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Revision 3663 by gezelter, Thu Oct 21 16:24:13 2010 UTC

+%% http://bibdesk.sourceforge.net/
-<
+%% Created for Kelsey Stocker at 2010-09-22 15:53:28 -0400
->
+%% Created for Dan Gezelter at 2010-10-21 12:23:58 -0400
+%% Saved with string encoding Unicode (UTF-8)
+@string{prl = {Phys. Rev. Lett.}}
+@string{rmp = {Rev. Mod. Phys.}}
-+
-+
-+
+@misc{Qhull,
-+
+        Date-Added = {2010-10-21 12:05:09 -0400},
-+
+        Date-Modified = {2010-10-21 12:05:09 -0400},
-+
+        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. $\mathtt{http://www.geom.umn.edu/software/qhull/}$},
-+
+        Title = {Qhull},
-+
+        Year = 1993}
-+
-+
+@article{Sun:2008fk,
-+
+        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.},
-+
+        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
-+
+        Author = {Sun, Xiuquan and Lin, Teng and Gezelter, J. Daniel},
-+
+        Date-Added = {2010-10-21 12:04:05 -0400},
-+
+        Date-Modified = {2010-10-21 12:04:05 -0400},
-+
+        Doi = {DOI 10.1063/1.2936991},
-+
+        Isi = {000256936700007},
-+
+        Isi-Recid = {171639081},
-+
+        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},
-+
+        Journal = {Journal of Chemical Physics},
-+
+        Month = jun,
-+
+        Number = {23},
-+
+        Publisher = {AMER INST PHYSICS},
-+
+        Times-Cited = {2},
-+
+        Title = {Langevin dynamics for rigid bodies of arbitrary shape},
-+
+        Volume = {128},
-+
+        Year = {2008},
-+
+        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000256936700007}}
-+
-+
+@article{ISI:000167766600035,
-+
+        Abstract = {Molecular dynamics simulations are used to
-+
+                  investigate the separation of water films adjacent
-+
+                  to a hot metal surface. The simulations clearly show
-+
+                  that the water layers nearest the surface overheat
-+
+                  and undergo explosive boiling. For thick films, the
-+
+                  expansion of the vaporized molecules near the
-+
+                  surface forces the outer water layers to move away
-+
+                  from the surface. These results are of interest for
-+
+                  mass spectrometry of biological molecules, steam
-+
+                  cleaning of surfaces, and medical procedures.},
-+
+        Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
-+
+        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.},
-+
+        Author = {Dou, YS and Zhigilei, LV and Winograd, N and Garrison, BJ},
-+
+        Date-Added = {2010-10-21 12:02:39 -0400},
-+
+        Date-Modified = {2010-10-21 12:02:39 -0400},
-+
+        Doc-Delivery-Number = {416ED},
-+
+        Issn = {1089-5639},
-+
+        Journal = {J. Phys. Chem. A},
-+
+        Journal-Iso = {J. Phys. Chem. A},
-+
+        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},
-+
+        Language = {English},
-+
+        Month = {MAR 29},
-+
+        Number = {12},
-+
+        Number-Of-Cited-References = {65},
-+
+        Pages = {2748-2755},
-+
+        Publisher = {AMER CHEMICAL SOC},
-+
+        Subject-Category = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
-+
+        Times-Cited = {66},
-+
+        Title = {Explosive boiling of water films adjacent to heated surfaces: A microscopic description},
-+
+        Type = {Article},
-+
+        Unique-Id = {ISI:000167766600035},
-+
+        Volume = {105},
-+
+        Year = {2001}}
-+
-+
+@article{wolf:8254,
-+
+        Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
-+
+        Date-Added = {2010-10-21 12:02:26 -0400},
-+
+        Date-Modified = {2010-10-21 12:02:26 -0400},
-+
+        Doi = {10.1063/1.478738},
-+
+        Journal = {J. Chem. Phys.},
-+
+        Keywords = {POTENTIAL ENERGY; COULOMB FIELD; COULOMB ENERGY; LATTICE PARAMETERS; potential energy functions; lattice dynamics; lattice energy},
-+
+        Number = {17},
-+
+        Pages = {8254-8282},
-+
+        Publisher = {AIP},
-+
+        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r[sup -1] summation},
-+
+        Url = {http://link.aip.org/link/?JCP/110/8254/1},
-+
+        Volume = {110},
-+
