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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2010-10-19 10:14:21 -0400
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# Line 57 | Line 57
57   @string{rmp = {Rev. Mod. Phys.}}
58  
59  
60 + @article{Dey:2003ts,
61 +        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.},
62 +        Address = {175 FIFTH AVE, NEW YORK, NY 10010 USA},
63 +        Author = {Dey, TK and Giesen, J and Goswami, S and Zhao, WL},
64 +        Date = {APR 2003},
65 +        Date-Added = {2010-11-04 11:11:29 -0400},
66 +        Date-Modified = {2010-11-04 11:11:29 -0400},
67 +        Doi = {DOI 10.1007/s00454-002-2838-9},
68 +        Journal = {Discrete \& Computational Geometry},
69 +        Pages = {419-434},
70 +        Publisher = {SPRINGER-VERLAG},
71 +        Timescited = {3},
72 +        Title = {Shape dimension and approximation from samples},
73 +        Volume = {29},
74 +        Year = {2003},
75 +        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00454-002-2838-9}}
76 +
77 + @article{EDELSBRUNNER:1994oq,
78 +        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.},
79 +        Address = {1515 BROADWAY, NEW YORK, NY 10036},
80 +        Author = {EDELSBRUNNER, H and MUCKE, EP},
81 +        Date = {JAN 1994},
82 +        Date-Added = {2010-11-04 11:11:14 -0400},
83 +        Date-Modified = {2010-11-04 11:11:14 -0400},
84 +        Journal = {Acm Transactions On Graphics},
85 +        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
86 +        Pages = {43-72},
87 +        Publisher = {ASSOC COMPUTING MACHINERY},
88 +        Timescited = {270},
89 +        Title = {3-DIMENSIONAL ALPHA-SHAPES},
90 +        Volume = {13},
91 +        Year = {1994}}
92 +
93 + @article{EDELSBRUNNER:1995cj,
94 +        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.},
95 +        Address = {175 FIFTH AVE, NEW YORK, NY 10010},
96 +        Author = {EDELSBRUNNER, H},
97 +        Date = {APR-JUN 1995},
98 +        Date-Added = {2010-11-04 11:11:14 -0400},
99 +        Date-Modified = {2010-11-04 11:11:14 -0400},
100 +        Journal = {Discrete \& Computational Geometry},
101 +        Pages = {415-440},
102 +        Publisher = {SPRINGER VERLAG},
103 +        Timescited = {65},
104 +        Title = {THE UNION OF BALLS AND ITS DUAL SHAPE},
105 +        Volume = {13},
106 +        Year = {1995}}
107 +
108 + @article{Barber96,
109 +        Author = {C.~B. Barber and D.~P. Dobkin and H.~T. Huhdanpaa},
110 +        Date-Added = {2010-10-27 12:52:57 -0400},
111 +        Date-Modified = {2010-10-27 12:52:57 -0400},
112 +        Journal = {ACM Trans. Math. Software},
113 +        Pages = {469-483},
114 +        Title = {The Quickhull Algorithm for Convex Hulls},
115 +        Volume = 22,
116 +        Year = 1996}
117 +
118 + @article{delaunay,
119 +        Author = {B. Delaunay},
120 +        Date-Added = {2010-10-27 12:48:48 -0400},
121 +        Date-Modified = {2010-10-27 12:49:35 -0400},
122 +        Journal = {Bull. Acad. Science USSR VII:Class. Sci. Mat. Nat.},
123 +        Pages = {793-800},
124 +        Title = {Sur la sph{\`e}re vide},
125 +        Year = {1934}}
126 +
127 + @article{springerlink:10.1007/BF00977785,
128 +        Author = {Lee, D. T. and Schachter, B. J.},
129 +        Date-Added = {2010-10-27 12:44:24 -0400},
130 +        Date-Modified = {2010-10-27 12:44:24 -0400},
131 +        Issn = {0885-7458},
132 +        Issue = {3},
133 +        Journal = {International Journal of Parallel Programming},
134 +        Keyword = {Computer Science},
135 +        Note = {10.1007/BF00977785},
136 +        Pages = {219-242},
137 +        Publisher = {Springer Netherlands},
138 +        Title = {Two algorithms for constructing a Delaunay triangulation},
139 +        Url = {http://dx.doi.org/10.1007/BF00977785},
140 +        Volume = {9},
141 +        Year = {1980},
142 +        Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00977785}}
143 +
144 + @misc{Qhull,
145 +        Date-Added = {2010-10-21 12:05:09 -0400},
146 +        Date-Modified = {2010-10-21 12:05:09 -0400},
