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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2008-05-16 10:19:07 -0400
5 > %% Created for Kelsey Stocker at 2010-11-22 12:25:03 -0500
6  
7  
8 < %% Saved with string encoding Western (ASCII)
8 > %% Saved with string encoding Unicode (UTF-8)
9  
10  
11   @string{acp = {Adv. Chem. Phys.}}
# Line 47 | Line 47
47   @string{rmp = {Rev. Mod. Phys.}}
48  
49  
50 + @article{Kohanoff:2005qm,
51 +        Abstract = {We present a method for simulating clusters or, molecules subjected to an external pressure, which is exerted by a pressure-transmitting medium. It is based on the canoninical Langevin thermostat, but extended in such a way that the Brownian forces are allowed to operate only from the region exterior to the cluster. We show that the frictional force of the Langevin thermostat is linked to the pressure of the reservoir in a unique way, and that this property manifests itself when the particle it acts upon is not pointlike but has finite dimensions. By choosing appropriately the strength of the random forces and the friction coefficient, both temperature and pressure can be controlled independently. We illustrate the capabilities of this new method by calculating the compressibility of small gold clusters under pressure.},
52 +        Address = {PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY},
53 +        Author = {Kohanoff, J and Caro, A and Finnis, MW},
54 +        Date = {SEP 5 2005},
55 +        Date-Added = {2010-11-22 12:24:56 -0500},
56 +        Date-Modified = {2010-11-22 12:24:56 -0500},
57 +        Doi = {DOI 10.1002/cphc.200400607},
58 +        Journal = {ChemPhysChem},
59 +        Keywords = {clusters; gold; nanostructures; pressure; simulation},
60 +        Pages = {1848-1852},
61 +        Publisher = {WILEY-V C H VERLAG GMBH},
62 +        Timescited = {2},
63 +        Title = {An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters},
64 +        Volume = {6},
65 +        Year = {2005},
66 +        Bdsk-Url-1 = {http://dx.doi.org/10.1002/cphc.200400607}}
67 +
68 + @article{springerlink:10.1007/BF00977785,
69 +        Author = {Lee, D. T. and Schachter, B. J.},
70 +        Date-Added = {2010-11-22 12:24:49 -0500},
71 +        Date-Modified = {2010-11-22 12:24:49 -0500},
72 +        Issn = {0885-7458},
73 +        Issue = {3},
74 +        Journal = {International Journal of Parallel Programming},
75 +        Keyword = {Computer Science},
76 +        Note = {10.1007/BF00977785},
77 +        Pages = {219-242},
78 +        Publisher = {Springer Netherlands},
79 +        Title = {Two algorithms for constructing a Delaunay triangulation},
80 +        Url = {http://dx.doi.org/10.1007/BF00977785},
81 +        Volume = {9},
82 +        Year = {1980},
83 +        Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00977785}}
84 +
85 + @article{delaunay,
86 +        Author = {B. Delaunay},
87 +        Date-Added = {2010-11-22 12:24:45 -0500},
88 +        Date-Modified = {2010-11-22 12:24:45 -0500},
89 +        Journal = {Bull. Acad. Science USSR VII:Class. Sci. Mat. Nat.},
90 +        Pages = {793-800},
91 +        Title = {Sur la sph{\`e}re vide},
92 +        Year = {1934}}
93 +
94 + @article{EDELSBRUNNER:1994oq,
95 +        Abstract = {Frequently, data in scientific computing is in its abstract form a finite point set in space, and it is sometimes useful or required to compute what one might call the ''shape'' of the set. For that purpose, this article introduces the formal notion of the family of alpha-shapes of a finite point set in R3. Each shape is a well-defined polytope, derived from the Delaunay triangulation of the point set, with a parameter alpha is-an-element-of R controlling the desired level of detail. An algorithm is presented that constructs the entire family of shapes for a given set of size n in time O(n2), worst case. A robust implementation of the algorithm is discussed, and several applications in the area of scientific computing are mentioned.},
96 +        Address = {1515 BROADWAY, NEW YORK, NY 10036},
97 +        Author = {Edelsbrunner, H and Mucke, E.~P.},
98 +        Date = {JAN 1994},
99 +        Date-Added = {2010-11-22 12:24:34 -0500},
100 +        Date-Modified = {2010-11-22 12:24:34 -0500},
101 +        Journal = {ACM Transactions On Graphics},
102 +        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
103 +        Pages = {43-72},
104 +        Publisher = {ASSOC COMPUTING MACHINERY},
105 +        Timescited = {270},
106 +        Title = {3-DIMENSIONAL ALPHA-SHAPES},
107 +        Volume = {13},
108 +        Year = {1994}}
109 +
110 + @article{Barber96,
111 +        Author = {C.~B. Barber and D.~P. Dobkin and H.~T. Huhdanpaa},
112 +        Date-Added = {2010-11-22 12:24:25 -0500},
113 +        Date-Modified = {2010-11-22 12:24:25 -0500},
114 +        Journal = {ACM Trans. Math. Software},
115 +        Pages = {469-483},
116 +        Title = {The Quickhull Algorithm for Convex Hulls},
117 +        Volume = 22,
118 +        Year = 1996}
119 +
120 + @book{Schlick2002,
121 +        Address = {Secaucus, NJ, USA},
122 +        Author = {Tamar Schlick},
123 +        Date-Added = {2010-11-22 12:24:11 -0500},
124 +        Date-Modified = {2010-11-22 12:24:11 -0500},
125 +        Isbn = {038795404X},
126 +        Publisher = {Springer-Verlag New York, Inc.},
127 +        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
128 +        Year = {2002}}
129 +
130 + @article{Sun:2008fk,
131 +        Abstract = {We present an algorithm for carrying out Langevin dynamics simulations on complex rigid bodies by incorporating the hydrodynamic resistance tensors for arbitrary shapes into an advanced rotational integration scheme. The integrator gives quantitative agreement with both analytic and approximate hydrodynamic theories for a number of model rigid bodies and works well at reproducing the solute dynamical properties (diffusion constants and orientational relaxation times) obtained from explicitly solvated simulations. (C) 2008 American Institute of Physics.},
132 +        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
133 +        Author = {Sun, Xiuquan and Lin, Teng and Gezelter, J. Daniel},
134 +        Date-Added = {2010-11-22 12:24:00 -0500},
135 +        Date-Modified = {2010-11-22 12:24:00 -0500},
136 +        Doi = {DOI 10.1063/1.2936991},
137 +        Isi = {000256936700007},
138 +        Isi-Recid = {171639081},
