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2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2010-10-27 12:54:30 -0400
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7  
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# Line 57 | Line 57
57   @string{rmp = {Rev. Mod. Phys.}}
58  
59  
60 + @unpublished{QSC,
61 +        Author = {Y. Kimura and T. Cagin and W. A. {Goddard III}},
62 +        Date-Added = {2010-11-11 16:40:36 -0500},
63 +        Date-Modified = {2010-11-11 16:40:36 -0500},
64 +        Note = {Downloaded from: $\mathtt{http://wag.caltech.edu/home-pages/tahir/psfiles/51.ps}$},
65 +        Title = {The Quantum Sutton-Chen Many Body Potential for Properties of FCC metals},
66 +        Url = {http://wag.caltech.edu/home-pages/tahir/psfiles/51.ps},
67 +        Year = {1998},
68 +        Bdsk-Url-1 = {citeseer.ist.psu.edu/150963.html}}
69 +
70 + @article{Zhu:2008fk,
71 +        Abstract = {Two simple models are developed to accurately account for short-range solvation effects in molecular dynamics simulations of biomolecular systems in water. The methods limit the amount of solvent that must be treated explicitly to two or three solvation shells, thereby eliminating the need for periodic boundary conditions, which significantly reduces the computational complexity. In the dynamic boundary model, a confining potential is imposed on the solvent that responds dynamically to fluctuations in the solvent distribution and conformations of the biomolecular solute. In the exchange boundary solvation model, the molecules at the surface of the explicit solvation shell are allowed to undergo pairwise exchanges with the bulk to maintain a uniform hydration of the solute. The models are used to study the solvation thermodynamics of a 11-residue polyalanine helix in water. A broad range of structural and dynamic properties characterizing both the protein and the surrounding solvent are computed. Comparison with the results obtained from conventional periodic boundary condition simulations shows excellent agreement, and the new solvation models are found to improve computational efficiency by up two orders of magnitude. (C) 2008 Elsevier B.V. All rights reserved.},
72 +        Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
73 +        Author = {Zhu, Wusheng and Krilov, Goran},
74 +        Date-Added = {2010-11-11 16:29:05 -0500},
75 +        Date-Modified = {2010-11-11 16:29:05 -0500},
76 +        Doi = {DOI 10.1016/j.theochem.2008.05.035},
77 +        Isi = {000259719400006},
78 +        Isi-Recid = {173553934},
79 +        Isi-Ref-Recids = {45853871 70732554 152291148 104489423 104489429 65322851 87480881 90163797 93668415 39889551 46774919 72549485 282445 41538860 50985260 52031423 118060314 121628598 148959020 62737851 93573488 134643892 36862872 83010484 105744290 91472272 110749892 118461739 120957948 134599612 114633021 70197537 107985288 146240895 127089201 143385646 150932516 142444198 121603296 109842709 125496094 107255659 134599616 102272218 75630818 101084982 44754957 149298475 117544086 124879696 62609631 67033562 149633382 109842663 63091485 111340113 105035661 73139919 173553935 107383980 104342509 125966406 104156158 89313539 37068368 57373279 29138640 53172669 136485000 126777112 134886755},
80 +        Journal = {Journal of Molecular Structure-Theochem},
81 +        Keywords = {molecular dynamics; hybrid solvation; polyalanine; non-periodic boundary conclicion},
82 +        Month = sep,
83 +        Number = {1-3},
84 +        Pages = {31--41},
85 +        Publisher = {ELSEVIER SCIENCE BV},
86 +        Times-Cited = {0},
87 +        Title = {New flexible boundary hybrid solvation models for efficient biomolecular simulations},
88 +        Volume = {864},
89 +        Year = {2008},
90 +        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000259719400006}}
91 +
92 + @article{PhysRevB.33.7983,
93 +        Author = {Foiles, S. M. and Baskes, M. I. and Daw, M. S.},
