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%% Created for Dan Gezelter at 2010-11-11 16:41:08 -0500 |
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%% Saved with string encoding Unicode (UTF-8) |
| 55 |
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@string{prl = {Phys. Rev. Lett.}} |
| 56 |
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| 57 |
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@string{rmp = {Rev. Mod. Phys.}} |
| 58 |
+ |
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| 59 |
+ |
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| 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@unpublished{QSC, |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 |
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| 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 |
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|
| 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 |
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Author = {Guy C. Brown}, |
| 121 |
|
Date-Added = {2010-11-09 15:01:26 -0500}, |
| 378 |
|
Volume = {6}, |
| 379 |
|
Year = {2005}, |
| 380 |
|
Bdsk-Url-1 = {http://dx.doi.org/10.1002/cphc.200400607}} |
| 322 |
– |
|
| 323 |
– |
@article{Zhu:xw, |
| 324 |
– |
Author = {Zhu, Wusheng and Krilov, Goran}, |
| 325 |
– |
Date-Added = {2010-10-19 10:13:55 -0400}, |
| 326 |
– |
Date-Modified = {2010-10-19 10:13:55 -0400}, |
| 327 |
– |
Journal = {Journal of Molecular Structure: THEOCHEM}, |
| 328 |
– |
Keywords = {Molecular dynamics; Hybrid solvation; Polyalanine; Non-periodic boundary condition}, |
| 329 |
– |
Pages = {--}, |
| 330 |
– |
Title = {New flexible boundary hybrid solvation models for efficient biomolecular simulations}, |
| 331 |
– |
Ty = {JOUR}, |
| 332 |
– |
Url = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c}, |
| 333 |
– |
Volume = {In Press}, |
| 334 |
– |
Year = {2008}, |
| 335 |
– |
Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TGT-4SPC0K0-6/1/ffff9c19dc09fefbeda9efaf0652c91c}} |
| 381 |
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| 382 |
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@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.}, |
| 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}} |
| 466 |
|
|
| 422 |
– |
@article{doi:10.1021/jp046852t, |
| 423 |
– |
Author = {Li, Yuhui and Krilov, Goran and Berne, B. J.}, |
| 424 |
– |
Date-Added = {2010-10-19 08:58:54 -0400}, |
| 425 |
– |
Date-Modified = {2010-10-19 08:58:54 -0400}, |
| 426 |
– |
Doi = {10.1021/jp046852t}, |
| 427 |
– |
Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp046852t}, |
| 428 |
– |
Journal = {The Journal of Physical Chemistry B}, |
| 429 |
– |
Note = {PMID: 16851037}, |
| 430 |
– |
Number = {1}, |
| 431 |
– |
Pages = {463-470}, |
| 432 |
– |
Title = {Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems: Application to Liquid Argon}, |
| 433 |
– |
Url = {http://pubs.acs.org/doi/abs/10.1021/jp046852t}, |
| 434 |
– |
Volume = {109}, |
| 435 |
– |
Year = {2005}, |
| 436 |
– |
Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp046852t}, |
| 437 |
– |
Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp046852t}} |
| 438 |
– |
|
| 467 |
|
@article{ISI:A1984TQ73500045, |
| 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}, |
| 745 |
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Year = {1993}, |
| 746 |
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| 747 |
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|
| 720 |
– |
@article{Li2005, |
| 721 |
– |
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.}, |
| 722 |
– |
Author = {Li, Y. and Krilov, G. and Berne, B.J.}, |
| 723 |
– |
Date-Added = {2010-09-08 16:48:01 -0400}, |
| 724 |
– |
Date-Modified = {2010-09-08 16:48:01 -0400}, |
| 725 |
– |
Journal = {J. Phys. Chem. B}, |
| 726 |
– |
Keywords = {Elastic bag; dewetting}, |
| 727 |
– |
Pages = {463-470}, |
| 728 |
– |
Title = {Elastic bag model for molecular dynamics simulations of solvated systems: Application to liquid argon}, |
| 729 |
– |
Volume = {109}, |
| 730 |
– |
Year = {2005}, |
| 731 |
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| 732 |
– |
|
| 748 |
|
@article{Debenedetti1986, |
| 749 |
|
Author = {Debenedetti, P.G.}, |
| 750 |
|
Date-Added = {2010-09-08 16:48:01 -0400}, |
| 862 |
|
Year = {2009}, |
| 863 |
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| 864 |
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| 850 |
– |
@article{Baltazar2006, |
| 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 = {Comp. Mat. Sci.}, |
| 855 |
– |
Keywords = {NPT}, |
| 856 |
– |
Pages = {526-536}, |
| 857 |
– |
Title = {Assessment of isobaric-isothermal (NPT) simulations for finite systems}, |
| 858 |
– |
Volume = {37}, |
| 859 |
– |
Year = {2006}, |
| 860 |
– |
Bdsk-File-1 = {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}} |
| 861 |
– |
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| 865 |
|
@article{Urquidi1999, |
| 866 |
|
Author = {J. Urquidi and S. Singh and C.H. Cho and G.W. Robinson}, |
| 867 |
|
Date-Added = {2010-09-08 16:48:01 -0400}, |
| 2639 |
|
Volume = 29, |
| 2640 |
|
Year = 1984} |
| 2641 |
|
|
| 2639 |
– |
@article{Foiles86, |
| 2640 |
– |
Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw}, |
| 2641 |
– |
Date-Added = {2008-01-08 14:58:56 -0500}, |
| 2642 |
– |
Date-Modified = {2008-01-08 14:58:58 -0500}, |
| 2643 |
– |
Journal = prb, |
| 2644 |
– |
Number = 12, |
| 2645 |
– |
Pages = 7983, |
| 2646 |
– |
Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, |
| 2647 |
– |
Volume = 33, |
| 2648 |
– |
Year = 1986} |
| 2649 |
– |
|
| 2642 |
|
@article{Zahn02, |
| 2643 |
|
Author = {D. Zahn and B. Schilling and S.~M. Kast}, |
| 2644 |
|
Date-Added = {2008-01-08 14:58:56 -0500}, |