139 +        Isi-Ref-Recids = {74848920 50663994 119330651 134477260 22939933 131802420 114632880 64190493 55802797 21189309 75892319 21406638 110293282 113408519 96782216 130078852 17359022 100665361 113671463 49951397 123367767 123367728 154386980 102422498 35241737 32391149 6325223 127852571 58929276 95157449 32334819 42562624 12736689 163240533 130556111 122778971 51825394 49588888 145030437 101277182 101670714 148588118 73818708 142688207 124629108 18817706 103995016 149522882 50793 47098 109491995 114073447 108180005 98728780 112132273 16915130 31384453 127055599 134786719 131544581 124299358 1555937 160750161 85968524 163240534},
140 +        Journal = {J. Chem. Phys.},
141 +        Month = jun,
142 +        Number = {23},
143 +        Publisher = {AMER INST PHYSICS},
144 +        Times-Cited = {2},
145 +        Title = {Langevin dynamics for rigid bodies of arbitrary shape},
146 +        Volume = {128},
147 +        Year = {2008},
148 +        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000256936700007}}
149 +
150 + @article{GarciadelaTorreJ2002,
151 +        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
152 +        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.},
153 +        Date-Added = {2010-11-22 12:23:52 -0500},
154 +        Date-Modified = {2010-11-22 12:23:52 -0500},
155 +        Journal = {Biopolymers},
156 +        Number = {3},
157 +        Pages = {163-167},
158 +        Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits},
159 +        Volume = {63},
160 +        Year = {2002}}
161 +
162 + @article{Garcia-de-la-Torre:2001wd,
163 +        Abstract = { The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program () which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.},
164 +        Author = {{Garc\'{i}a de la Torre}, Jose},
165 +        Date-Added = {2010-11-22 12:23:48 -0500},
166 +        Date-Modified = {2010-11-22 12:23:48 -0500},
167 +        Journal = {Biophysical Chemistry},
168 +        Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure},
169 +        Number = {3},
170 +        Pages = {265--274},
171 +        Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape},
172 +        Ty = {JOUR},
173 +        Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953},
174 +        Volume = {94},
175 +        Year = {2001},
176 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}}
177 +
178 + @article{JoseGarciadelaTorre02012000,
179 +        Abstract = {The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.
180 + },
181 +        Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz},
182 +        Date-Added = {2010-11-22 12:23:36 -0500},
183 +        Date-Modified = {2010-11-22 12:23:36 -0500},
184 +        Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf},
185 +        Journal = bj,
186 +        Number = {2},
187 +        Pages = {719-730},
188 +        Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}},
189 +        Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719},
190 +        Volume = {78},
191 +        Year = {2000},
192 +        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/78/2/719}}
193 +
194   @article{Fennell06,
195          Author = {C.~J. Fennell and J.~D. Gezelter},
196          Date-Added = {2008-05-16 10:19:01 -0400},
# Line 148 | Line 292
292          Journal = prl,
293          Number = 21,
294          Pages = {4648-4651},
295 <        Title = {Connected Network of Minima as a Model Glass: Long                   Time Dynamics},
295 >        Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
296          Volume = 81,
297          Year = 1998}
298  
# Line 175 | Line 319
319          Journal = jcp,
320          Number = 6,
321          Pages = {2742-2746},
322 <        Title = {The effect of density on the inherent structure in                   liquids},
322 >        Title = {The effect of density on the inherent structure in liquids},
323          Volume = 80,
324          Year = 1984}
325  
# Line 184 | Line 328
328          Journal = jcp,
329          Number = 9,
330          Pages = {4767-4775},
331 <        Title = {Inherent structure theory of liquids in the                   hard-sphere limit},
331 >        Title = {Inherent structure theory of liquids in the hard-sphere limit},
332          Volume = 83,
333          Year = 1985}
334  
# Line 192 | Line 336
336          Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
337          Journal = {Nature},
338          Pages = {554-557},
339 <        Title = {Signatures of distinct dynamical regimes in the                   energy landscape of a glass-forming liquid},
339 >        Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
340          Volume = 393,
341          Year = 1998}
342  
# Line 201 | Line 345
345          Journal = jcp,
346          Number = 6,
347          Pages = {2698-2704},
348 <        Title = {Dense liquids. I. The effect of density and                   temperature on viscosity of tetramethylsilane and                   benzene-$\mbox{D}_6$},
348 >        Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
349          Volume = 63,
350          Year = 1975}
351  
# Line 210 | Line 354
354          Journal = jcp,
355          Number = 6,
356          Pages = {2705-2709},
357 <        Title = {Dense liquids. II. The effect of density and                   temperature on viscosity of tetramethylsilane and                   benzene },
357 >        Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
358          Volume = 63,
359          Year = 1975}
360  
# Line 218 | Line 362
362          Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
363          Journal = {J. Chem. Soc. - Faraday Transactions},
364          Pages = {613-619},
365 <        Title = {Antibiotic activity of valinomycin - Molecular                   dynamics simulations involving the water/membrane                   interface},
365 >        Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
366          Volume = 93,
367          Year = 1997}
368  
# Line 226 | Line 370
370          Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
371          Journal = bj,
372          Pages = {2786-2801},
373 <        Title = {A molecular dynamics study of the pores formed by                   Escherichia coli OmpF porin in a fully hydrated                   palmitoyloleoylphosphatidylcholine bilayer},
373 >        Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
374          Volume = 74,
375          Year = 1998}
376  
# Line 234 | Line 378
378          Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
379          Journal = {J. Phys. Chem. B},
380          Pages = {625-631},
381 <        Title = {Anaesthetic mechanism on a model biological                   membrane: A molecular dynamics simulation study},