147 +        Note = {Software Library Is Available From the National Science and Technology Research Center for Computation and Visualization of Geometric Structures (The Geometry Center), University of Minnesota. $\mathtt{http://www.geom.umn.edu/software/qhull/}$},
148 +        Title = {Qhull},
149 +        Year = 1993}
150 +
151 + @article{Sun:2008fk,
152 +        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.},
153 +        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
154 +        Author = {Sun, Xiuquan and Lin, Teng and Gezelter, J. Daniel},
155 +        Date-Added = {2010-10-21 12:04:05 -0400},
156 +        Date-Modified = {2010-10-21 12:04:05 -0400},
157 +        Doi = {DOI 10.1063/1.2936991},
158 +        Isi = {000256936700007},
159 +        Isi-Recid = {171639081},
160 +        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},
161 +        Journal = {Journal of Chemical Physics},
162 +        Month = jun,
163 +        Number = {23},
164 +        Publisher = {AMER INST PHYSICS},
165 +        Times-Cited = {2},
166 +        Title = {Langevin dynamics for rigid bodies of arbitrary shape},
167 +        Volume = {128},
168 +        Year = {2008},
169 +        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000256936700007}}
170 +
171 + @article{ISI:000167766600035,
172 +        Abstract = {Molecular dynamics simulations are used to
173 +                  investigate the separation of water films adjacent
174 +                  to a hot metal surface. The simulations clearly show
175 +                  that the water layers nearest the surface overheat
176 +                  and undergo explosive boiling. For thick films, the
177 +                  expansion of the vaporized molecules near the
178 +                  surface forces the outer water layers to move away
179 +                  from the surface. These results are of interest for
180 +                  mass spectrometry of biological molecules, steam
181 +                  cleaning of surfaces, and medical procedures.},
182 +        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
183 +        Affiliation = {Garrison, BJ (Reprint Author), Penn State Univ, Dept Chem, University Pk, PA 16802 USA. Penn State Univ, Dept Chem, University Pk, PA 16802 USA. Penn State Univ, Inst Mat Res, University Pk, PA 16802 USA. Univ Virginia, Dept Mat Sci \& Engn, Charlottesville, VA 22903 USA.},
184 +        Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
185 +        Date-Added = {2010-10-21 12:02:39 -0400},
186 +        Date-Modified = {2010-10-21 12:02:39 -0400},
187 +        Doc-Delivery-Number = {416ED},
188 +        Issn = {1089-5639},
189 +        Journal = {J. Phys. Chem. A},
190 +        Journal-Iso = {J. Phys. Chem. A},
191 +        Keywords-Plus = {MOLECULAR-DYNAMICS SIMULATIONS; ASSISTED LASER-DESORPTION; FROZEN AQUEOUS-SOLUTIONS; COMPUTER-SIMULATION; ORGANIC-SOLIDS; VELOCITY DISTRIBUTIONS; PARTICLE BOMBARDMENT; MASS-SPECTROMETRY; PHASE EXPLOSION; LIQUID WATER},
192 +        Language = {English},
193 +        Month = {MAR 29},
194 +        Number = {12},
195 +        Number-Of-Cited-References = {65},
196 +        Pages = {2748-2755},
197 +        Publisher = {AMER CHEMICAL SOC},
198 +        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
199 +        Times-Cited = {66},
200 +        Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
201 +        Type = {Article},
202 +        Unique-Id = {ISI:000167766600035},
203 +        Volume = {105},
204 +        Year = {2001}}
205 +
206 + @article{wolf:8254,
207 +        Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
208 +        Date-Added = {2010-10-21 12:02:26 -0400},
209 +        Date-Modified = {2010-10-21 12:02:26 -0400},
210 +        Doi = {10.1063/1.478738},
211 +        Journal = {J. Chem. Phys.},
212 +        Keywords = {POTENTIAL ENERGY; COULOMB FIELD; COULOMB ENERGY; LATTICE PARAMETERS; potential energy functions; lattice dynamics; lattice energy},
213 +        Number = {17},
214 +        Pages = {8254-8282},
215 +        Publisher = {AIP},
216 +        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r[sup -1] summation},
217 +        Url = {http://link.aip.org/link/?JCP/110/8254/1},
218 +        Volume = {110},
219 +        Year = {1999},
220 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/110/8254/1},
