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Revision 3663 by gezelter, Thu Oct 21 16:24:13 2010 UTC vs.
Revision 3684 by gezelter, Tue Nov 9 21:13:27 2010 UTC

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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2010-10-21 12:23:58 -0400
5 > %% Created for Dan Gezelter at 2010-11-09 15:04:22 -0500
6  
7  
8   %% Saved with string encoding Unicode (UTF-8)
# Line 57 | Line 57
57   @string{rmp = {Rev. Mod. Phys.}}
58  
59  
60 + @article{Brown1991195,
61 +        Author = {Guy C. Brown},
62 +        Date-Added = {2010-11-09 15:01:26 -0500},
63 +        Date-Modified = {2010-11-09 15:01:26 -0500},
64 +        Doi = {DOI: 10.1016/S0022-5193(05)80422-9},
65 +        Issn = {0022-5193},
66 +        Journal = {Journal of Theoretical Biology},
67 +        Number = {2},
68 +        Pages = {195 - 203},
69 +        Title = {Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells},
70 +        Url = {http://www.sciencedirect.com/science/article/B6WMD-4KDGTFP-4/2/db99c5d9b22a51b80eaf218762c3c514},
71 +        Volume = {153},
72 +        Year = {1991},
73 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WMD-4KDGTFP-4/2/db99c5d9b22a51b80eaf218762c3c514},
74 +        Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0022-5193(05)80422-9}}
75 +
76 + @article{Asthagiri20053300,
77 +        Author = {D. Asthagiri and A. Paliwal and D. Abras and A.M. Lenhoff and M.E. Paulaitis},
78 +        Date-Added = {2010-11-09 14:38:13 -0500},
79 +        Date-Modified = {2010-11-09 14:38:13 -0500},
80 +        Doi = {DOI: 10.1529/biophysj.104.058859},
81 +        Issn = {0006-3495},
82 +        Journal = {Biophysical Journal},
83 +        Number = {5},
84 +        Pages = {3300 - 3309},
85 +        Title = {A Consistent Experimental and Modeling Approach to Light-Scattering Studies of Protein-Protein Interactions in Solution},
86 +        Url = {http://www.sciencedirect.com/science/article/B94RW-4V40XMK-W/2/e216be642ad376c3e507cc19a623a474},
87 +        Volume = {88},
88 +        Year = {2005},
89 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B94RW-4V40XMK-W/2/e216be642ad376c3e507cc19a623a474},
90 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.058859}}
91 +
92 + @article{Dey:2003ts,
93 +        Abstract = {There are many scientific and engineering applications where an automatic detection of shape dimension from sample data is necessary. Topological dimensions of shapes constitute an important global feature of them. We present a Voronoi-based dimension detection algorithm that assigns a dimension to a sample point which is the topological dimension of the manifold it belongs to. Based on this dimension detection, we also present an algorithm to approximate shapes of arbitrary dimension from their samples. Our empirical results with data sets in three dimensions support our theory.},
94 +        Address = {175 FIFTH AVE, NEW YORK, NY 10010 USA},
95 +        Author = {Dey, TK and Giesen, J and Goswami, S and Zhao, WL},
96 +        Date = {APR 2003},
97 +        Date-Added = {2010-11-04 11:11:29 -0400},
98 +        Date-Modified = {2010-11-04 11:11:29 -0400},
99 +        Doi = {DOI 10.1007/s00454-002-2838-9},
100 +        Journal = {Discrete \& Computational Geometry},
101 +        Pages = {419-434},
102 +        Publisher = {SPRINGER-VERLAG},
103 +        Timescited = {3},
104 +        Title = {Shape dimension and approximation from samples},
105 +        Volume = {29},
106 +        Year = {2003},
107 +        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00454-002-2838-9}}
108 +
109 + @article{EDELSBRUNNER:1994oq,
110 +        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.},
111 +        Address = {1515 BROADWAY, NEW YORK, NY 10036},
112 +        Author = {Edelsbrunner, H and Mucke, E.~P.},
113 +        Date = {JAN 1994},
