     Title = {A REVIEW OF THE PACKING PROBLEM},
1269     Volume = 15,
1270     Year = 1986}
1271    
1272     @article{Bonnier1993,
1273     Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
1274     Journal = {Physica A},
1275     Pages = {1-10},
1276     Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
1277     Volume = 198,
1278     Year = 1993}
1279    
1280     @book{Frenkel1996,
1281     Address = {New York},
1282     Author = {D. Frenkel and B. Smit},
1283     Publisher = {Academic Press},
1284     Title = {Understanding Molecular Simulation : From Algorithms to Applications},
1285     Year = 1996}
1286    
1287     @article{Dullweber1997,
1288     Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
1289     Journal = jcp,
1290     Number = 15,
1291     Pages = {5840-5851},
1292     Title = {Symplectic splitting methods for rigid body molecular dynamics},
1293     Volume = 107,
1294     Year = 1997}
1295    
1296     @article{Siepmann1998,
1297     Author = {M. Martin and J.~I. Siepmann},
1298     Journal = jpcB,
1299     Pages = {2569-2577},
1300     Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
1301     Volume = 102,
1302     Year = 1998}
1303    
1304     @article{Marrink01,
1305     Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
1306     Journal = jacs,
1307     Pages = {8638-8639},
1308     Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
1309     Volume = 123,
1310     Year = 2001}
1311    
1312     @article{liu96:new_model,
1313     Author = {Y. Liu and T. Ichiye},
1314     Journal = jpc,
1315     Pages = {2723-2730},
1316     Title = {Soft sticky dipole potential for liquid water: a new model},
1317     Volume = 100,
1318     Year = 1996}
1319    
1320     @article{liu96:monte_carlo,
1321     Author = {Y. Liu and T. Ichiye},
1322     Journal = cpl,
1323     Pages = {334-340},
1324     Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
1325     Volume = 256,
1326     Year = 1996}
1327    
1328     @article{chandra99:ssd_md,
1329     Author = {A. Chandra and T. Ichiye},
1330     Journal = jcp,
1331     Number = 6,
1332     Pages = {2701-2709},
1333     Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
1334     Volume = 111,
1335     Year = 1999}
1336    
1337     @book{allen87:csl,
1338     Address = {New York},
1339     Author = {M.~P. Allen and D.~J. Tildesley},
1340     Publisher = {Oxford University Press},
1341     Title = {Computer Simulations of Liquids},
1342     Year = 1987}
1343    
1344     @book{leach01:mm,
1345     Address = {Harlow, England},
1346     Author = {A. Leach},
1347     Edition = {2nd},
1348     Publisher = {Pearson Educated Limited},
1349     Title = {Molecular Modeling: Principles and Applications},
1350     Year = 2001}
1351    
1352     @article{katsaras00,
1353     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},
1354     Journal = pre,
1355     Number = 5,
1356     Pages = {5668-5677},
1357     Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
1358     Volume = 61,
1359     Year = 2000}
1360    
1361     @article{sengupta00,
1362     Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
1363     Journal = {Europhysics Letters},
1364     Number = 6,
1365     Pages = {722-728},
1366     Title = {Novel structural Features of the ripple phase of phospholipids},
1367     Volume = 49,
1368     Year = 2000}
1369    
1370     @article{venable00,
1371     Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
1372     Journal = jcp,
1373     Number = 10,
1374     Pages = {4822-4832},
1375     Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
1376     Volume = 112,
1377     Year = 2000}
1378    
1379     @article{lindahl00,
1380     Author = {E. Lindahl and O. Edholm},
1381     Journal = bj,
1382     Month = {July},
1383     Pages = {426-433},
1384     Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
1385     Volume = 79,
1386     Year = 2000}
1387    
1388     @article{saiz02,
1389     Author = {L. Saiz and M. Klein},
1390     Journal = jcp,
1391     Number = 7,
1392     Pages = {3052-3057},
1393     Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
1394     Volume = 116,