381 >        Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
382          Volume = 102,
383          Year = 1998}
384  
# Line 242 | Line 386
386          Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
387          Journal = {J. Am. Chem. Soc.},
388          Pages = {4118-4129},
389 <        Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID                   BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
389 >        Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
390          Volume = 117,
391          Year = 1995}
392  
# Line 250 | Line 394
394          Author = {H.~E. Alper and T.~R. Stouch},
395          Journal = {J. Phys. Chem.},
396          Pages = {5724-5731},
397 <        Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN                   BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
397 >        Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
398          Volume = 99,
399          Year = 1995}
400  
# Line 258 | Line 402
402          Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
403          Journal = {J. Chem. Phys.},
404          Pages = {4699-4704},
405 <        Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF                   SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
405 >        Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
406          Volume = 96,
407          Year = 1992}
408  
# Line 266 | Line 410
410          Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
411          Journal = prl,
412          Pages = {3649},
413 <        Title = {Direct Observation of Stretched-Exponential                   Relaxation in Low-Temperature Lennard-Jones Systems                   Using the Cage Correlation Function},
413 >        Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
414          Volume = 82,
415          Year = {1999}}
416  
# Line 274 | Line 418
418          Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
419          Journal = {J. Chem. Phys.},
420          Pages = {6867-6876},
421 <        Title = {Calculating the hopping rate for self-diffusion on                   rough potential energy surfaces: Cage correlations},
421 >        Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
422          Volume = 107,
423          Year = 1997}
424  
# Line 282 | Line 426
426          Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
427          Journal = jcp,
428          Pages = 3444,
429 <        Title = {Methods for calculating the hopping rate for                   orientational and spatial diffusion in a molecular                   liquid: $\mbox{CS}_{2}$},
429 >        Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
430          Volume = 110,
431          Year = 1999}
432  
# Line 290 | Line 434
434          Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
435          Journal = jcp,
436          Pages = 4695,
437 <        Title = {Response to 'Comment on a Critique of the                   Instantaneous Normal Mode (INM) Approach to                   Diffusion'},
437 >        Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
438          Volume = 109,
439          Year = 1998}
440  
# Line 298 | Line 442
442          Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
443          Journal = jcp,
444          Pages = 4618,
445 <        Title = {Can imaginary instantaneous normal mode frequencies                   predict barriers to self-diffusion?},
445 >        Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
446          Volume = 107,
447          Year = 1997}
448  
# Line 306 | Line 450
450          Author = {R. Zwanzig},
451          Journal = jcp,
452          Pages = {4507-4508},
453 <        Title = {On the relation between self-diffusion and viscosity                   of liquids},
453 >        Title = {On the relation between self-diffusion and viscosity of liquids},
454          Volume = 79,
455          Year = 1983}
456  
# Line 322 | Line 466
466          Author = {F.~H. Stillinger},
467          Journal = {Science},
468          Pages = {1935-1939},
469 <        Title = {A Topographic View of Supercooled Liquids and Glass                   Formation},
469 >        Title = {A Topographic View of Supercooled Liquids and Glass Formation},
470          Volume = 267,
471          Year = 1995}
472  
# Line 332 | Line 476
476          Booktitle = {Relaxations in Complex Systems},
477          Editor = {K.~Ngai and G.~B. Wright},
478          Pages = 1,
479 <        Publisher = {National Technical Information Service,                   U.S. Department of Commerce},
479 >        Publisher = {National Technical Information Service, U.S. Department of Commerce},
480          Title = {unknown},
481          Year = 1985}
482  
# Line 348 | Line 492
492          Author = {X. Sun and W.~H. Miller},
493          Journal = jcp,
494          Pages = 6346,
495 <        Title = {Semiclassical initial value representation for                   electronically nonadiabatic molecular dynamics},
495 >        Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
496          Volume = 106,
497          Year = 1997}
498  
# Line 356 | Line 500
500          Author = {B.~W. Spath and W.~H. Miller},
501          Journal = jcp,
502          Pages = 95,
503 <        Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION                   PROBABILITIES},
503 >        Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
504          Volume = 104,
505          Year = 1996}
506  
# Line 364 | Line 508
508          Address = {New York},
509          Author = {Arieh Warshel},
510          Publisher = {Wiley},
511 <        Title = {Computer modeling of chemical reactions in enzymes                   and solutions},
511 >        Title = {Computer modeling of chemical reactions in enzymes and solutions},
512          Year = 1991}
513  
514   @article{Vuilleumier97,
515          Author = {Rodolphe Vuilleumier and Daniel Borgis},
516          Journal = jpc,
517 <        Title = {Molecular Dynamics of an excess proton in water                   using a non-additive valence bond force field},
517 >        Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
518          Volume = {in press},
519          Year = 1997}
520  
# Line 378 | Line 522
522          Author = {W. Kob and H.~C. Andersen},
523          Journal = pre,
524          Pages = {4626-4641},
525 <        Title = {Testing mode-coupling theory for a supercooled                   binary Lennard-Jones mixtures: The van Hove                   corraltion function},
525 >        Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
526          Volume = 51,
