New Algorithms for Macromolecular Simulation

By: B. Leimkuhler, Benedict Leimkuhler (Editor), Christophe Chipot (Editor)

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Paperback | 20 December 2005

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384 Pages

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22.86 x 15.24 x 1.27

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Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

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You Can Find This Book In

Non-Fiction Mathematics Algebra Applied Mathematics Computing & I.T.Computer Science Science Physics Biology, Life Sciences Biochemistry Graphical & Digital Media Applications 3D Graphics & Modelling

Chemistry Analytical Chemistry Medicine Pre-Clinical Medicine & Basic Sciences Engineering & Technology Technology in General Engineering in General

Membrane protein simulations : modelling a complex environment	p. 3
Modeling and simulation based approaches for investigating allosteric regulation in enzymes	p. 21
Exploring the connection between synthetic and natural RNAs in genomes via a novel computational approach	p. 35
Learning to align sequences : a maximum-margin approach	p. 57
Overcoming energetic and time scale barriers using the potential energy surface	p. 73
The protein folding problem	p. 89
Biomolecular sampling : algorithms, test molecules, and metrics	p. 103
Approach to thermal equilibrium in biomolecular simulation	p. 125
The targeted shadowing hybrid Monte Carlo (TSHMC) method	p. 141
The Langevin equation for generalized coordinates	p. 155
Metastability and dominant eigenvalues of transfer operators	p. 167
Free energy calculations in biological systems : how useful are they in practice?	p. 185
Numerical methods for calculating the potential of mean force	p. 213
Replica-exchange-based free-energy methods	p. 251
Implicit solvent electrostatics in biomolecular simulation	p. 263
New distributed multipole metdhods for accurate electrostatics in large-scale biomolecular simulations	p. 297
Towards fast and reliable quantum chemical modelling of macromolecules	p. 315
Quantum chemistry simulations of glycopeptide antibiotics	p. 343
Table of Contents provided by Blackwell. All Rights Reserved.

New Algorithms for Macromolecular Simulation

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