Get Bridging Time Scales: Molecular Simulations for the Next PDF

By Edo Kussell, Jun Shimada, Eugene I. Shakhnovich (auth.), Peter Nielaba, Michel Mareschal, Giovanni Ciccotti (eds.)

ISBN-10: 3540443177

ISBN-13: 9783540443179

ISBN-10: 3540458379

ISBN-13: 9783540458371

The behaviour of many advanced fabrics extends over the years- and lengthscales well past those who can usually be defined utilizing regular molecular dynamics or Monte Carlo simulation recommendations. As development is coming extra via subtle simulation tools than from elevated desktop energy, this quantity is meant as either an creation and a evaluate of all appropriate smooth tools that would form molecular simulation within the coming near near decade. Written as a collection of instructional stories, the publication may be of use to experts and nonspecialists alike.

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Baker: Nature Struct. Biol. 7, 669–673 (2000). S. Nauli, B. Kuhlman, D. Baker: Nature Struct. Biol. 8, 602–605 (2001). S. Park, M. C. R. Shastry, H. Roder: Nature Struct. Biol. 6, 943–947 (1999). J. Shimada, E. Kussell, E. I. Shakhnovich: J. Mol. Biol. 308, 79–95 (2001). P. G. Bolhuis, D. Chandler, C. Dellago, P. L. Geissler: Annu. Rev. Phys. Chem. submitted (2002). A. R. Fersht: Proc. Natl. Acad. Sci. USA 92, 10869–10873 (1995). T. R. Sosnick, L. Mayne, S. W. Englander: Proteins 24, 413–426 (1996).

Both power-law [34] and stretched-exponential [35] behavior can emerge depending on the nature of the barriers. In the lattice simulations, we observed a power-law or highly stretched exponential relaxation at long times. The landscape for slow sidechain equilibration thus seems to be one of increasingly deeper wells, rather than a single cooperative transition to nativity. This places sidechain relaxation within the set of phenomena that can be characterized as a glass. Classic lattice models without sidechain states, however, do not exhibit a glass transition at any reasonable temperature [8].

The highest frequency motions are typically bond vibrations involving hydrogen. Since these fast motions are approximately decoupled from the rest of the system, they undergo many oscillations on the time scale of the remainder of the system. Hence their interaction with the remainder of the system is roughly governed by their average location, which is at the equilibrium bond length. There are algorithms, such as shake and rattle, which constrain these high frequency bonds to remain fixed at their equilibrium extensions, thereby eliminating the stiffest motions and allowing the time step to be increased.

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Bridging Time Scales: Molecular Simulations for the Next Decade by Edo Kussell, Jun Shimada, Eugene I. Shakhnovich (auth.), Peter Nielaba, Michel Mareschal, Giovanni Ciccotti (eds.)

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