+        Year = {1999},
-+
+        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/110/8254/1},
-+
+        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.478738}}
-+
-+
+@article{Fennell06,
-+
+        Author = {C.~J. Fennell and J.~D. Gezelter},
-+
+        Date-Added = {2010-10-21 12:02:17 -0400},
-+
+        Date-Modified = {2010-10-21 12:02:17 -0400},
-+
+        Doi = {10.1063/1.2206581},
-+
+        Journal = {J. Chem. Phys.},
-+
+        Number = {23},
-+
+        Pages = {234104(12)},
-+
+        Rating = {5},
-+
+        Read = {Yes},
-+
+        Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
-+
+        Volume = {124},
-+
+        Year = {2006},
-+
+        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}
-+
-+
+@article{PhysRevB.59.3527,
-+
+        Author = {Qi, Yue and \c{C}a\v{g}in, Tahir and Kimura, Yoshitaka and {Goddard III}, William A.},
-+
+        Date-Added = {2010-10-21 12:02:07 -0400},
-+
+        Date-Modified = {2010-10-21 12:02:07 -0400},
-+
+        Doi = {10.1103/PhysRevB.59.3527},
-+
+        Journal = {Phys. Rev. B},
-+
+        Local-Url = {file://localhost/Users/charles/Documents/Papers/Qi/1999.pdf},
-+
+        Month = {Feb},
-+
+        Number = {5},
-+
+        Numpages = {6},
-+
+        Pages = {3527-3533},
-+
+        Publisher = {American Physical Society},
-+
+        Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals:\quad{}{C}u-{A}g and {C}u-{N}i},
-+
+        Volume = {59},
-+
+        Year = {1999},
-+
+        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevB.59.3527}}
-+
-+
+@article{Baltazar:2006ru,
-+
+        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.},
-+
+        Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
-+
+        Author = {Baltazar, S. E. and Romero, A. H. and Rodriguez-Lopez, J. L. and Terrones, H. and Martonak, R.},
-+
+        Date = {OCT 2006},
-+
+        Date-Added = {2010-10-19 10:14:13 -0400},
-+
+        Date-Modified = {2010-10-19 10:14:13 -0400},
-+
+        Doi = {DOI 10.1016/j.commatsci.2005.12.028},
-+
+        Journal = {Computational Materials Science},
-+
+        Keywords = {high pressures; finite systems; volume; molecular dynamics},
-+
+        Pages = {526-536},
-+
+        Publisher = {ELSEVIER SCIENCE BV},
-+
+        Timescited = {3},
-+
+        Title = {Assessment of isobaric-isothermal (NPT) simulations for finite systems},
-+
+        Volume = {37},
-+
+        Year = {2006},
-+
+        Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.commatsci.2005.12.028}}
-+
-+
+@article{Kohanoff:2005qm,
-+
+        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.},
-+
+        Address = {PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY},
-+
+        Author = {Kohanoff, J and Caro, A and Finnis, MW},
-+
+        Date = {SEP 5 2005},
-+
+        Date-Added = {2010-10-19 10:14:05 -0400},
-+
+        Date-Modified = {2010-10-19 10:14:05 -0400},
-+
+        Doi = {DOI 10.1002/cphc.200400607},
-+
+        Journal = {Chemphyschem},
-+
+        Keywords = {clusters; gold; nanostructures; pressure; simulation},
-+
+        Pages = {1848-1852},
-+
+        Publisher = {WILEY-V C H VERLAG GMBH},
-+
+        Timescited = {2},
-+
+        Title = {An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters},
-+
+        Volume = {6},
-+
+        Year = {2005},
-+
+        Bdsk-Url-1 = {http://dx.doi.org/10.1002/cphc.200400607}}
-+
-+
+@article{Zhu:xw,
-+
+        Author = {Zhu, Wusheng and Krilov, Goran},
-+
+        Date-Added = {2010-10-19 10:13:55 -0400},
-+
+        Date-Modified = {2010-10-19 10:13:55 -0400},
-+
+        Journal = {Journal of Molecular Structure: THEOCHEM},
-+
+        Keywords = {Molecular dynamics; Hybrid solvation; Polyalanine; Non-periodic boundary condition},
-+
+        Pages = {--},
-+
+        Title = {New flexible boundary hybrid solvation models for efficient biomolecular simulations},
-+
+        Ty = {JOUR},
-+
+        Url = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c},
-+
+        Volume = {In Press},
-+
+        Year = {2008},
-+
+        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c}}
-+
-+
+@article{LiY._jp046852t,
-+
+        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.},
