ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/langevinHull/langevinHull.bib
(Generate patch)

Comparing trunk/langevinHull/langevinHull.bib (file contents):
Revision 3652 by gezelter, Mon Oct 18 18:27:24 2010 UTC vs.
Revision 3653 by gezelter, Tue Oct 19 16:13:01 2010 UTC

# Line 2 | Line 2
2   %% http://bibdesk.sourceforge.net/
3  
4  
5 < %% Created for Dan Gezelter at 2010-10-18 13:05:47 -0400
5 > %% Created for Dan Gezelter at 2010-10-19 10:14:21 -0400
6  
7  
8   %% Saved with string encoding Unicode (UTF-8)
# Line 55 | Line 55
55   @string{prl = {Phys. Rev. Lett.}}
56  
57   @string{rmp = {Rev. Mod. Phys.}}
58 +
59 +
60 + @article{Baltazar:2006ru,
61 +        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.},
62 +        Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
63 +        Author = {Baltazar, S. E. and Romero, A. H. and Rodriguez-Lopez, J. L. and Terrones, H. and Martonak, R.},
64 +        Date = {OCT 2006},
65 +        Date-Added = {2010-10-19 10:14:13 -0400},
66 +        Date-Modified = {2010-10-19 10:14:13 -0400},
67 +        Doi = {DOI 10.1016/j.commatsci.2005.12.028},
68 +        Journal = {Computational Materials Science},
69 +        Keywords = {high pressures; finite systems; volume; molecular dynamics},
70 +        Pages = {526-536},
71 +        Publisher = {ELSEVIER SCIENCE BV},
72 +        Timescited = {3},
73 +        Title = {Assessment of isobaric-isothermal (NPT) simulations for finite systems},
74 +        Volume = {37},
75 +        Year = {2006},
76 +        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.commatsci.2005.12.028}}
77 +
78 + @article{Kohanoff:2005qm,
79 +        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.},
80 +        Address = {PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY},
81 +        Author = {Kohanoff, J and Caro, A and Finnis, MW},
82 +        Date = {SEP 5 2005},
83 +        Date-Added = {2010-10-19 10:14:05 -0400},
84 +        Date-Modified = {2010-10-19 10:14:05 -0400},
85 +        Doi = {DOI 10.1002/cphc.200400607},
86 +        Journal = {Chemphyschem},
87 +        Keywords = {clusters; gold; nanostructures; pressure; simulation},
88 +        Pages = {1848-1852},
89 +        Publisher = {WILEY-V C H VERLAG GMBH},
90 +        Timescited = {2},
91 +        Title = {An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters},
92 +        Volume = {6},
93 +        Year = {2005},
94 +        Bdsk-Url-1 = {http://dx.doi.org/10.1002/cphc.200400607}}
95 +
96 + @article{Zhu:xw,
97 +        Author = {Zhu, Wusheng and Krilov, Goran},
98 +        Date-Added = {2010-10-19 10:13:55 -0400},
99 +        Date-Modified = {2010-10-19 10:13:55 -0400},
100 +        Journal = {Journal of Molecular Structure: THEOCHEM},
101 +        Keywords = {Molecular dynamics; Hybrid solvation; Polyalanine; Non-periodic boundary condition},
102 +        Pages = {--},
103 +        Title = {New flexible boundary hybrid solvation models for efficient biomolecular simulations},
104 +        Ty = {JOUR},
105 +        Url = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c},
106 +        Volume = {In Press},
107 +        Year = {2008},
108 +        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c}}
109 +
110 + @article{LiY._jp046852t,
111 +        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.},
112 +        Affiliation = {Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027},
113 +        Author = {Li, Y. and Krilov, G. and Berne, B.J.},
114 +        Date-Added = {2010-10-19 10:13:46 -0400},
115 +        Date-Modified = {2010-10-19 10:13:46 -0400},
116 +        Issn = {1520-6106},
117 +        Journal = jpcb,
118 +        Number = {1},
119 +        Pages = {463-470},
120 +        Title = {Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems: Application to Liquid Argon},
121 +        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp046852t},
122 +        Volume = {109},
123 +        Year = {2005},
124 +        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp046852t}}
125 +
126 + @article{beglov:9050,
127 +        Author = {Dmitrii Beglov and Beno\^{i}t Roux},
128 +        Date-Added = {2010-10-19 09:49:30 -0400},
129 +        Date-Modified = {2010-10-19 09:49:30 -0400},
130 +        Doi = {10.1063/1.466711},
131 +        Journal = {The Journal of Chemical Physics},
132 +        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},
133 +        Number = {12},
134 +        Pages = {9050-9063},
135 +        Publisher = {AIP},
136 +        Title = {Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations},
137 +        Url = {http://link.aip.org/link/?JCP/100/9050/1},
138 +        Volume = {100},