527          Year = 1995}
528  
# Line 386 | Line 530
530          Author = {W. Kob and H.~C. Andersen},
531          Journal = pre,
532          Pages = {4134-4153},
533 <        Title = {Testing mode-coupling theory for a supercooled                   binary Lennard-Jones mixtures. II. Intermediate                   scattering function and dynamic susceptibility},
533 >        Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
534          Volume = 52,
535          Year = 1995}
536  
# Line 405 | Line 549
549          Author = {X. Sun and W.~H. Miller},
550          Journal = jcp,
551          Pages = 916,
552 <        Title = {Mixed semiclassical-classical approaches to the                   dynamics of complex molecular systems},
552 >        Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
553          Year = 1997}
554  
555   @article{Keshavamurthy94,
# Line 428 | Line 572
572          Author = {Y.-T. Chang and W.~H. Miller},
573          Journal = jpc,
574          Pages = {5884-5888},
575 <        Title = {An Empirical Valence Bond Model for Constructing                   Global Potential Energy Surfaces for Chemical                   Reactions of Polyatomic Molecular Systems},
575 >        Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
576          Volume = 94,
577          Year = 1990}
578  
# Line 436 | Line 580
580          Author = {P.W. Shor},
581          Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
582          Pages = {124-134},
583 <        Title = {Algorithms for quantum computation: discrete                   logarithms and factoring},
583 >        Title = {Algorithms for quantum computation: discrete logarithms and factoring},
584          Year = 1994}
585  
586   @article{Feynman82,
# Line 451 | Line 595
595          Author = {L.~K. Grover},
596          Journal = prl,
597          Pages = {4709-4712},
598 <        Title = {Quantum computers can search arbitrarily large                   databases by a single query},
598 >        Title = {Quantum computers can search arbitrarily large databases by a single query},
599          Volume = 79,
600          Year = 1997}
601  
# Line 464 | Line 608
608          Year = 1998}
609  
610   @article{Monroe95,
611 <        Author = {C. Monroe and D.~M. Meekhof and B.~E. King and                   W.~M. Itano and D.~J. Wineland},
611 >        Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
612          Journal = prl,
613          Pages = 4714,
614          Title = {Demonstration of a fundamental quantum logic gate},
# Line 472 | Line 616
616          Year = 1995}
617  
618   @article{Lent93,
619 <        Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and                   G.~H. Bernstein},
619 >        Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
620          Journal = {Nanotechnology},
621          Pages = {49-57},
622          Title = {Quantum Cellular Automata},
# Line 480 | Line 624
624          Year = 1993}
625  
626   @article{Barenco95,
627 <        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},
627 >        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},
628          Journal = {Phys. Rev. A},
629          Pages = {3457-3467},
630          Title = {elementary gates for quantum computation},
# Line 491 | Line 635
635          Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
636          Journal = jcp,
637          Pages = {457-466},
638 <        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},
638 >        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},
639          Volume = 106,
640          Year = 1997}
641  
# Line 499 | Line 643
643          Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
644          Journal = prl,
645          Pages = 77,
646 <        Title = {A perfect quantum error correcting code: 5 bit code                   correcting a general 1 qubit error to encode 1 qubit                   of information},
646 >        Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
647          Volume = 98,
648          Year = 1996}
649  
# Line 531 | Line 675
675          Author = {J.~D. Gezelter and W.~H. Miller},
676          Journal = jcp,
677          Pages = {7868-7876},
678 <        Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE                   RATE OF KETENE ISOMERIZATION},
678 >        Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
679          Volume = 103,
680          Year = 1995}
681  
# Line 544 | Line 688
688          Year = 1992}
689  
690   @article{Paula96,
691 <        Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and                   T.~H. Haines and D.~W. Deamer},
691 >        Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
692          Journal = bj,
693          Pages = {339-348},
694 <        Title = {Permeation of protons, potassium ions, and small                   polar molecules through phospholipid bilayers as a                   function of membrane thickness},
694 >        Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
695          Volume = 70,
696          Year = 1996}
697  
# Line 555 | Line 699
699          Author = {H.~J. Little},
700          Journal = {Pharmacology \& Therapeutics},
701          Pages = {37-58},
702 <        Title = {How has molecular pharmacology contributed to our                   understanding of the mechanism(s) of general                   anesthesia?},
702 >        Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
703          Volume = 69,
704          Year = 1996}
705  
# Line 563 | Line 707
707          Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
708          Journal = jpc,
709          Pages = {10497-10506},
710 <        Title = {Nonequilibrium Molecular Dynamics Simulation of                   Oxygen Diffusion through Hexadecane Monolayers with                   Varying Concentrations of Cholesterol},
710 >        Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
711          Volume = 96,
712          Year = 1992}
713  
714   @article{Venable93,
715 <        Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and                   R.~W. Pastor},
715 >        Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
716          Journal = {Science},
717          Pages = {223-226},
718 <        Title = {Molecular Dynamics Simulations of a Lipid Bilayer                   and of Hexadecane: An Investigation of Membrane Fluidity},
718 >        Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
719          Volume = 262,
720          Year = 1993}
721  
# Line 579 | Line 723
723          Author = {U. Essmann and M.~L. Berkowitz},
724          Journal = bj,