94 +        Date-Added = {2010-11-11 16:24:12 -0500},
95 +        Date-Modified = {2010-11-11 16:24:12 -0500},
96 +        Doi = {10.1103/PhysRevB.33.7983},
97 +        Journal = {Phys. Rev. B},
98 +        Local-Url = {file://localhost/Users/charles/Documents/Papers/p7983_1.pdf},
99 +        Month = {Jun},
100 +        Number = {12},
101 +        Numpages = {8},
102 +        Pages = {7983-7991},
103 +        Publisher = {American Physical Society},
104 +        Title = {Embedded-atom-method functions for the fcc metals {C}u, {A}g, {A}u, {N}i, {P}d, {P}t, and their alloys},
105 +        Volume = {33},
106 +        Year = {1986},
107 +        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.33.7983}}
108 +
109 + @article{Chen90,
110 +        Author = {A.~P. Sutton and J. Chen},
111 +        Date-Added = {2010-11-11 16:23:18 -0500},
112 +        Date-Modified = {2010-11-11 16:23:18 -0500},
113 +        Journal = {Phil. Mag. Lett.},
114 +        Pages = {139-146},
115 +        Title = {Long-Range Finnis Sinclair Potentials},
116 +        Volume = 61,
117 +        Year = {1990}}
118 +
119 + @article{Brown1991195,
120 +        Author = {Guy C. Brown},
121 +        Date-Added = {2010-11-09 15:01:26 -0500},
122 +        Date-Modified = {2010-11-09 15:01:26 -0500},
123 +        Doi = {DOI: 10.1016/S0022-5193(05)80422-9},
124 +        Issn = {0022-5193},
125 +        Journal = {Journal of Theoretical Biology},
126 +        Number = {2},
127 +        Pages = {195 - 203},
128 +        Title = {Total cell protein concentration as an evolutionary constraint on the metabolic control distribution in cells},
129 +        Url = {http://www.sciencedirect.com/science/article/B6WMD-4KDGTFP-4/2/db99c5d9b22a51b80eaf218762c3c514},
130 +        Volume = {153},
131 +        Year = {1991},
132 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WMD-4KDGTFP-4/2/db99c5d9b22a51b80eaf218762c3c514},
133 +        Bdsk-Url-2 = {http://dx.doi.org/10.1016/S0022-5193(05)80422-9}}
134 +
135 + @article{Asthagiri20053300,
136 +        Author = {D. Asthagiri and A. Paliwal and D. Abras and A.M. Lenhoff and M.E. Paulaitis},
137 +        Date-Added = {2010-11-09 14:38:13 -0500},
138 +        Date-Modified = {2010-11-09 14:38:13 -0500},
139 +        Doi = {DOI: 10.1529/biophysj.104.058859},
140 +        Issn = {0006-3495},
141 +        Journal = {Biophysical Journal},
142 +        Number = {5},
143 +        Pages = {3300 - 3309},
144 +        Title = {A Consistent Experimental and Modeling Approach to Light-Scattering Studies of Protein-Protein Interactions in Solution},
145 +        Url = {http://www.sciencedirect.com/science/article/B94RW-4V40XMK-W/2/e216be642ad376c3e507cc19a623a474},
146 +        Volume = {88},
147 +        Year = {2005},
148 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B94RW-4V40XMK-W/2/e216be642ad376c3e507cc19a623a474},
149 +        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.058859}}
150 +
151 + @article{Dey:2003ts,
152 +        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.},
153 +        Address = {175 FIFTH AVE, NEW YORK, NY 10010 USA},
154 +        Author = {Dey, TK and Giesen, J and Goswami, S and Zhao, WL},
155 +        Date = {APR 2003},
156 +        Date-Added = {2010-11-04 11:11:29 -0400},
157 +        Date-Modified = {2010-11-04 11:11:29 -0400},
158 +        Doi = {DOI 10.1007/s00454-002-2838-9},
159 +        Journal = {Discrete \& Computational Geometry},
160 +        Pages = {419-434},
161 +        Publisher = {SPRINGER-VERLAG},
162 +        Timescited = {3},
163 +        Title = {Shape dimension and approximation from samples},
164 +        Volume = {29},
165 +        Year = {2003},
166 +        Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00454-002-2838-9}}
167 +
168 + @article{EDELSBRUNNER:1994oq,
169 +        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.},
170 +        Address = {1515 BROADWAY, NEW YORK, NY 10036},
171 +        Author = {Edelsbrunner, H and Mucke, E.~P.},
172 +        Date = {JAN 1994},