1395     Year = 2002}
1396    
1397     @article{stevens95,
1398     Author = {M.~J. Stevens and G.~S. Grest},
1399     Journal = pre,
1400     Number = 6,
1401     Pages = {5976-5983},
1402     Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
1403     Volume = 51,
1404     Year = 1995}
1405    
1406     @article{darden93:pme,
1407     Author = {T. Darden and D. York and L. Pedersen},
1408     Journal = jcp,
1409     Number = 12,
1410     Pages = {10089-10092},
1411     Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
1412     Volume = 98,
1413     Year = 1993}
1414    
1415     @article{goetz98,
1416     Author = {R. Goetz and R. Lipowsky},
1417     Journal = jcp,
1418     Number = 17,
1419     Pages = 7397,
1420     Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
1421     Volume = 108,
1422     Year = 1998}
1423    
1424     @article{marrink01:undulation,
1425     Author = {S.~J. Marrink and A.~E. Mark},
1426     Journal = jpcB,
1427     Pages = {6122-6127},
1428     Title = {Effect of undulations on surface tension in simulated bilayers},
1429     Volume = 105,
1430     Year = 2001}
1431    
1432     @article{lindahl00:undulation,
1433     Author = {E. Lindahl and O. Edholm},
1434     Journal = bj,
1435     Pages = {426-433},
1436     Title = {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation},
1437     Volume = 79,
1438     Year = 2000}
1439    
1440     @article{metropolis:1949,
1441     Author = {N. Metropolis and S. Ulam},
1442     Journal = {J. Am. Stat. Ass.},
1443     Pages = {335-341},
1444     Title = {The $\mbox{Monte Carlo}$ Method},
1445     Volume = 44,
1446     Year = 1949}
1447    
1448     @article{metropolis:1953,
1449     Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
1450     Journal = jcp,
1451     Pages = {1087-1092},
1452     Title = {Equation of State Calculations by Fast Computing Machines},
1453     Volume = 21,
1454     Year = 1953}
1455    
1456     @article{born:1912,
1457     Author = {M. Born and Th. Von~Karman},
1458     Journal = {Physik Z.},
1459     Number = {297-309},
1460     Title = {Uber Schwingungen in Raumgittern},
1461     Volume = 13,
1462     Year = 1912}
1463    
1464     @book{chandler:1987,
1465     Author = {David Chandler},
1466     Publisher = {Oxford University Press},
1467     Title = {Introduction to Modern Statistical Mechanics},
1468     Year = 1987}
1469    
1470     @article{pearlman:1995,
1471     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},
1472     Journal = cpc,
1473     Pages = {1-41},
1474     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},
1475     Volume = 91,
1476     Year = 1995}
1477    
1478     @book{Goldstein01,
1479     Address = {San Francisco},
1480     Author = {H. Goldstein and C. Poole and J. Safko},
1481     Edition = {3rd},
1482     Publisher = {Addison Wesley},
1483     Title = {Classical Mechanics},
1484     Year = 2001}
1485    
1486     @article{Bratko85,
1487     Author = {D. Bratko and L. Blum and A. Luzar},
1488     Journal = jcp,
1489     Number = 12,
1490     Pages = {6367-6370},
1491     Title = {A simple model for the intermolecular potential of water},
1492     Volume = 83,
1493     Year = 1985}
1494    
1495     @article{Bratko95,
1496     Author = {L. Blum and F. Vericat and D. Bratko},
1497     Journal = jcp,
1498     Number = 3,
1499     Pages = {1461-1462},
1500     Title = {Towards an analytical model of water: The octupolar model},
1501     Volume = 102,
1502     Year = 1995}
1503    
1504     @article{Ichiye03,
1505     Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
1506     Journal = cpl,
1507     Pages = {646-652},
1508     Title = {A temperature of maximum density in soft sticky dipole water},
1509     Volume = 376,
1510     Year = 2003}
1511    
1512     @article{Soper86,
1513     Author = {A.~K. Soper and M.~G. Phillips},
1514     Journal = cp,
1515     Number = 1,
1516     Pages = {47-60},
1517     Title = {A new determination of the structure of water at 298K},
1518     Volume = 107,
1519     Year = 1986}
1520    
1521     @article{plimpton95,
1522     Author = {S. Plimpton},
1523     Journal = {J. Comp. Phys.},