-+
+        Affiliation = {Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027},
-+
+        Author = {Li, Y. and Krilov, G. and Berne, B.J.},
-+
+        Date-Added = {2010-10-19 10:13:46 -0400},
-+
+        Date-Modified = {2010-10-19 10:13:46 -0400},
-+
+        Issn = {1520-6106},
-+
+        Journal = jpcb,
-+
+        Number = {1},
-+
+        Pages = {463-470},
-+
+        Title = {Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems: Application to Liquid Argon},
-+
+        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp046852t},
-+
+        Volume = {109},
-+
+        Year = {2005},
-+
+        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp046852t}}
-+
-+
+@article{beglov:9050,
-+
+        Author = {Dmitrii Beglov and Beno\^{i}t Roux},
-+
+        Date-Added = {2010-10-19 09:49:30 -0400},
-+
+        Date-Modified = {2010-10-19 09:49:30 -0400},
-+
+        Doi = {10.1063/1.466711},
-+
+        Journal = {The Journal of Chemical Physics},
-+
+        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},
-+
+        Number = {12},
-+
+        Pages = {9050-9063},
-+
+        Publisher = {AIP},
-+
+        Title = {Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations},
-+
+        Url = {http://link.aip.org/link/?JCP/100/9050/1},
-+
+        Volume = {100},
-+
+        Year = {1994},
-+
+        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/100/9050/1},
-+
+        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.466711}}
-+
-+
+@article{Beglov:1995fk,
-+
+        Author = {Beglov, D. and Roux, B.},
-+
+        Date-Added = {2010-10-19 09:47:43 -0400},
-+
+        Date-Modified = {2010-10-19 09:47:43 -0400},
-+
+        Do = {10.1002/bip.360350205},
-+
+        Isbn = {1097-0282},
-+
+        Journal = {Biopolymers},
-+
+        Journal1 = {Biopolymers},
-+
+        Number = {2},
-+
+        Pages = {171--178},
-+
+        Publisher = {Wiley Subscription Services, Inc., A Wiley Company},
-+
+        Title = {Dominant solvation effects from the primary shell of hydration: Approximation for molecular dynamics simulations},
-+
+        Ty = {JOUR},
-+
+        Url = {http://dx.doi.org/10.1002/bip.360350205},
-+
+        Volume = {35},
-+
+        Year = {1995},
-+
+        Bdsk-Url-1 = {http://dx.doi.org/10.1002/bip.360350205}}
-+
-+
+@article{king:3647,
-+
+        Author = {Gregory King and Arieh Warshel},
-+
+        Date-Added = {2010-10-19 09:30:46 -0400},
-+
+        Date-Modified = {2010-10-19 09:30:46 -0400},
-+
+        Doi = {10.1063/1.456845},
-+
+        Journal = {The Journal of Chemical Physics},
-+
+        Keywords = {AQUEOUS SOLUTIONS; LIQUID STRUCTURE; SOLVATION; INTERMOLECULAR FORCES; PROTEINS; BOUNDARY CONDITIONS; CONSTRAINTS; DIELECTRIC PROPERTIES; MOLECULAR DYNAMICS CALCULATIONS; COMPUTERIZED SIMULATION},
-+
+        Number = {6},
-+
+        Pages = {3647-3661},
-+
+        Publisher = {AIP},
-+
+        Title = {A surface constrained all-atom solvent model for effective simulations of polar solutions},
-+
+        Url = {http://link.aip.org/link/?JCP/91/3647/1},
-+
+        Volume = {91},
-+
+        Year = {1989},
-+
+        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/91/3647/1},
-+
+        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.456845}}
-+
-+
+@article{iii:6312,
-+
+        Author = {C. L. Brooks III and Martin Karplus},
-+
+        Date-Added = {2010-10-19 09:14:01 -0400},
-+
+        Date-Modified = {2010-10-19 09:14:01 -0400},
-+
+        Doi = {10.1063/1.445724},
-+
+        Journal = {The Journal of Chemical Physics},
-+
+        Keywords = {DISTRIBUTION FUNCTIONS; ARGON; THERMODYNAMIC PROPERTIES; COMPUTERIZED SIMULATION; STRUCTURE FACTORS; LIQUID STRUCTURE},
-+
+        Number = {12},
-+
+        Pages = {6312-6325},
-+
+        Publisher = {AIP},
-+
+        Title = {Deformable stochastic boundaries in molecular dynamics},
-+
+        Url = {http://link.aip.org/link/?JCP/79/6312/1},
-+
+        Volume = {79},
-+
+        Year = {1983},
-+
+        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/6312/1},
-+
+        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.445724}}
-+
-+
+@article{doi:10.1021/jp046852t,
-+