173 +        Date-Added = {2010-11-04 11:11:14 -0400},
174 +        Date-Modified = {2010-11-04 11:11:14 -0400},
175 +        Journal = {ACM Transactions On Graphics},
176 +        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
177 +        Pages = {43-72},
178 +        Publisher = {ASSOC COMPUTING MACHINERY},
179 +        Timescited = {270},
180 +        Title = {3-DIMENSIONAL ALPHA-SHAPES},
181 +        Volume = {13},
182 +        Year = {1994}}
183 +
184 + @article{EDELSBRUNNER:1995cj,
185 +        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.},
186 +        Address = {175 FIFTH AVE, NEW YORK, NY 10010},
187 +        Author = {Edelsbrunner, H},
188 +        Date = {APR-JUN 1995},
189 +        Date-Added = {2010-11-04 11:11:14 -0400},
190 +        Date-Modified = {2010-11-04 11:11:14 -0400},
191 +        Journal = {Discrete \& Computational Geometry},
192 +        Pages = {415-440},
193 +        Publisher = {SPRINGER VERLAG},
194 +        Timescited = {65},
195 +        Title = {THE UNION OF BALLS AND ITS DUAL SHAPE},
196 +        Volume = {13},
197 +        Year = {1995}}
198 +
199   @article{Barber96,
200          Author = {C.~B. Barber and D.~P. Dobkin and H.~T. Huhdanpaa},
201          Date-Added = {2010-10-27 12:52:57 -0400},
# Line 93 | Line 232
232          Year = {1980},
233          Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00977785}}
234  
96 – @article{EDELSBRUNNER:1994oq,
97 –        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.},
98 –        Address = {1515 BROADWAY, NEW YORK, NY 10036},
99 –        Author = {EDELSBRUNNER, H and MUCKE, EP},
100 –        Date = {JAN 1994},
101 –        Date-Added = {2010-10-27 12:32:43 -0400},
102 –        Date-Modified = {2010-10-27 12:32:43 -0400},
103 –        Journal = {Acm Transactions On Graphics},
104 –        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
105 –        Pages = {43-72},
106 –        Publisher = {ASSOC COMPUTING MACHINERY},
107 –        Timescited = {270},
108 –        Title = {3-DIMENSIONAL ALPHA-SHAPES},
109 –        Volume = {13},
110 –        Year = {1994}}
111 –
235   @misc{Qhull,
236          Date-Added = {2010-10-21 12:05:09 -0400},
237          Date-Modified = {2010-10-21 12:05:09 -0400},
# Line 126 | Line 249
249          Isi = {000256936700007},
250          Isi-Recid = {171639081},
251          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},
252 <        Journal = {Journal of Chemical Physics},
252 >        Journal = {J. Chem. Phys.},
253          Month = jun,
254          Number = {23},
255          Publisher = {AMER INST PHYSICS},
# Line 246 | Line 369
369          Date-Added = {2010-10-19 10:14:05 -0400},
370          Date-Modified = {2010-10-19 10:14:05 -0400},
371          Doi = {DOI 10.1002/cphc.200400607},
372 <        Journal = {Chemphyschem},
372 >        Journal = {ChemPhysChem},
373          Keywords = {clusters; gold; nanostructures; pressure; simulation},
374          Pages = {1848-1852},
375          Publisher = {WILEY-V C H VERLAG GMBH},
# Line 256 | Line 379
379          Year = {2005},
380          Bdsk-Url-1 = {http://dx.doi.org/10.1002/cphc.200400607}}
381  
259 – @article{Zhu:xw,
260 –        Author = {Zhu, Wusheng and Krilov, Goran},
261 –        Date-Added = {2010-10-19 10:13:55 -0400},
262 –        Date-Modified = {2010-10-19 10:13:55 -0400},
263 –        Journal = {Journal of Molecular Structure: THEOCHEM},
264 –        Keywords = {Molecular dynamics; Hybrid solvation; Polyalanine; Non-periodic boundary condition},
265 –        Pages = {--},
266 –        Title = {New flexible boundary hybrid solvation models for efficient biomolecular simulations},
267 –        Ty = {JOUR},
268 –        Url = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c},
269 –        Volume = {In Press},
270 –        Year = {2008},
271 –        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c}}
272 –
382   @article{LiY._jp046852t,