1524     Pages = {1-19},
1525     Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
1526     Volume = 117,
1527     Year = 1995}
1528    
1529     @article{Ercolessi02,
1530     Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
1531     Journal = prb,
1532     Pages = 241406,
1533     Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
1534     Volume = 65,
1535     Year = 2002}
1536    
1537     @article{Ercolessi88,
1538     Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
1539     Journal = {Phil. Mag. A},
1540     Pages = {213-226},
1541     Title = {Simulation of Gold in the Glue Model.},
1542     Volume = 58,
1543     Year = 1988}
1544    
1545     @article{Finnis84,
1546     Author = {M.~W Finnis and J.~E. Sinclair },
1547     Journal = {Phil. Mag. A},
1548     Pages = {45-55},
1549     Title = {A Simple Empirical N-Body Potential for Transition-Metals},
1550     Volume = 50,
1551     Year = 1984}
1552    
1553     @article{FBD86,
1554     Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
1555     Journal = prb,
1556     Number = 12,
1557     Pages = 7983,
1558     Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
1559     Volume = 33,
1560     Year = 1986}
1561    
1562     @article{EAM93,
1563     Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
1564     Journal = {Mat. Sci. Rep.},
1565     Pages = {251-310},
1566     Title = {The embededd-atom method},
1567     Volume = 9,
1568     Year = 1993}
1569    
1570     @article{johnson89,
1571     Author = {R.~A. Johnson},
1572     Journal = prb,
1573     Number = 17,
1574     Pages = 12554,
1575     Title = {Alloy models with the embedded-atom method},
1576     Volume = 39,
1577     Year = 1989}
1578    
1579     @article{Laird97,
1580     Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
1581     Journal = jcp,
1582     Number = 7,
1583     Pages = {2580-2588},
1584     Title = {A symplectic method for rigid-body molecular simulation},
1585     Volume = 107,
1586     Year = 1997}
1587    
1588     @article{hoover85,
1589     Author = {W.~G. Hoover},
1590     Journal = pra,
1591     Pages = 1695,
1592     Title = {Canonical dynamics: Equilibrium phase-space distributions},
1593     Volume = 31,
1594     Year = 1985}
1595    
1596     @article{Roux91,
1597     Author = {B. Roux and M. Karplus},
1598     Journal = jpc,
1599     Number = 15,
1600     Pages = {4856-4868},
1601     Title = {Ion transport in a Gramicidin-like channel: dynamics and mobility},
1602     Volume = 95,
1603     Year = 1991}
1604    
1605     @article{Marrink94,
1606     Author = {S.~J Marrink and H.~J.~C. Berendsen},
1607     Journal = jpc,
1608     Number = 15,
1609     Pages = {4155-4168},
1610     Title = {Simulation of water transport through a lipid membrane},
1611     Volume = 98,
1612     Year = 1994}
1613    
1614     @article{Daw89,
1615     Author = {Murray~S. Daw},
1616     Journal = prb,
1617     Pages = {7441-7452},
1618     Title = {Model of metallic cohesion: The embedded-atom method},
1619     Volume = 39,
1620     Year = 1989}
1621    
1622     @inbook{voter,
1623     Author = {A.~F. Voter},
1624     Chapter = 4,
1625     Editor = {J.~H. Westbrook and R.~L. Fleischer},
1626     Pages = 77,
1627     Publisher = {John Wiley and Sons Ltd},
1628     Title = {Intermetallic Compounds: Principles and Practice},
1629     Volume = 1,
1630     Year = 1995}
1631    
1632     @article{marrink:2002,
1633     Author = {S.~J. Marrink and D.~P. Teileman},
1634     Journal = bj,
1635     Pages = {2386-2392},
1636     Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
1637     Volume = 83,
1638     Year = 2002}
1639    
1640     @article{sum:2003,
1641     Author = {A.~K. Sum and J.~J. de~Pablo},
1642     Journal = bj,
1643     Pages = {3636-3645},
1644     Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
1645     Volume = 85,
1646     Year = 2003}
1647    
1648     @article{gomez:2003,
1649     Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
1650     Journal = {Eur. Biophys. J.},
1651     Pages = {217-227},
1652     Title = {Setting up and optimization of membrane protein simulations},
1653     Volume = 31,