725          Pages = {2081-2089},
726 <        Title = {Dynamical properties of phospholipid bilayers from                   computer simulation},
726 >        Title = {Dynamical properties of phospholipid bilayers from computer simulation},
727          Volume = 76,
728          Year = 1999}
729  
# Line 587 | Line 731
731          Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
732          Journal = bj,
733          Pages = {2123-2134},
734 <        Title = {Effects of anesthetics on the structure of a                   phospholipid bilayer: Molecular dynamics                   investigation of halothane in the hydrated liquid                   crystal phase of dipalmitoylphosphatidylcholine},
734 >        Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
735          Volume = 75,
736          Year = 1998}
737  
# Line 595 | Line 739
739          Author = {R. Pomes and B. Roux},
740          Journal = bj,
741          Pages = {19-39},
742 <        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},
742 >        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},
743          Volume = 71,
744          Year = 1996}
745  
# Line 603 | Line 747
747          Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
748          Journal = {J. Appl. Phys.},
749          Pages = {1136-1137},
750 <        Title = {Continuous Series of Metastable Solid Solutions in                   Silver-Copper Alloys},
750 >        Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
751          Volume = 31,
752          Year = 1960}
753  
# Line 611 | Line 755
755          Author = {A. Peker and W.~L. Johnson},
756          Journal = {Appl. Phys. Lett.},
757          Pages = {2342-2344},
758 <        Title = {A highly processable metallic-glass -                   $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
758 >        Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
759          Volume = 63,
760          Year = 1993}
761  
# Line 624 | Line 768
768          Year = 1997}
769  
770   @article{Sun96,
771 <        Author = {X. Sun and S. Schneider and U. Geyer and                   W.~L. Johnson and M.~A. Nicolet},
771 >        Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
772          Journal = {J. Mater. Res.},
773          Pages = {2738-2743},
774 <        Title = {Oxidation and crystallization of an amorphous                   $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
774 >        Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
775          Volume = 11,
776          Year = 1996}
777  
# Line 635 | Line 779
779          Author = {H. Heller and M. Schaefer and K. Schulten},
780          Journal = jpc,
781          Pages = {8343-8360},
782 <        Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200                   LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
782 >        Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
783          Volume = 97,
784          Year = 1993}
785  
# Line 651 | Line 795
795          Author = {R. Berardi and S. Orlandi and C Zannoni},
796          Journal = cpl,
797          Pages = {357-362},
798 <        Title = {Antiphase structures in polar smectic liquid                   crystals and their molecular origin},
798 >        Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
799          Volume = 261,
800          Year = 1996}
801  
# Line 659 | Line 803
803          Author = {R. Berardi and S. Orlandi and C. Zannoni},
804          Journal = {Int. J. Mod. Phys. C},
805          Pages = {477-484},
806 <        Title = {Monte Carlo simulations of rod-like Gay-Berne                   mesogens with transverse dipoles},
806 >        Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
807          Volume = 10,
808          Year = 1999}
809  
# Line 667 | Line 811
811          Author = {K. Pasterny and E. Gwozdz and A. Brodka},
812          Journal = {J. Mol. Liq.},
813          Pages = {173-184},
814 <        Title = {Properties of a model liquid crystal: Polar                   Gay-Berne particles},
814 >        Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
815          Volume = 85,
816          Year = 2000}
817  
818   @article{Jorgensen83,
819 <        Author = {W.~L. Jorgensen and J. Chandrasekhar and                   J.~D. Madura and R.~W. Impey and M.~L. Klein},
819 >        Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
820          Journal = jcp,
821          Pages = {926-935},
822 <        Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR                   SIMULATING LIQUID WATER},
822 >        Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
823          Volume = 79,
824          Year = 1983}
825  
# Line 691 | Line 835
835          Author = {G.~R. Luckhurst and R.~A. Stephens and R.~W. Phippen},
836          Journal = {Liquid Crystals},
837          Pages = {451-464},
838 <        Title = {Computer simulation studies of anisotropic systems                   {XIX}. Mesophases formed by the Gay-Berne model mesogen},
838 >        Title = {Computer simulation studies of anisotropic systems {XIX}. Mesophases formed by the Gay-Berne model mesogen},
839          Volume = 8,
840          Year = 1990}
841  
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843          Author = {J.~G. Gay and B.~J. Berne},
844          Journal = jcp,
845          Pages = {3316-3319},
846 <        Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A                   LINEAR SITE-SITE POTENTIAL},
846 >        Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
847          Volume = 74,
848          Year = 1981}
849  
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856          Year = 1972}
857  
858   @article{Perram96,
859 <        Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and                   J.~L. Lebowitz},
859 >        Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
860          Journal = pre,
861          Pages = {6565-6572},
862 <        Title = {Ellipsoid contact potential: Theory and relation to                   overlap potentials},
862 >        Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
863          Volume = 54,
864          Year = 1996}
865  
866   @article{Cornell95,
867 <        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},
867 >        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},
868          Journal = jacs,
869          Pages = {5179-5197},
870 <        Title = {A second generation force field for the simulation                   of proteins and nucleic acids},
870 >        Title = {A second generation force field for the simulation of proteins and nucleic acids},
871          Volume = 117,
872          Year = 1995}
873  
874   @article{Brooks83,
875 <        Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson                   and D.~J. States and S. Swaminathan and M. Karplus},
875 >        Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
876          Journal = jcc,
877          Pages = {187-217},
878          Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
# Line 737 | Line 881
881  
882   @incollection{MacKerell98,
883          Address = {New York},
884 <        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},
884 >        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},
885          Booktitle = {The Encyclopedia of Computational Chemistry},
886          Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
887          Pages = {271-277},
888          Publisher = {John Wiley \& Sons},
889 <        Title = {{\sc charmm}: The Energy Function and Its Parameterization                   with an Overview of the Program},
889 >        Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
890          Volume = 1,
891          Year = 1998}
892  
# Line 761 | Line 905
905          Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
906          Journal = prl,
907          Pages = 467,
908 <        Title = {Reply to `Comment on ``Direct Observation of                   Stretched-Exponential Relaxation in Low-Temperature                   Lennard-Jones Systems Using th eCage Correlation                   Function'' '},
908 >        Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
909          Volume = 85,
910          Year = 2000}
911  
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920          Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
921          Journal = {J. Biol. Chem.},
922          Pages = {6068-6078},
923 <        Title = {Temperature and Compositional Dependence of the                   Structure of Hydrated Dimyristoyl Lecithin},
923 >        Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
924          Volume = 254,
925          Year = 1979}
926  
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928          Address = {Tucson},
929          Author = {Sheila Tobias},
930          Publisher = {Research Corp.},
931 <        Title = {They're not Dumb. They're Different: Stalking the                   Second Tier},
931 >        Title = {They're not Dumb. They're Different: Stalking the Second Tier},
932          Year = 1990}
933  
934   @article{Mazur92,
935          Author = {E. Mazur},
936          Journal = {Optics and Photonics News},
937          Pages = 38,
938 <        Title = {Qualitative vs. Quantititative Thinking: Are we                   teaching the right thing? },
938 >        Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing?},
939          Volume = 3,
940          Year = 1992}
941  
# Line 806 | Line 950
950          Author = {E.~P. Wigner},
951          Journal = {Annals of Mathematics},
952          Pages = {548-564},
953 <        Title = {Characteristic Vectors of Bordered Matrices with                   Infinite Dimensions},
953 >        Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
954          Volume = 62,
955          Year = 1955}
956  
# Line 814 | Line 958
958          Author = {C. Gaukel and H.~R. Schober},
959          Journal = {Solid State Comm.},
960          Pages = {1-5},
961 <        Title = {Diffusion Mechanisms in under-cooled Binary Metal                   Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
961 >        Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
962          Volume = 107,
963          Year = 1998}
964  
965   @article{Qi99,
966 <        Author = {Y. Qi and T. \c{C}a\v{g}in and Y.                   Kimura and W.~A. {Goddard III}},
966 >        Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
967          Journal = prb,
968          Number = 5,
969          Pages = {3527-3533},
970 <        Title = {Molecular-dynamics simulations of glass formation                   and crystallization in binary liquid metals: $\mbox{Cu-Ag}$                   and $\mbox{Cu-Ni}$},
970 >        Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
971          Volume = 59,
972          Year = 1999}
973  
# Line 853 | Line 997
997  
998   @inproceedings{Barker80,
999          Author = {J.~A. Barker},
1000 <        Booktitle = {The problem of long-range forces in the computer                   simulation of condensed matter},
1000 >        Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
1001          Editor = {D. Ceperley},
1002          Pages = {45-6},
1003          Series = {NRCC Workshop Proceedings},
# Line 874 | Line 1018
1018          Journal = prb,
1019          Number = 12,
1020          Pages = {6443-6453},
1021 <        Title = {Embedded-atom method: Derivation and application to                   impurities, surfaces, and other defects in metals},
1021 >        Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
1022          Volume = 29,
1023          Year = 1984}
1024  
# Line 890 | Line 1034
1034          Author = {J. Lu and J.~A. Szpunar},
1035          Journal = {Phil. Mag. A},
1036          Pages = {1057-1066},
1037 <        Title = {Applications of the embedded-atom method to glass                   formation and crystallization of liquid and glass                   transition-metal nickel},
1037 >        Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
1038          Volume = {75},
1039          Year = {1997}}
1040  
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1058          Author = {A. Blumen and J. Klafter and G. Zumofen},
1059          Journal = {Phys. Rev. B},
1060          Pages = {3429-3435},
1061 <        Title = {Recombination in amorphous materials as a                   continuous-time random-walk problem},
1061 >        Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
1062          Volume = 27,
1063          Year = 1983}
1064  
# Line 922 | Line 1066
1066          Author = {J. Klafter and G. Zumofen},
1067          Journal = jpc,
1068          Pages = {7366-7370},
1069 <        Title = {Probability Distributions for Continuous-Time Random                   Walks with Long Tails},
1069 >        Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
1070          Volume = 98,
1071          Year = 1994}
1072  
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1074          Author = {M. Dzugutov},
1075          Journal = pra,
1076          Pages = {R2984-R2987},
1077 <        Title = {Glass formation in a simple monatomic liquid with                   icosahedral inherent local order},