383          Abstract = {Abstract: A new approach is developed to study the dynamics of the localized process in solutions and other condensed phase systems. The approach employs a fluctuating elastic boundary (FEB) model which encloses the simulated system in an elastic bag that mimics the effects of the bulk solvent. This alleviates the need for periodic boundary conditions and allows for a reduction in the number of solvent molecules that need to be included in the simulation. The boundary bag is modeled as a mesh of quasi-particles connected by elastic bonds. The FEB model allows for volume and density fluctuations characteristic of the bulk system, and the shape of the boundary fluctuates during the course of the simulation to adapt to the configuration fluctuations of the explicit solute-solvent system inside. The method is applied to the simulation of a Lennard-Jones model of liquid argon. Various structural and dynamical quantities are computed and compared with those obtained from conventional periodic boundary simulations. The agreement between the two is excellent in most cases, thus validating the viability of the FEB method.},
384          Affiliation = {Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027},
# Line 291 | Line 400
400          Date-Added = {2010-10-19 09:49:30 -0400},
401          Date-Modified = {2010-10-19 09:49:30 -0400},
402          Doi = {10.1063/1.466711},
403 <        Journal = {The Journal of Chemical Physics},
403 >        Journal = {J. Chem. Phys.},
404          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},
405          Number = {12},
406          Pages = {9050-9063},
# Line 326 | Line 435
435          Date-Added = {2010-10-19 09:30:46 -0400},
436          Date-Modified = {2010-10-19 09:30:46 -0400},
437          Doi = {10.1063/1.456845},
438 <        Journal = {The Journal of Chemical Physics},
438 >        Journal = {J. Chem. Phys.},
439          Keywords = {AQUEOUS SOLUTIONS; LIQUID STRUCTURE; SOLVATION; INTERMOLECULAR FORCES; PROTEINS; BOUNDARY CONDITIONS; CONSTRAINTS; DIELECTRIC PROPERTIES; MOLECULAR DYNAMICS CALCULATIONS; COMPUTERIZED SIMULATION},
440          Number = {6},
441          Pages = {3647-3661},
# Line 339 | Line 448
448          Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.456845}}
449  
450   @article{iii:6312,
451 <        Author = {C. L. Brooks III and Martin Karplus},
451 >        Author = {C.~L. {Brooks III} and Martin Karplus},
452          Date-Added = {2010-10-19 09:14:01 -0400},
453          Date-Modified = {2010-10-19 09:14:01 -0400},
454          Doi = {10.1063/1.445724},
455 <        Journal = {The Journal of Chemical Physics},
455 >        Journal = {J. Chem. Phys.},
456          Keywords = {DISTRIBUTION FUNCTIONS; ARGON; THERMODYNAMIC PROPERTIES; COMPUTERIZED SIMULATION; STRUCTURE FACTORS; LIQUID STRUCTURE},
457          Number = {12},
458          Pages = {6312-6325},
# Line 354 | Line 463
463          Year = {1983},
464          Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/6312/1},
465          Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.445724}}
357 –
358 – @article{doi:10.1021/jp046852t,
359 –        Author = {Li, Yuhui and Krilov, Goran and Berne, B. J.},
360 –        Date-Added = {2010-10-19 08:58:54 -0400},
361 –        Date-Modified = {2010-10-19 08:58:54 -0400},
362 –        Doi = {10.1021/jp046852t},
363 –        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp046852t},
364 –        Journal = {The Journal of Physical Chemistry B},
365 –        Note = {PMID: 16851037},
366 –        Number = {1},
367 –        Pages = {463-470},
368 –        Title = {Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems:  Application to Liquid Argon},
369 –        Url = {http://pubs.acs.org/doi/abs/10.1021/jp046852t},
370 –        Volume = {109},
371 –        Year = {2005},
372 –        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp046852t},
373 –        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp046852t}}
466  
467   @article{ISI:A1984TQ73500045,