1654     Year = 2002}
1655    
1656     @article{smondyrev:1999,
1657     Author = {A.~M. Smondyrev and M.~L. Berkowitz},
1658     Journal = bj,
1659     Pages = {2472-2478},
1660     Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
1661     Volume = 76,
1662     Year = 1999}
1663    
1664     @article{nina:2002,
1665     Author = {M. Nina and T. Simonson},
1666     Journal = jpcB,
1667     Pages = {3696-3705},
1668     Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
1669     Volume = 106,
1670     Year = 2002}
1671    
1672     @article{norberg:2000,
1673     Author = {J. Norberg and L. Nilsson},
1674     Journal = bj,
1675     Pages = {1537-1553},
1676     Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
1677     Volume = 79,
1678     Year = 2000}
1679    
1680     @article{patra:2003,
1681     Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
1682     Journal = bj,
1683     Pages = {3636-3645},
1684     Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
1685     Volume = 84,
1686     Year = 2003}
1687    
1688     @article{marrink04,
1689     Author = {S.~J. Marrink and A.~H. {de~Vries} and A.~E. Mark},
1690     Journal = jpcB,
1691     Pages = {750-760},
1692     Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
1693     Volume = 108,
1694     Year = 2004}
1695    
1696     @article{andersen83,
1697     Author = {H.~C. Andersen},
1698     Journal = {J. Comp. Phys.},
1699     Pages = {24-34},
1700     Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
1701     Volume = 52,
1702     Year = 1983}
1703    
1704     @article{hura00,
1705     Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
1706     Journal = jcp,
1707     Pages = {9140-9148},
1708     Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
1709     Volume = 113,
1710     Year = 2000}
1711    
1712     @article{ryckaert77,
1713     Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
1714     Journal = {J. Comp. Phys.},
1715     Pages = {327-341},
1716     Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
1717     Volume = 23,
1718     Year = 1977}
1719    
1720     @inbook{fowles99:lagrange,
1721     Author = {G.~R. Fowles and G.~L. Cassiday},
1722     Chapter = 10,
1723     Edition = {6th},
1724     Publisher = {Saunders College Publishing},
1725     Title = {Analytical Mechanics},
1726     Year = 1999}
1727    
1728     @article{petrache00,
1729     Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
1730     Journal = bj,
1731     Pages = {3172-3192},
1732     Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
1733     Volume = 79,
1734     Year = 2000}
1735    
1736     @article{egberts88,
1737     Author = {E. Egberts and H.~J.~C. Berendsen},
1738     Journal = jcp,
1739     Pages = {3718-3732},
1740     Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
1741     Volume = 89,
1742     Year = 1988}
1743    
1744     @article{Holz00,
1745     Author = {M. Holz and S.~R. Heil and A. Sacco},
1746     Journal = {Phys. Chem. Chem. Phys.},
1747     Pages = {4740-4742},
1748     Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1749     Volume = 2,
1750     Year = 2000}
1751    
1752     @incollection{zannoni94,
1753     Author = {C. Zannoni},
1754     Booktitle = {The Molecular Dynamics of Liquid Crstals},
1755     Chapter = 6,
1756     Editor = {G.~R. Luckhurst and C.~A. Veracini},
1757     Pages = {139-169},
1758     Publisher = {Kluwer Academic Publishers},
1759     Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
1760     Year = 1994}
1761    
1762     @article{melchionna93,
1763     Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
1764     Journal = {Mol. Phys.},
1765     Pages = {533-544},
1766     Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
1767     Volume = 78,
1768     Year = 1993}
1769    
1770     @article{fennell04,
1771     Author = {C.~J. Fennell and J.~D. Gezelter},
1772     Journal = jcp,
1773     Number = 19,
1774     Pages = {9175-9184},
1775     Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
1776     Volume = 120,
1777     Year = 2004}
1778    
1779     @article{klein01,
1780     Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