1077 >        Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
1078          Volume = 46,
1079          Year = 1992}
1080  
# Line 938 | Line 1082
1082          Author = {P. Moore and T. Keyes},
1083          Journal = jcp,
1084          Pages = 6709,
1085 <        Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity                   Correlation Functions and Self-Diffusion Constants},
1085 >        Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
1086          Volume = 100,
1087          Year = 1994}
1088  
# Line 954 | Line 1098
1098          Author = {B. Madan and T. Keyes and G. Seeley},
1099          Journal = jcp,
1100          Pages = {7565-7569},
1101 <        Title = {Diffusion in supercooled liquids via normal mode                   analysis},
1101 >        Title = {Diffusion in supercooled liquids via normal mode analysis},
1102          Volume = 92,
1103          Year = 1990}
1104  
# Line 962 | Line 1106
1106          Author = {B. Madan and T. Keyes and G. Seeley},
1107          Journal = jcp,
1108          Pages = {6762-6769},
1109 <        Title = {Normal mode analysis of the velocity correlation                   function in supercooled liquids},
1109 >        Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
1110          Volume = 94,
1111          Year = 1991}
1112  
# Line 970 | Line 1114
1114          Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
1115          Journal = jcp,
1116          Pages = {8522-8535},
1117 <        Title = {The short-time dynamics of molecular                   liquids. Instantaneous-normal-mode theory},
1117 >        Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
1118          Volume = 97,
1119          Year = 1992}
1120  
# Line 978 | Line 1122
1122          Author = {Yi. Wan and R.~M. Stratt},
1123          Journal = jcp,
1124          Pages = {5123-5138},
1125 <        Title = {Liquid theory for the instantaneous normal modes of                   a liquid},
1125 >        Title = {Liquid theory for the instantaneous normal modes of a liquid},
1126          Volume = 100,
1127          Year = 1994}
1128  
# Line 994 | Line 1138
1138          Author = {G.~V. Vijayadamodar and A. Nitzan},
1139          Journal = jcp,
1140          Pages = {2169-2177},
1141 <        Title = {On the application of instantaneous normal mode                   analysis to long time dynamics of liquids},
1141 >        Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
1142          Volume = 103,
1143          Year = 1995}
1144  
# Line 1010 | Line 1154
1154          Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
1155          Journal = jcp,
1156          Pages = {4693-4694},
1157 <        Title = {Comment on a critique of the instantaneous normal                   mode (INM) approach to diffusion                   (J. Chem. Phys. {\bf 107}, 4618 (1997))},
1157 >        Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
1158          Volume = 109,
1159          Year = 1998}
1160  
# Line 1018 | Line 1162
1162          Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
1163          Journal = jcp,
1164          Pages = {5175-5176},
1165 <        Title = {Transport coefficients of liquid transition metals:                   A computer simulation study using the embedded atom                   model},
1165 >        Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
1166          Volume = 109,
1167          Year = 1998}
1168  
1169   @article{Belonoshko00,
1170 <        Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and                   B. Johansson},
1170 >        Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
1171          Journal = prb,
1172          Pages = {3838-3844},
1173          Title = {Quasi ab initio molecular dynamic study of Cu melting},
# Line 1031 | Line 1175
1175          Year = 2000}
1176  
1177   @article{Banhart92,
1178 <        Author = {J. Banhart and H. Ebert and R. Kuentzler and                   J. Voitl\"{a}nder},
1178 >        Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
1179          Journal = prb,
1180          Pages = {9968-9975},
1181 <        Title = {Electronic properties of single-phased metastable                   Ag-Cu alloys},
1181 >        Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
1182          Volume = 46,
1183          Year = 1992}
1184  
# Line 1063 | Line 1207
1207  
1208   @book{pliny,
1209          Author = {Pliny},
1066 –        Publisher = { },
1210          Title = {Hist. Nat.},
1211 <        Volume = {XXXVI},
1069 <        Year = { }}
1211 >        Volume = {XXXVI}}
1212  
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1214          Author = {K. Anheuser and J.P. Northover},
# Line 1088 | Line 1230
1230          Author = {K.~L. Ngai and F.-S. Liu},
1231          Journal = prb,
1232          Pages = {1049-1065},
1233 <        Title = {Dispersive diffusion transport and noise,                   time-dependent diffusion coefficient, generalized                   Einstein-Nernst relation, and dispersive                   diffusion-controlled unimolecular and bimolecular                   reactions},
1233 >        Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
1234          Volume = 24,
1235          Year = 1981}
1236  
# Line 1121 | Line 1263
1263          Year = 1920}
1264  
1265   @article{Nagel96,
1266 <        Author = {M.D. Ediger and  C.A. Angell and Sidney R. Nagel},
1266 >        Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
1267          Journal = jpc,
1268          Pages = 13200,
1269          Title = {Supercooled Liquids and Glasses},
# Line 1151 | Line 1293
1293          Author = {J. Klafter and M.~F. Shlesinger},
1294          Journal = {Proc. Natl. Acad. Sci. USA},
1295          Pages = {848-851},
1296 <        Title = {On the relationship among three theories of                   relaxation in disordered systems},
1296 >        Title = {On the relationship among three theories of relaxation in disordered systems},
1297          Volume = 83,
1298          Year = 1986}
1299  
# Line 1159 | Line 1301
1301          Author = {Z. Li and M. Lieberman and W. Hill},
1302          Journal = {Langmuir},
1303          Pages = {4887-4894},
1304 <        Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine                   Monolayers: umbrella vs. octopus design strategies                   for formation of oriented {\sc sam}s},
1304 >        Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
1305          Volume = 17,
1306          Year = 2001}
1307  
# Line 1210 | Line 1352
1352          Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1353          Journal = jpc,