468 <        Author = {BERENDSEN, HJC and POSTMA, JPM and VANGUNSTEREN, WF and DINOLA, A and HAAK, JR},
468 >        Author = {Berendsen, H.~J.~C. and Postma, J.~P.~M. and VanGunsteren, W.~F. and Dinola, A and Haak, J.~R.},
469          Date-Added = {2010-10-18 13:04:11 -0400},
470          Date-Modified = {2010-10-18 13:04:11 -0400},
471 <        Journal = {JOURNAL OF CHEMICAL PHYSICS},
380 <        Journal-Iso = {J. Chem. Phys.},
471 >        Journal = {J. Chem. Phys.},
472          Number = {8},
473          Pages = {3684-3690},
474 <        Title = {MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH},
474 >        Title = {molecular-dynamics with coupling to an external bath},
475          Volume = {81},
476          Year = {1984}}
477  
478   @article{ANDERSEN:1980vn,
479          Address = {WOODBURY},
480 <        Author = {ANDERSEN, H. C.},
480 >        Author = {Andersen, H.~C.},
481          Cited-Reference-Count = {29},
482          Date-Added = {2010-10-18 13:01:27 -0400},
483          Date-Modified = {2010-10-18 13:01:27 -0400},
# Line 395 | Line 486
486          Isi-Document-Delivery-Number = {JK068},
487          Iso-Source-Abbreviation = {J. Chem. Phys.},
488          Issn = {0021-9606},
489 <        Journal = {JOURNAL OF CHEMICAL PHYSICS},
489 >        Journal = {J. Chem. Phys.},
490          Language = {English},
491          Number = {4},
492          Page-Count = {10},
# Line 420 | Line 511
511          Isi = {000085345300002},
512          Isi-Recid = {113793583},
513          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},
514 <        Journal = {Journal of Chemical Physics},
514 >        Journal = {J. Chem. Phys.},
515          Month = feb,
516          Number = {8},
517          Pages = {3474--3482},
# Line 434 | Line 525
525   @article{FELLER:1995fk,
526          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.},
527          Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
528 <        Author = {FELLER, SE and ZHANG, YH and PASTOR, RW and BROOKS, BR},
528 >        Author = {Feller, S.~E. and Zhang, Y.~H. and Pastor, R.~W. and Brooks, B.~R.},
529          Date-Added = {2010-10-18 12:59:12 -0400},
530          Date-Modified = {2010-10-18 12:59:12 -0400},
531          Isi = {A1995RU11000023},
532          Isi-Recid = {92912418},
533          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},
534 <        Journal = {Journal of Chemical Physics},
534 >        Journal = {J. Chem. Phys.},
535          Month = sep,
536          Number = {11},
537          Pages = {4613--4621},
# Line 461 | Line 552
552          Isi = {000228287900056},
553          Isi-Recid = {143814862},
554          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},
555 <        Journal = {Journal of Chemical Physics},
555 >        Journal = {J. Chem. Phys.},
556          Month = mar,
557          Number = {12},
558          Publisher = {AMER INST PHYSICS},
# Line 653 | Line 744 | can be very different from that of small hydrophobic m
744          Volume = {70},
745          Year = {1993},
746          Bdsk-File-1 = {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}}
656 –
657 – @article{Li2005,
658 –        Abstract = {A new approach is developed to study the dynamics of the localized process in solutions and other condensed phase systems. The approach employs a fluctuating elastic boundary (FEB) model which encloses the simulated system in an elastic bag that mimics the effects of the bulk solvent. This alleviates the need for periodic boundary conditions and allows for a reduction in the number of solvent molecules that need to be included in the simulation. The boundary bag is modeled as a mesh of quasi-particles connected by elastic bonds. The FEB model allows for volume and density fluctuations characteristic of the bulk system, and the shape of the boundary fluctuates during the course of the simulation to adapt to the configuration fluctuations of the explicit solute-solvent system inside. The method is applied to the simulation of a Lennard-Jones model of liquid argon. Various structural and dynamical quantities are computed and compared with those obtained from conventional periodic boundary simulations. The agreement between the two is excellent in most cases, thus validating the viability of the FEB method.},
659 –        Author = {Li, Y. and Krilov, G. and Berne, B.J.},
660 –        Date-Added = {2010-09-08 16:48:01 -0400},
661 –        Date-Modified = {2010-09-08 16:48:01 -0400},
662 –        Journal = {J. Phys. Chem. B},
663 –        Keywords = {Elastic bag; dewetting},
664 –        Pages = {463-470},
665 –        Title = {Elastic bag model for molecular dynamics simulations of solvated systems: Application to liquid argon},
666 –        Volume = {109},
667 –        Year = {2005},
668 –        Bdsk-File-1 = {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}}
747  
748   @article{Debenedetti1986,
749          Author = {Debenedetti, P.G.},
# Line 783 | Line 861 | can be very different from that of small hydrophobic m
861          Volume = {483},
862          Year = {2009},
863          Bdsk-File-1 = {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}}
786 –
787 – @article{Baltazar2006,
788 –        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},
789 –        Date-Added = {2010-09-08 16:48:01 -0400},
790 –        Date-Modified = {2010-09-08 16:48:01 -0400},
791 –        Journal = {Computational Materials Science},
792 –        Keywords = {NPT},
793 –        Pages = {526-536},
794 –        Title = {Assessment of isobaric-isothermal (NPT) simulations for finite systems},
795 –        Volume = {37},
796 –        Year = {2006},
797 –        Bdsk-File-1 = {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}}
864  
865   @article{Urquidi1999,
866          Author = {J. Urquidi and S. Singh and C.H. Cho and G.W. Robinson},
# Line 981 | Line 1047 | can be very different from that of small hydrophobic m
1047          Bdsk-File-1 = {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}}
1048  
1049   @article{Brooks1983a,
1050 <        Author = {Brooks, C.L III and Karplus, M.},
1050 >        Author = {Brooks, C.~L.~III and Karplus, M.},
1051          Date-Added = {2010-09-08 16:48:01 -0400},
1052          Date-Modified = {2010-09-08 16:48:38 -0400},
1053          Journal = {J. Chem. Phys.},
# Line 1434 | Line 1500 | can be very different from that of small hydrophobic m
1500          Date-Added = {2008-01-11 16:16:43 -0500},
1501          Date-Modified = {2008-01-11 16:16:43 -0500},
1502          Journal = jcp,
1503 <        Journal1 = {The Journal of Chemical Physics},
1503 >        Journal1 = {J. Chem. Phys.},
1504          Journal2 = {J. Chem. Phys.},
1505          Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
1506          Number = 5,
# Line 1916 | Line 1982 | can be very different from that of small hydrophobic m
1982          Title = {Aspects of Structural Glass Transitions},
1983          Volume = {I},
1984          Year = 1989,
1985 <        Bdsk-File-1 = {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}}
1985 >        Bdsk-File-1 = {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}}
1986  
1987   @article{Lewis91,
1988          Author = {L.~J. Lewis},
# Line 2573 | Line 2639 | can be very different from that of small hydrophobic m
2639          Volume = 29,
2640          Year = 1984}
2641  
2576 – @article{Foiles86,
2577 –        Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
2578 –        Date-Added = {2008-01-08 14:58:56 -0500},
2579 –        Date-Modified = {2008-01-08 14:58:58 -0500},
2580 –        Journal = prb,
2581 –        Number = 12,
2582 –        Pages = 7983,
2583 –        Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
2584 –        Volume = 33,
2585 –        Year = 1986}
2586 –
2642   @article{Zahn02,
2643          Author = {D. Zahn and B. Schilling and S.~M. Kast},
2644          Date-Added = {2008-01-08 14:58:56 -0500},

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