139 +        Year = {1994},
140 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/100/9050/1},
141 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.466711}}
142  
143 + @article{Beglov:1995fk,
144 +        Author = {Beglov, D. and Roux, B.},
145 +        Date-Added = {2010-10-19 09:47:43 -0400},
146 +        Date-Modified = {2010-10-19 09:47:43 -0400},
147 +        Do = {10.1002/bip.360350205},
148 +        Isbn = {1097-0282},
149 +        Journal = {Biopolymers},
150 +        Journal1 = {Biopolymers},
151 +        Number = {2},
152 +        Pages = {171--178},
153 +        Publisher = {Wiley Subscription Services, Inc., A Wiley Company},
154 +        Title = {Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations},
155 +        Ty = {JOUR},
156 +        Url = {http://dx.doi.org/10.1002/bip.360350205},
157 +        Volume = {35},
158 +        Year = {1995},
159 +        Bdsk-Url-1 = {http://dx.doi.org/10.1002/bip.360350205}}
160  
161 + @article{king:3647,
162 +        Author = {Gregory King and Arieh Warshel},
163 +        Date-Added = {2010-10-19 09:30:46 -0400},
164 +        Date-Modified = {2010-10-19 09:30:46 -0400},
165 +        Doi = {10.1063/1.456845},
166 +        Journal = {The Journal of Chemical Physics},
167 +        Keywords = {AQUEOUS SOLUTIONS; LIQUID STRUCTURE; SOLVATION; INTERMOLECULAR FORCES; PROTEINS; BOUNDARY CONDITIONS; CONSTRAINTS; DIELECTRIC PROPERTIES; MOLECULAR DYNAMICS CALCULATIONS; COMPUTERIZED SIMULATION},
168 +        Number = {6},
169 +        Pages = {3647-3661},
170 +        Publisher = {AIP},
171 +        Title = {A surface constrained all-atom solvent model for effective simulations of polar solutions},
172 +        Url = {http://link.aip.org/link/?JCP/91/3647/1},
173 +        Volume = {91},
174 +        Year = {1989},
175 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/91/3647/1},
176 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.456845}}
177 +
178 + @article{iii:6312,
179 +        Author = {C. L. Brooks III and Martin Karplus},
180 +        Date-Added = {2010-10-19 09:14:01 -0400},
181 +        Date-Modified = {2010-10-19 09:14:01 -0400},
182 +        Doi = {10.1063/1.445724},
183 +        Journal = {The Journal of Chemical Physics},
184 +        Keywords = {DISTRIBUTION FUNCTIONS; ARGON; THERMODYNAMIC PROPERTIES; COMPUTERIZED SIMULATION; STRUCTURE FACTORS; LIQUID STRUCTURE},
185 +        Number = {12},
186 +        Pages = {6312-6325},
187 +        Publisher = {AIP},
188 +        Title = {Deformable stochastic boundaries in molecular dynamics},
189 +        Url = {http://link.aip.org/link/?JCP/79/6312/1},
190 +        Volume = {79},
191 +        Year = {1983},
192 +        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/6312/1},
193 +        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.445724}}
194 +
195 + @article{doi:10.1021/jp046852t,
196 +        Author = {Li, Yuhui and Krilov, Goran and Berne, B. J.},
197 +        Date-Added = {2010-10-19 08:58:54 -0400},
198 +        Date-Modified = {2010-10-19 08:58:54 -0400},
199 +        Doi = {10.1021/jp046852t},
200 +        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp046852t},
201 +        Journal = {The Journal of Physical Chemistry B},
202 +        Note = {PMID: 16851037},
203 +        Number = {1},
204 +        Pages = {463-470},
205 +        Title = {Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems:  Application to Liquid Argon},
206 +        Url = {http://pubs.acs.org/doi/abs/10.1021/jp046852t},
207 +        Volume = {109},
208 +        Year = {2005},
209 +        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp046852t},
210 +        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp046852t}}
211 +
212   @article{ISI:A1984TQ73500045,
213          Author = {BERENDSEN, HJC and POSTMA, JPM and VANGUNSTEREN, WF and DINOLA, A and HAAK, JR},
214          Date-Added = {2010-10-18 13:04:11 -0400},
# Line 67 | Line 219
219          Pages = {3684-3690},
220          Title = {MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH},
221          Volume = {81},
222 <        Year = {1984}
71 < }
222 >        Year = {1984}}
223  
224   @article{ANDERSEN:1980vn,
225          Address = {WOODBURY},
# Line 1601 | Line 1752 | can be very different from that of small hydrophobic m
1752          Publisher = {North-Holland},
1753          Title = {Aspects of Structural Glass Transitions},
1754          Volume = {I},
1755 <        Year = 1989}
1755 >        Year = 1989,
1756 >        Bdsk-File-1 = {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}}
1757  
1758   @article{Lewis91,
1759          Author = {L.~J. Lewis},

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines