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Revision: 3708
Committed: Mon Nov 22 22:34:45 2010 UTC (13 years, 9 months ago) by kstocke1
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added documentation for Langevin Hull

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# User Rev Content
1 gezelter 3607 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
3    
4    
5 kstocke1 3708 %% Created for Kelsey Stocker at 2010-11-22 12:25:03 -0500
6 gezelter 3607
7    
8 kstocke1 3708 %% Saved with string encoding Unicode (UTF-8)
9 gezelter 3607
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 kstocke1 3708 @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 gezelter 3607 @article{Fennell06,
195     Author = {C.~J. Fennell and J.~D. Gezelter},
196     Date-Added = {2008-05-16 10:19:01 -0400},
197     Date-Modified = {2008-05-16 10:19:01 -0400},
198     Doi = {10.1063/1.2206581},
199     Journal = jcp,
200     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_PairwiseSummationMethods_06.pdf},
201     Number = {23},
202     Pages = {234104(12)},
203     Rating = {5},
204     Read = {Yes},
205     Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
206     Volume = {124},
207     Year = {2006},
208     Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}
209    
210     @article{Heyes81,
211     Author = {D.~M. Heyes},
212     Date-Added = {2008-05-16 10:18:50 -0400},
213     Date-Modified = {2008-05-16 10:18:50 -0400},
214     Journal = jcp,
215     Keywords = {Empty Keywords},
216     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
217     Number = {3},
218     Pages = {1924-1929},
219     Title = {Electrostatic potentials and fields in infinite point charge lattices},
220     Volume = {74},
221     Year = {1981}}
222    
223     @article{Jones56,
224     Author = {R.~E. Jones and D.~H. Templeton},
225     Date-Added = {2008-05-16 10:18:41 -0400},
226     Date-Modified = {2008-05-16 10:18:41 -0400},
227     Journal = jcp,
228     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
229     Number = {5},
230     Pages = {1062-1063},
231     Title = {Optimum Atomic Shape for \uppercase{B}ertaut Series},
232     Volume = {25},
233     Year = {1956}}
234    
235     @book{Allen87,
236     Address = {New York},
237     Author = {M.~P. Allen and D.~J. Tildesley},
238     Date-Added = {2008-05-16 10:18:32 -0400},
239     Date-Modified = {2008-05-16 10:18:32 -0400},
240     Publisher = {Oxford University Press},
241     Title = {Computer Simulations of Liquids},
242     Year = 1987}
243    
244     @article{Wolf99,
245     Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
246     Date-Added = {2008-05-16 10:18:22 -0400},
247     Date-Modified = {2008-05-16 10:18:22 -0400},
248     Journal = jcp,
249     Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
250     Number = {17},
251     Pages = {8254-8282},
252     Rating = {0},
253     Read = {No},
254     Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
255     Volume = {110},
256     Year = {1999}}
257    
258     @book{Berne90,
259     Address = {Malabar, Florida},
260     Author = {B.~J. Berne and R. Pecora},
261     Publisher = {Robert E. Krieger Publishing Company, Inc.},
262     Title = {Dynamic Light Scattering},
263     Year = 1990}
264    
265     @article{Evans77,
266     Author = {D.~J. Evans},
267     Journal = {Mol. Phys.},
268     Pages = {317-325},
269     Title = {On the representation of orientation space},
270     Volume = 34,
271     Year = 1977}
272    
273     @article{Tuckerman92,
274     Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
275     Journal = jcp,
276     Pages = {1990-2001},
277     Title = {Reversible multiple time scale molecular dynamics},
278     Volume = 97,
279     Year = 1992}
280    
281     @book{Hansen86,
282     Address = {London},
283     Author = {J.~P. Hansen and I.~R. McDonald},
284     Chapter = 7,
285     Pages = {199-206},
286     Publisher = {Academic Press},
287     Title = {Theory of Simple Liquids},
288     Year = 1986}
289    
290     @article{Angelani98,
291     Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
292     Journal = prl,
293     Number = 21,
294     Pages = {4648-4651},
295 kstocke1 3708 Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
296 gezelter 3607 Volume = 81,
297     Year = 1998}
298    
299     @article{Stillinger82,
300     Author = {F.~H. Stillinger and T.~A. Weber},
301     Journal = pra,
302     Number = 2,
303     Pages = {978-989},
304     Title = {Hidden structure in liquids},
305     Volume = 25,
306     Year = 1982}
307    
308     @article{Stillinger83,
309     Author = {F.~H. Stillinger and T.~A. Weber},
310     Journal = pra,
311     Number = 4,
312     Pages = {2408-2416},
313     Title = {Dynamics of structural transitions in liquids},
314     Volume = 28,
315     Year = 1983}
316    
317     @article{Weber84,
318     Author = {T.~A. Weber and F.~H. Stillinger},
319     Journal = jcp,
320     Number = 6,
321     Pages = {2742-2746},
322 kstocke1 3708 Title = {The effect of density on the inherent structure in liquids},
323 gezelter 3607 Volume = 80,
324     Year = 1984}
325    
326     @article{Stillinger85,
327     Author = {F.~H. Stillinger and T.~A. Weber},
328     Journal = jcp,
329     Number = 9,
330     Pages = {4767-4775},
331 kstocke1 3708 Title = {Inherent structure theory of liquids in the hard-sphere limit},
332 gezelter 3607 Volume = 83,
333     Year = 1985}
334    
335     @article{Stillinger98,
336     Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
337     Journal = {Nature},
338     Pages = {554-557},
339 kstocke1 3708 Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
340 gezelter 3607 Volume = 393,
341     Year = 1998}
342    
343     @article{Parkhurst75a,
344     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
345     Journal = jcp,
346     Number = 6,
347     Pages = {2698-2704},
348 kstocke1 3708 Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
349 gezelter 3607 Volume = 63,
350     Year = 1975}
351    
352     @article{Parkhurst75b,
353     Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
354     Journal = jcp,
355     Number = 6,
356     Pages = {2705-2709},
357 kstocke1 3708 Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
358 gezelter 3607 Volume = 63,
359     Year = 1975}
360    
361     @article{Forester97,
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 kstocke1 3708 Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
366 gezelter 3607 Volume = 93,
367     Year = 1997}
368    
369     @article{Tieleman98,
370     Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
371     Journal = bj,
372     Pages = {2786-2801},
373 kstocke1 3708 Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
374 gezelter 3607 Volume = 74,
375     Year = 1998}
376    
377     @article{Cascales98,
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 kstocke1 3708 Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
382 gezelter 3607 Volume = 102,
383     Year = 1998}
384    
385     @article{Bassolino95,
386     Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
387     Journal = {J. Am. Chem. Soc.},
388     Pages = {4118-4129},
389 kstocke1 3708 Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
390 gezelter 3607 Volume = 117,
391     Year = 1995}
392    
393     @article{Alper95,
394     Author = {H.~E. Alper and T.~R. Stouch},
395     Journal = {J. Phys. Chem.},
396     Pages = {5724-5731},
397 kstocke1 3708 Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
398 gezelter 3607 Volume = 99,
399     Year = 1995}
400    
401     @article{Sok92,
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 kstocke1 3708 Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
406 gezelter 3607 Volume = 96,
407     Year = 1992}
408    
409     @article{Rabani99,
410     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
411     Journal = prl,
412     Pages = {3649},
413 kstocke1 3708 Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
414 gezelter 3607 Volume = 82,
415     Year = {1999}}
416    
417     @article{Rabani97,
418     Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
419     Journal = {J. Chem. Phys.},
420     Pages = {6867-6876},
421 kstocke1 3708 Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
422 gezelter 3607 Volume = 107,
423     Year = 1997}
424    
425     @article{Gezelter99,
426     Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
427     Journal = jcp,
428     Pages = 3444,
429 kstocke1 3708 Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
430 gezelter 3607 Volume = 110,
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