+        Author = {Li, Yuhui and Krilov, Goran and Berne, B. J.},
-+
+        Date-Added = {2010-10-19 08:58:54 -0400},
-+
+        Date-Modified = {2010-10-19 08:58:54 -0400},
-+
+        Doi = {10.1021/jp046852t},
-+
+        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp046852t},
-+
+        Journal = {The Journal of Physical Chemistry B},
-+
+        Note = {PMID: 16851037},
-+
+        Number = {1},
-+
+        Pages = {463-470},
-+
+        Title = {Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems:  Application to Liquid Argon},
-+
+        Url = {http://pubs.acs.org/doi/abs/10.1021/jp046852t},
-+
+        Volume = {109},
-+
+        Year = {2005},
-+
+        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp046852t},
-+
+        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp046852t}}
-+
-+
+@article{ISI:A1984TQ73500045,
-+
+        Author = {BERENDSEN, HJC and POSTMA, JPM and VANGUNSTEREN, WF and DINOLA, A and HAAK, JR},
-+
+        Date-Added = {2010-10-18 13:04:11 -0400},
-+
+        Date-Modified = {2010-10-18 13:04:11 -0400},
-+
+        Journal = {JOURNAL OF CHEMICAL PHYSICS},
-+
+        Journal-Iso = {J. Chem. Phys.},
-+
+        Number = {8},
-+
+        Pages = {3684-3690},
-+
+        Title = {MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH},
-+
+        Volume = {81},
-+
+        Year = {1984}}
-+
-+
+@article{ANDERSEN:1980vn,
-+
+        Address = {WOODBURY},
-+
+        Author = {ANDERSEN, H. C.},
-+
+        Cited-Reference-Count = {29},
-+
+        Date-Added = {2010-10-18 13:01:27 -0400},
-+
+        Date-Modified = {2010-10-18 13:01:27 -0400},
-+
+        Document-Type = {Article},
-+
+        Isi = {ISI:A1980JK06800026},
-+
+        Isi-Document-Delivery-Number = {JK068},
-+
+        Iso-Source-Abbreviation = {J. Chem. Phys.},
-+
+        Issn = {0021-9606},
-+
+        Journal = {JOURNAL OF CHEMICAL PHYSICS},
-+
+        Language = {English},
-+
+        Number = {4},
-+
+        Page-Count = {10},
-+
+        Pages = {2384--2393},
-+
+        Publication-Type = {J},
-+
+        Publisher = {AMER INST PHYSICS},
-+
+        Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
-+
+        Reprint-Address = {ANDERSEN, HC, STANFORD UNIV,DEPT CHEM,STANFORD,CA 94305.},
-+
+        Source = {J CHEM PHYS},
-+
+        Subject-Category = {Physics, Atomic, Molecular & Chemical},
-+
+        Times-Cited = {2017},
-+
+        Title = {MOLECULAR-DYNAMICS SIMULATIONS AT CONSTANT PRESSURE AND-OR TEMPERATURE},
-+
+        Volume = {72},
-+
+        Year = {1980}}
-+
-+
+@article{Sturgeon:2000kx,
-+
+        Abstract = {We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nose-Poincare thermostat, recently developed by Bond, Leimkuhler, and Laird [J. Comp. Phys. 151, 114 (1999)]. This Nose-Poincare-Andersen (NPA) formulation has advantages over the Nose-Hoover-Andersen approach in that the NPA is Hamiltonian and can take advantage of symplectic integration schemes, which lead to enhanced stability for long-time simulations. The equations of motion are integrated using a generalized leapfrog algorithm (GLA) and the method is easy to implement, symplectic, explicit, and time reversible. To demonstrate the superior stability of the method we show results for test simulations using a model for aluminum and compare it to a recently developed time-reversible algorithm for Nose-Hoover-Anderson. In addition, an extension of the NPA to multiple time steps is outlined and a symplectic and time-reversible integration algorithm, based on the GLA, is given. (C) 2000 American Institute of Physics. [S0021-9606(00)51307-5].},
-+
+        Address = {2 HUNTINGTON QUADRANGLE, STE 1NO1, MELVILLE, NY 11747-4501 USA},
-+
+        Author = {Sturgeon, JB and Laird, BB},
-+
+        Date-Added = {2010-10-18 13:00:24 -0400},
-+
+        Date-Modified = {2010-10-18 13:00:24 -0400},
-+
+        Isi = {000085345300002},
-+
+        Isi-Recid = {113793583},
-+
+        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},
-+
+        Journal = {Journal of Chemical Physics},
-+
+        Month = feb,
-+
+        Number = {8},
-+
+        Pages = {3474--3482},
-+
+        Publisher = {AMER INST PHYSICS},
-+
+        Times-Cited = {46},
-+
