By Charles L. Brooks, Martin Karplus, B. Montgomery Pettitt

Featuring a wide-ranging view of present advancements in protein study, the papers during this assortment, each one written through extremely popular specialists within the box, study numerous features of protein constitution, features, dynamics, and experimentation. themes comprise dynamical simulation tools, the organic position of atom fluctuations, protein folding, impacts on protein dynamics, and numerous analytical innovations, similar to X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. this is often a part of a chain dedicated to delivering normal details on a wide selection of subject matters in chemical physics as a way to stimulate new learn and to function a textual content for rookies in a selected zone of chemical physics.

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Additional info for Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. (Advances in Chemical Physics)(Vol. 71.)

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Thus they are not adequately sampled in conventional simulation approaches. Activated dynamics methods provide one alternative that overcomes this sampling problem, although stochastic dynamics has also been applied to barrier crossing phenomena (see Chapt. 3). Special simulation techniques have been developed which make possible the efficient determination of trajectories of relevance in calculating the rates for activated p r o c e s ~ e s . These ~ ~ ~ -techniques, ~~~ which were earlier applied to small-moleculecollision dynamics125-127and to vacancy diffusion dynamics in regular solids,128 represent a synthesis of molecular dynamics methods and transition-state theory that can be used with the more general dynamics techniques discussed above.

RN)refer to the N atoms in the reaction zone. 44 DYNAMICAL SIMULATION METHODS These modified equations of motion are solved numerically using a Verlet type of algorithm which includes the effect due to the presence of Langevin forceswJo2(see Chapt. G). There are some limitations to the stochastic boundary molecular dynamics approach in its present form. Since the method is limited to a local region, it neglects explicit effects of the rest of the system. Extensions of the theory to include the influence of low-frequency motions and fluctuating long-range electrostatic interactions on the local dynamics are possible.

Brooks, Martin Karplus, B. Montgomery Pettitt Copyright © 1988 by John Wiley & Sons, Inc. CHAPTER TV DYNAMICAL SIMULATION METHODS The simulation methodologies described here are designed to study structural, dynamical, and thermodynamic properties of biological macromolecules. The most exact and detailed information is provided by molecular dynamics simulations, in which one uses a computer to solve the Newtonian equations of motion for the atoms of the macromolecules and, in principle, the surrounding solvent.

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