114 +        Date-Added = {2010-11-04 11:11:14 -0400},
115 +        Date-Modified = {2010-11-04 11:11:14 -0400},
116 +        Journal = {ACM Transactions On Graphics},
117 +        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
118 +        Pages = {43-72},
119 +        Publisher = {ASSOC COMPUTING MACHINERY},
120 +        Timescited = {270},
121 +        Title = {3-DIMENSIONAL ALPHA-SHAPES},
122 +        Volume = {13},
123 +        Year = {1994}}
124 +
125 + @article{EDELSBRUNNER:1995cj,
126 +        Abstract = {Efficient algorithms are described for computing topological, combinatorial, and metric properties of the union of finitely many spherical balls in R(d) These algorithms are based on a simplicial complex dual to a decomposition of the union of balls using Voronoi cells, and on short inclusion-exclusion formulas derived from this complex. The algorithms are most relevant in R(3) where unions of finitely many balls are commonly used as models of molecules.},
127 +        Address = {175 FIFTH AVE, NEW YORK, NY 10010},
128 +        Author = {Edelsbrunner, H},
129 +        Date = {APR-JUN 1995},
130 +        Date-Added = {2010-11-04 11:11:14 -0400},
131 +        Date-Modified = {2010-11-04 11:11:14 -0400},
132 +        Journal = {Discrete \& Computational Geometry},
133 +        Pages = {415-440},
134 +        Publisher = {SPRINGER VERLAG},
135 +        Timescited = {65},
136 +        Title = {THE UNION OF BALLS AND ITS DUAL SHAPE},
137 +        Volume = {13},
138 +        Year = {1995}}
139 +
140 + @article{Barber96,
141 +        Author = {C.~B. Barber and D.~P. Dobkin and H.~T. Huhdanpaa},
142 +        Date-Added = {2010-10-27 12:52:57 -0400},
143 +        Date-Modified = {2010-10-27 12:52:57 -0400},
144 +        Journal = {ACM Trans. Math. Software},
145 +        Pages = {469-483},
146 +        Title = {The Quickhull Algorithm for Convex Hulls},
147 +        Volume = 22,
148 +        Year = 1996}
149 +
150 + @article{delaunay,
151 +        Author = {B. Delaunay},
152 +        Date-Added = {2010-10-27 12:48:48 -0400},
153 +        Date-Modified = {2010-10-27 12:49:35 -0400},
154 +        Journal = {Bull. Acad. Science USSR VII:Class. Sci. Mat. Nat.},
155 +        Pages = {793-800},
156 +        Title = {Sur la sph{\`e}re vide},
157 +        Year = {1934}}
158 +
159 + @article{springerlink:10.1007/BF00977785,
160 +        Author = {Lee, D. T. and Schachter, B. J.},
161 +        Date-Added = {2010-10-27 12:44:24 -0400},
162 +        Date-Modified = {2010-10-27 12:44:24 -0400},
163 +        Issn = {0885-7458},
164 +        Issue = {3},
165 +        Journal = {International Journal of Parallel Programming},
166 +        Keyword = {Computer Science},
167 +        Note = {10.1007/BF00977785},
168 +        Pages = {219-242},
169 +        Publisher = {Springer Netherlands},
170 +        Title = {Two algorithms for constructing a Delaunay triangulation},
171 +        Url = {http://dx.doi.org/10.1007/BF00977785},
172 +        Volume = {9},
173 +        Year = {1980},
174 +        Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00977785}}
175 +
176   @misc{Qhull,
177          Date-Added = {2010-10-21 12:05:09 -0400},
178          Date-Modified = {2010-10-21 12:05:09 -0400},
# Line 74 | Line 190
190          Isi = {000256936700007},
191          Isi-Recid = {171639081},
192          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},
193 <        Journal = {Journal of Chemical Physics},
193 >        Journal = {J. Chem. Phys.},
194          Month = jun,
195          Number = {23},
196          Publisher = {AMER INST PHYSICS},
# Line 194 | Line 310
310          Date-Added = {2010-10-19 10:14:05 -0400},
311          Date-Modified = {2010-10-19 10:14:05 -0400},
312          Doi = {DOI 10.1002/cphc.200400607},
313 <        Journal = {Chemphyschem},
313 >        Journal = {ChemPhysChem},
314          Keywords = {clusters; gold; nanostructures; pressure; simulation},
315          Pages = {1848-1852},
316          Publisher = {WILEY-V C H VERLAG GMBH},
# Line 239 | Line 355
355          Date-Added = {2010-10-19 09:49:30 -0400},
356          Date-Modified = {2010-10-19 09:49:30 -0400},
357          Doi = {10.1063/1.466711},
358 <        Journal = {The Journal of Chemical Physics},
358 >        Journal = {J. Chem. Phys.},
359          Keywords = {COMPUTERIZED SIMULATION; SOLVENTS; POTENTIALS; CALCULATION METHODS; SOLVATION; FREE ENERGY; SOLUTES; MOLECULAR CLUSTERS; RADII; SPHERES; INTEGRALS; BOLTZMANN EQUATION; VAN DER WAALS FORCES; COULOMB FIELD; CONFORMATIONAL CHANGES; EQUILIBRIUM; SAMPLING; BUTANE; HYDRATION; ALANINES; PEPTIDES},
360          Number = {12},
361          Pages = {9050-9063},
# Line 274 | Line 390
390          Date-Added = {2010-10-19 09:30:46 -0400},
391          Date-Modified = {2010-10-19 09:30:46 -0400},
392          Doi = {10.1063/1.456845},
393 <        Journal = {The Journal of Chemical Physics},
393 >        Journal = {J. Chem. Phys.},
394          Keywords = {AQUEOUS SOLUTIONS; LIQUID STRUCTURE; SOLVATION; INTERMOLECULAR FORCES; PROTEINS; BOUNDARY CONDITIONS; CONSTRAINTS; DIELECTRIC PROPERTIES; MOLECULAR DYNAMICS CALCULATIONS; COMPUTERIZED SIMULATION},
395          Number = {6},
396          Pages = {3647-3661},
# Line 287 | Line 403
403          Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.456845}}
404  
405   @article{iii:6312,
406 <        Author = {C. L. Brooks III and Martin Karplus},
406 >        Author = {C.~L. {Brooks III} and Martin Karplus},
407          Date-Added = {2010-10-19 09:14:01 -0400},
408          Date-Modified = {2010-10-19 09:14:01 -0400},
409          Doi = {10.1063/1.445724},
410 <        Journal = {The Journal of Chemical Physics},
410 >        Journal = {J. Chem. Phys.},
411          Keywords = {DISTRIBUTION FUNCTIONS; ARGON; THERMODYNAMIC PROPERTIES; COMPUTERIZED SIMULATION; STRUCTURE FACTORS; LIQUID STRUCTURE},
412          Number = {12},
413          Pages = {6312-6325},
# Line 321 | Line 437
437          Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp046852t}}
438  
439   @article{ISI:A1984TQ73500045,
440 <        Author = {BERENDSEN, HJC and POSTMA, JPM and VANGUNSTEREN, WF and DINOLA, A and HAAK, JR},
440 >        Author = {Berendsen, H.~J.~C. and Postma, J.~P.~M. and VanGunsteren, W.~F. and Dinola, A and Haak, J.~R.},
441          Date-Added = {2010-10-18 13:04:11 -0400},
442          Date-Modified = {2010-10-18 13:04:11 -0400},
443 <        Journal = {JOURNAL OF CHEMICAL PHYSICS},
328 <        Journal-Iso = {J. Chem. Phys.},
443 >        Journal = {J. Chem. Phys.},
444          Number = {8},
445          Pages = {3684-3690},
446 <        Title = {MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH},
446 >        Title = {molecular-dynamics with coupling to an external bath},
447          Volume = {81},
448          Year = {1984}}
449  
450   @article{ANDERSEN:1980vn,
451          Address = {WOODBURY},
452 <        Author = {ANDERSEN, H. C.},
452 >        Author = {Andersen, H.~C.},
453          Cited-Reference-Count = {29},
454          Date-Added = {2010-10-18 13:01:27 -0400},
455          Date-Modified = {2010-10-18 13:01:27 -0400},
# Line 343 | Line 458
458          Isi-Document-Delivery-Number = {JK068},
459          Iso-Source-Abbreviation = {J. Chem. Phys.},
460          Issn = {0021-9606},
461 <        Journal = {JOURNAL OF CHEMICAL PHYSICS},
461 >        Journal = {J. Chem. Phys.},
462          Language = {English},
463          Number = {4},
464          Page-Count = {10},
# Line 368 | Line 483
483          Isi = {000085345300002},
484          Isi-Recid = {113793583},
485          Isi-Ref-Recids = {81972786 39595345 109970205 51854999 66009108 53306123 99223832 60134148 54857943 67654925 80228604 52514734 52893114 79704395 68016955 83328866 101670717 73702456 44796632 88334077 95381668 80404775},