1354          Pages = {5212-5218},
1355 <        Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC                   PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1355 >        Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
1356          Volume = 97,
1357          Year = 1992}
1358  
# Line 1218 | Line 1360
1360          Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1361          Journal = {Physica A},
1362          Pages = {248-252},
1363 <        Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION                   OF VERY ELONGATED PARTICLES},
1363 >        Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
1364          Volume = 191,
1365          Year = 1992}
1366  
# Line 1233 | Line 1375
1375          Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
1376          Journal = jcp,
1377          Pages = 1607,
1378 <        Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL                   ADSORPTION},
1378 >        Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
1379          Volume = 103,
1380          Year = 1995}
1381  
# Line 1241 | Line 1383
1383          Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
1384          Journal = {Physica A},
1385          Pages = {248-252},
1386 <        Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC                   PARTICLES},
1386 >        Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
1387          Volume = 191,
1388          Year = 1992}
1389  
# Line 1249 | Line 1391
1391          Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
1392          Journal = jcp,
1393          Pages = 9164,
1394 <        Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND                    EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1394 >        Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
1395          Volume = 101,
1396          Year = 1994}
1397  
# Line 1257 | Line 1399
1399          Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
1400          Journal = {Langmuir},
1401          Pages = {5127-5132},
1402 <        Title = {Diffusional Deposition of Charged Latex Particles on                   Water-Solid Interfaces at Low Ionic Strength},
1402 >        Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
1403          Volume = 14,
1404          Year = 1998}
1405  
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1415          Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
1416          Journal = {Physica A},
1417          Pages = {1-10},
1418 <        Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING                   D-DIMENSIONAL CUBES},
1418 >        Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
1419          Volume = 198,
1420          Year = 1993}
1421  
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1423          Address = {New York},
1424          Author = {D. Frenkel and B. Smit},
1425          Publisher = {Academic Press},
1426 <        Title = {Understanding Molecular Simulation : From Algorithms                   to Applications},
1426 >        Title = {Understanding Molecular Simulation : From Algorithms to Applications},
1427          Year = 1996}
1428  
1429   @article{Dullweber1997,
# Line 1289 | Line 1431
1431          Journal = jcp,
1432          Number = 15,
1433          Pages = {5840-5851},
1434 <        Title = {Symplectic splitting methods for rigid body molecular                    dynamics},
1434 >        Title = {Symplectic splitting methods for rigid body molecular dynamics},
1435          Volume = 107,
1436          Year = 1997}
1437  
# Line 1297 | Line 1439
1439          Author = {M. Martin and J.~I. Siepmann},
1440          Journal = jpcB,
1441          Pages = {2569-2577},
1442 <        Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom                   Description of n-Alkanes},
1442 >        Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
1443          Volume = 102,
1444          Year = 1998}
1445  
# Line 1305 | Line 1447
1447          Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
1448          Journal = jacs,
1449          Pages = {8638-8639},
1450 <        Title = {Simulations of the Spontaneous Aggregation of Phospholipids                    into Bilayers},
1450 >        Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
1451          Volume = 123,
1452          Year = 2001}
1453  
# Line 1502 | Line 1644
1644          Year = 1995}
1645  
1646   @article{Ichiye03,
1647 <        Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks                    and T. Ichiye},
1647 >        Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
1648          Journal = cpl,
1649          Pages = {646-652},
1650 <        Title = {A temperature of maximum density in soft sticky dipole                    water},
1650 >        Title = {A temperature of maximum density in soft sticky dipole water},
1651          Volume = 376,
1652          Year = 2003}
1653  
# Line 1535 | Line 1677
1677          Year = 2002}
1678  
1679   @article{Ercolessi88,
1680 <        Author = {F. Ercolessi  and M. Parrinello  and E. Tosatti},
1680 >        Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
1681          Journal = {Phil. Mag. A},
1682          Pages = {213-226},
1683          Title = {Simulation of Gold in the Glue Model.},
# Line 1543 | Line 1685
1685          Year = 1988}
1686  
1687   @article{Finnis84,
1688 <        Author = {M.~W Finnis and J.~E. Sinclair },
1688 >        Author = {M.~W Finnis and J.~E. Sinclair},
1689          Journal = {Phil. Mag. A},
1690          Pages = {45-55},
1691          Title = {A Simple Empirical N-Body Potential for Transition-Metals},
# Line 1745 | Line 1887
1887          Author = {M. Holz and S.~R. Heil and A. Sacco},
1888          Journal = {Phys. Chem. Chem. Phys.},
1889          Pages = {4740-4742},
1890 <        Title = {Temperature-dependent self-diffusion coefficients of                    water and six selected molecular liquids for calibration                    in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1890 >        Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
1891          Volume = 2,
1892          Year = 2000}
1893  
# Line 1890 | Line 2032
2032          Journal = {J. Mol. Graphics},
2033          Number = 3,
2034          Pages = {136-141},
2035 <        Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package },
2035 >        Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package},
2036          Volume = 14,
2037          Year = 1996}
2038  

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