1781     Journal = jpcB,
1782     Pages = {4464-4470},
1783     Title = {A coarse Grain Model for Phospholipid Simulations},
1784     Volume = 105,
1785     Year = 2001}
1786    
1787     @article{marrink03:vesicles,
1788     Author = {S.~J. Marrink and A.~E. Mark},
1789     Journal = jacs,
1790     Pages = {15233-15242},
1791     Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
1792     Volume = 125,
1793     Year = 2003}
1794    
1795     @article{FletcherReeves,
1796     Author = {R. Fletcher and C.~M. Reeves},
1797     Journal = {Comput. J.},
1798     Number = 2,
1799     Pages = {149-154},
1800     Title = {Function minimization by conjugate gradients},
1801     Volume = 7,
1802     Year = 1964}
1803    
1804     @article{PolakRibiere,
1805     Author = {E. Polak and G. Ribiere},
1806     Journal = {Rev. Fr. Inform. Rech. Oper.},
1807     Pages = {35-43},
1808     Title = {Note sur la convergence de methodes de directions conjugees},
1809     Volume = {16-R1},
1810     Year = 1969}
1811    
1812     @article{Voter:87,
1813     Author = {A.F. Voter and S.P. Chen},
1814     Journal = {Mat. Res. Soc. Symp. Proc.},
1815     Pages = {175},
1816     Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
1817     Volume = {82},
1818     Year = {1987}}
1819    
1820     @article{Hendrickson:95,
1821     Author = {Bruce Hendrickson and Steve Plimpton},
1822     Journal = {Journal of Parallel and Distributed Computing},
1823     Pages = {15-25},
1824     Title = {Parallel Many-body Simulations without All-to-All Communication},
1825     Volume = {27},
1826     Year = {1995}}
1827    
1828     @inproceedings{Paradyn,
1829     Address = {Pittsburgh, PA},
1830     Author = {S.~J. Plimpton and B.~A. Hendrickson},
1831     Booktitle = {Materials Theory and Modelling},
1832     Editor = {J. Broughton and P. Bristowe and J. Newsam},
1833     Pages = 37,
1834     Publisher = {Materials Research Society},
1835     Series = {MRS Proceedings},
1836     Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
1837     Volume = 291,
1838     Year = 1993}
1839    
1840     @article{Voter:95,
1841     Author = {A.F. Voter},
1842     Journal = {Intermetallic Compounds: Principles and Practice},
1843     Pages = {77},
1844     Title = {The Embedded-Atom Method},
1845     Volume = {1},
1846     Year = {1995}}
1847    
1848     @article{Heller:90,
1849     Author = {H. Heller and H. Grubmuller and K. Schulten},
1850     Journal = {Mol. Sim.},
1851     Pages = {133},
1852     Title = {Molecular dynamics simulation on a parallel computer},
1853     Volume = {5},
1854     Year = {1990}}
1855    
1856     @article{smd,
1857     Author = {H. Grubmuller and B. Heymann and P. Tavan},
1858     Journal = {Science},
1859     Pages = {997-999},
1860     Title = {Ligand Binding: Molecular Mechanics Calculation of The Streptavidin-Biotin Rupture Force},
1861     Volume = 271,
1862     Year = 1996}
1863    
1864     @book{Fox88,
1865     Address = {Englewood Cliffs, NJ},
1866     Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
1867     Publisher = {Prentice-Hall},
1868     Title = {Solving Promblems on Concurrent Processors},
1869     Volume = {I},
1870     Year = 1988}
1871    
1872     @article{Gromacs,
1873     Author = {H.~J.~C. Berendsen and D. {van~der~Spoel} and R. {van~Drunen}},
1874     Journal = cpc,
1875     Pages = {43-56},
1876     Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
1877     Volume = 91,
1878     Year = 1995}
1879    
1880     @article{Gromacs3,
1881     Author = {E. Lindahl and B. Hess and D. {van~der~Spoel}},
1882     Journal = {J. Mol. Modelling},
1883     Pages = {306-317},
1884     Title = {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
1885     Volume = 7,
1886     Year = 2001}
1887    
1888     @article{DL_POLY,
1889     Author = {W. Smith and T. Forester},
1890     Journal = {J. Mol. Graphics},
1891     Number = 3,
1892     Pages = {136-141},
1893     Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package },
1894     Volume = 14,
1895     Year = 1996}
1896    
1897     @article{Tinker,
1898     Author = {J.~W. Ponder and F.~M. Richards},
1899     Journal = jcc,
1900     Number = 7,
1901     Pages = {1016-1024},
1902     Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
1903     Volume = 8,
1904     Year = 1987}
1905    
1906     @article{namd,
1907     Author = {Laxmikant Kal\'{e} and Robert Skeel and Milind Bhandarkar and Robert Brunner and Attila Gursoy and Neal Krawetz and James Phillips and Aritomo Shinozaki and Krishnan Varadarajan and Klaus Schulten},
1908     Journal = {J. Comp. Phys.},
1909     Pages = {283-312},
1910     Title = {NAMD2: Greater scalability for parallel molecular dynamics},
1911     Volume = 151,
1912     Year = 1999}
1913    
1914     @article{macromodel,
1915     Author = {F. Mohamadi and N.~G.~J. Richards and W.~C. Guida and R. Liskamp and M. Lipton and C. Caufield and G. Chang and T. Hendrickson and W.~C. Still},
1916     Journal = jcc,
1917     Pages = 440,
1918     Title = {MacroModel-An Integrated Software System for Modeling Organic and Bioorganic Molecules using Molecular Mechanics},
1919     Volume = 11,
1920     Year = 1990}
1921    
1922     @article{Berendsen87,
1923     Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
1924     Journal = jpc,
1925     Pages = {6269-6271},
1926     Title = {The Missing Term in Effective Pair Potentials},
1927     Volume = 91,
1928     Year = 1987}
1929    
1930     @incollection{Berendsen81,
1931     Address = {Dordrecht},
1932     Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
1933     Booktitle = {Intermolecular Forces},
1934     Editor = {B. Pullman},
1935     Pages = 331,
1936     Publisher = {Reidel},
1937     Title = {Simple Point Charge Water},
1938     Year = 1981}
1939    
1940     @article{Mahoney00,
1941     Author = {M.~W. Mahoney and W.~L. Jorgensen},
1942     Journal = jcp,
1943     Number = 20,
1944     Pages = {8910-8922},
1945     Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
1946     Volume = 112,
1947     Year = 2000}
1948    
1949     @inproceedings{Alsing:00,
1950     Address = {Boston},
1951     Author = {Paul M. Alsing and Evangelos Coutsias and John McIver},
1952     Booktitle = {High Performance Computing in Engineering VI},
1953     Editor = {M. Ingber and H. Power and C.A. Brebbia},
1954     Pages = {81-90},
1955     Publisher = {WIT},
1956     Title = {The interfacial behavior of liquid water near hydrophobic surfaces: a parallel force decomposition molecular dynamics code},
1957     Year = {2000}}
1958    
1959     @article{Cygan04,
1960     Author = {R.~T. Cygan and J.-J. Liang and A.~G. Kalinichev},
1961     Journal = jpcb,
1962     Pages = {1255-1266},
1963     Title = {Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field},
1964     Volume = 108,
1965     Year = 2004}
1966    
1967     @article{Frenkel84,
1968     Author = {D. Frenkel and A.~J.~C. Ladd},
1969     Journal = jcp,
1970     Number = 7,
1971     Pages = {3188-3193},
1972     Title = {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
1973     Volume = 81,
1974     Year = 1984}
1975    
1976     @article{Hermens88,
1977     Author = {J. Hermans and A. Pathiaseril and A. Anderson},
1978     Journal = jacs,
1979     Pages = {5982-5986},
1980     Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
1981     Volume = 110,
1982     Year = 1988}
1983    
1984     @article{Meijer90,
1985     Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
1986     Journal = jcp,
1987     Number = 12,
1988     Pages = {7570-7575},
1989     Title = {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
1990     Volume = 92,
1991     Year = 1990}
1992    
1993     @article{Baez95a,
1994     Author = {L.~A. B\`{a}ez and P. Clancy},
1995     Journal = mp,
1996     Number = 3,
1997     Pages = {385-396},
1998     Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
1999     Volume = 86,
2000     Year = 1995}
2001    
2002     @article{Vlot99,
2003     Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
2004     Journal = jcp,
2005     Number = 1,
2006     Pages = {55-61},
2007     Title = {Free energy calculations on systems of rigid molecules: An application to the TIP4P model of H$_2$O},
2008     Volume = 110,
2009     Year = 1999}