+        Title = {Symplectic algorithm for constant-pressure molecular dynamics using a Nose-Poincare thermostat},
-+
+        Volume = {112},
-+
+        Year = {2000},
-+
+        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000085345300002}}
-+
-+
+@article{FELLER:1995fk,
-+
+        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.},
-+
+        Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
-+
+        Author = {FELLER, SE and ZHANG, YH and PASTOR, RW and BROOKS, BR},
-+
+        Date-Added = {2010-10-18 12:59:12 -0400},
-+
+        Date-Modified = {2010-10-18 12:59:12 -0400},
-+
+        Isi = {A1995RU11000023},
-+
+        Isi-Recid = {92912418},
-+
+        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},
-+
+        Journal = {Journal of Chemical Physics},
-+
+        Month = sep,
-+
+        Number = {11},
-+
+        Pages = {4613--4621},
-+
+        Publisher = {AMER INST PHYSICS},
-+
+        Times-Cited = {603},
-+
+        Title = {CONSTANT-PRESSURE MOLECULAR-DYNAMICS SIMULATION - THE LANGEVIN PISTON METHOD},
-+
+        Volume = {103},
-+
+        Year = {1995},
-+
+        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=A1995RU11000023}}
-+
+@article{Jakobsen:2005uq,
-+
+        Abstract = {We present a method for constant-pressure and constant-surface tension simulations in dissipative particle dynamics using a Langevin piston approach. We demonstrate that the corresponding equations of motion lead to the relevant ensembles and propose an appropriate scheme of integration. After having identified a suitable set of parameters for the approach, we demonstrate the feasibility of the approach by applying it to two different systems, a simple isotropic fluid and an anisotropic fluid lipid-bilayer membrane in water. Results are presented for, respectively, isothermal bulk compressibility, tracer diffusion coefficient, lipid head-group area, and isothermal area compressibility. We find that our Langevin piston approach leads to improvements over other approaches in terms of faster equilibration and shorter correlation times of various system variables.},
-+
+        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
-+
+        Author = {Jakobsen, AF},
-+
+        Date-Added = {2010-10-18 12:59:12 -0400},
-+
+        Date-Modified = {2010-10-18 12:59:12 -0400},
-+
+        Doi = {DOI 10.1063/1.1867374},
-+
+        Isi = {000228287900056},
-+
+        Isi-Recid = {143814862},
-+
+        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},
-+
+        Journal = {Journal of Chemical Physics},
-+
+        Month = mar,
-+
+        Number = {12},
-+
+        Publisher = {AMER INST PHYSICS},
-+
+        Times-Cited = {44},
-+
+        Title = {Constant-pressure and constant-surface tension simulations in dissipative particle dynamics},
-+
+        Volume = {122},
-+
+        Year = {2005},
-+
+        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000228287900056}}
-+
-+
+@misc{openmd,
-+
+        Author = {J. Daniel Gezelter and Shenyu Kuang and James Marr and Kelsey Stocker and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke},
-+
+        Date-Added = {2010-10-18 12:51:55 -0400},
-+
+        Date-Modified = {2010-10-18 12:51:55 -0400},
-+
+        Howpublished = {Available at {\tt http://openmd.net}},
-+
+        Title = {{OpenMD, an open source engine for molecular dynamics}}}
+@article{Fine1973,
+        Author = {Fine, Rana A. and Millero, Frank J.},
+        Publisher = {North-Holland},
+        Title = {Aspects of Structural Glass Transitions},
+        Volume = {I},
-<
+        Year = 1989}
->
+        Year = 1989,
->
+        Bdsk-File-1 = {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}}
+@article{Lewis91,
+        Author = {L.~J. Lewis},

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Comparing trunk/langevinHull/langevinHull.bib (file contents): Revision 3649 by kstocke1, Thu Sep 23 21:42:37 2010 UTC vs. Revision 3663 by gezelter, Thu Oct 21 16:24:13 2010 UTC

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Comparing trunk/langevinHull/langevinHull.bib (file contents):
Revision 3649 by kstocke1, Thu Sep 23 21:42:37 2010 UTC vs.
Revision 3663 by gezelter, Thu Oct 21 16:24:13 2010 UTC