486 <        Journal = {Journal of Chemical Physics},
486 >        Journal = {J. Chem. Phys.},
487          Month = feb,
488          Number = {8},
489          Pages = {3474--3482},
# Line 382 | Line 497
497   @article{FELLER:1995fk,
498          Abstract = {A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical ''ringing'' of the volume associated with the piston mass. In this way it is similar to the ''weak coupling algorithm'' developed by Berendsen and co-workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.},
499          Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
500 <        Author = {FELLER, SE and ZHANG, YH and PASTOR, RW and BROOKS, BR},
500 >        Author = {Feller, S.~E. and Zhang, Y.~H. and Pastor, R.~W. and Brooks, B.~R.},
501          Date-Added = {2010-10-18 12:59:12 -0400},
502          Date-Modified = {2010-10-18 12:59:12 -0400},
503          Isi = {A1995RU11000023},
504          Isi-Recid = {92912418},
505          Isi-Ref-Recids = {64516210 39595345 53816621 49016001 49016003 92912419 52031423 49377405 61751037 8052804 92912420 88334077 51117777 53442503 92912421 13886649 31384453 87659780 85624658 53101078 87752055 92912422},
506 <        Journal = {Journal of Chemical Physics},
506 >        Journal = {J. Chem. Phys.},
507          Month = sep,
508          Number = {11},
509          Pages = {4613--4621},
# Line 409 | Line 524
524          Isi = {000228287900056},
525          Isi-Recid = {143814862},
526          Isi-Ref-Recids = {72962882 39595345 143814863 91397367 92912418 110813457 111518806 49778585 102083652 120914607 80001319 54857943 111485260 88334077 95381668 130520135 41081337 135065719 126224491 120652643 108464729 123676541 127189050 123938968},
527 <        Journal = {Journal of Chemical Physics},
527 >        Journal = {J. Chem. Phys.},
528          Month = mar,
529          Number = {12},
530          Publisher = {AMER INST PHYSICS},
# Line 736 | Line 851 | can be very different from that of small hydrophobic m
851          Author = {S.E. Baltazar and A.H. Romero and J.L. Rodr{\'\i}guez-L{\'o}pez and H. Terrones and R. Marto{\v n}{\'a}k},
852          Date-Added = {2010-09-08 16:48:01 -0400},
853          Date-Modified = {2010-09-08 16:48:01 -0400},
854 <        Journal = {Computational Materials Science},
854 >        Journal = {Comp. Mat. Sci.},
855          Keywords = {NPT},
856          Pages = {526-536},
857          Title = {Assessment of isobaric-isothermal (NPT) simulations for finite systems},
# Line 929 | Line 1044 | can be very different from that of small hydrophobic m
1044          Bdsk-File-1 = {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}}
1045  
1046   @article{Brooks1983a,
1047 <        Author = {Brooks, C.L III and Karplus, M.},
1047 >        Author = {Brooks, C.~L.~III and Karplus, M.},
1048          Date-Added = {2010-09-08 16:48:01 -0400},
1049          Date-Modified = {2010-09-08 16:48:38 -0400},
1050          Journal = {J. Chem. Phys.},
# Line 1382 | Line 1497 | can be very different from that of small hydrophobic m
1497          Date-Added = {2008-01-11 16:16:43 -0500},
1498          Date-Modified = {2008-01-11 16:16:43 -0500},
1499          Journal = jcp,
1500 <        Journal1 = {The Journal of Chemical Physics},
1500 >        Journal1 = {J. Chem. Phys.},
1501          Journal2 = {J. Chem. Phys.},
1502          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
1503          Number = 5,
# Line 1864 | Line 1979 | can be very different from that of small hydrophobic m
1979          Title = {Aspects of Structural Glass Transitions},
1980          Volume = {I},
1981          Year = 1989,
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1983  
1984   @article{Lewis91,
1985          Author = {L.~J. Lewis},

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