221 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.478738}}
222 +
223 + @article{Fennell06,
224 +        Author = {C.~J. Fennell and J.~D. Gezelter},
225 +        Date-Added = {2010-10-21 12:02:17 -0400},
226 +        Date-Modified = {2010-10-21 12:02:17 -0400},
227 +        Doi = {10.1063/1.2206581},
228 +        Journal = {J. Chem. Phys.},
229 +        Number = {23},
230 +        Pages = {234104(12)},
231 +        Rating = {5},
232 +        Read = {Yes},
233 +        Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
234 +        Volume = {124},
235 +        Year = {2006},
236 +        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}
237 +
238 + @article{PhysRevB.59.3527,
239 +        Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
240 +        Date-Added = {2010-10-21 12:02:07 -0400},
241 +        Date-Modified = {2010-10-21 12:02:07 -0400},
242 +        Doi = {10.1103/PhysRevB.59.3527},
243 +        Journal = {Phys. Rev. B},
244 +        Local-Url = {file://localhost/Users/charles/Documents/Papers/Qi/1999.pdf},
245 +        Month = {Feb},
246 +        Number = {5},
247 +        Numpages = {6},
248 +        Pages = {3527-3533},
249 +        Publisher = {American Physical Society},
250 +        Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals:\quad{}{C}u-{A}g and {C}u-{N}i},
251 +        Volume = {59},
252 +        Year = {1999},
253 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}
254 +
255   @article{Baltazar:2006ru,
256          Abstract = {A compilation and an implementation of different methodologies to simulate NPT ensembles on finite systems is presented. In general, the methods discussed can be classified in two different groups depending on how the external pressure is applied to the system. The first approach is based on including the pressure with its conjugate thermodynamical variable, the volume, in the Lagrangian of the system. For this group four different volume definitions were considered and we assess their validity by studying the structural properties of small systems as function of pressure. In particular, we focus on the stability of the C-60 molecule as well as the amorphization process of a diamond-like cluster under pressure. In the second group, the finite system (C-60) is embedded in a classical fluid which serves as a pressure reservoir. We take the latter method as reference because it is closest to the experimental situation. The difficulties and the regimes where these methods can be used are also discussed. (c) 2005 Elsevier B.V. All rights reserved.},
257          Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
# Line 1753 | Line 1948 | can be very different from that of small hydrophobic m
1948          Title = {Aspects of Structural Glass Transitions},
1949          Volume = {I},
1950          Year = 1989,
1951 <        Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUIJidUJHRvcFgkb2JqZWN0c1gkdmVyc2lvblkkYXJjaGl2ZXLRBgdUcm9vdIABqAkKFRYXGyIjVSRudWxs0wsMDQ4RFFpOUy5vYmplY3RzV05TLmtleXNWJGNsYXNzog8QgASABqISE4ACgAOAB1lhbGlhc0RhdGFccmVsYXRpdmVQYXRo0hgNGRpXTlMuZGF0YU8RAbIAAAAAAbIAAgAABkZhbGNvbgAAAAAAAAAAAAAAAAAAAAAAAAAAAMcrh89IKwAAAAi6UB8xMC4xMDAyJTJGYmlwLjM2MDM1MDIwNS5lbncucmlzAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAArLqOyOMZnAAAAAAAAAAAAAMAAgAACSAAAAAAAAAAAAAAAAAAAAAJRG93bmxvYWRzAAAQAAgAAMcrzh8AAAARAAgAAMjjUdwAAAABAAwACLpQAAgULgAAkY0AAgA/RmFsY29uOlVzZXJzOmdlemVsdGVyOkRvd25sb2FkczoxMC4xMDAyJTJGYmlwLjM2MDM1MDIwNS5lbncucmlzAAAOAEAAHwAxADAALgAxADAAMAAyACUAMgBGAGIAaQBwAC4AMwA2ADAAMwA1ADAAMgAwADUALgBlAG4AdwAuAHIAaQBzAA8ADgAGAEYAYQBsAGMAbwBuABIAOFVzZXJzL2dlemVsdGVyL0Rvd25sb2Fkcy8xMC4xMDAyJTJGYmlwLjM2MDM1MDIwNS5lbncucmlzABMAAS8AABUAAgAP//8AAIAF0hwdHh9YJGNsYXNzZXNaJGNsYXNzbmFtZaMfICFdTlNNdXRhYmxlRGF0YVZOU0RhdGFYTlNPYmplY3RfEDIuLi8uLi8uLi9Eb3dubG9hZHMvMTAuMTAwMiUyRmJpcC4zNjAzNTAyMDUuZW53LnJpc9IcHSQloiUhXE5TRGljdGlvbmFyeRIAAYagXxAPTlNLZXllZEFyY2hpdmVyAAgAEQAWAB8AKAAyADUAOgA8AEUASwBSAF0AZQBsAG8AcQBzAHYAeAB6AHwAhgCTAJgAoAJWAlgCXQJmAnECdQKDAooCkwLIAs0C0ALdAuIAAAAAAAACAQAAAAAAAAAoAAAAAAAAAAAAAAAAAAAC9A==}}
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1952  
1953   @article{Lewis91,
1954          Author = {L.~J. Lewis},

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