New Algorithms for Macromolecular Simulation by Benedict LeimkuhlerNew Algorithms for Macromolecular Simulation by Benedict Leimkuhler

New Algorithms for Macromolecular Simulation

byBenedict LeimkuhlerEditorChristophe Chipot, Ron Elber

Paperback | December 20, 2005

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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.

Title:New Algorithms for Macromolecular SimulationFormat:PaperbackDimensions:367 pagesPublished:December 20, 2005Publisher:Springer-Verlag/Sci-Tech/TradeLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:3540255427

ISBN - 13:9783540255420


Table of Contents

Macromolecular Models: From Theories to Effective Algorithms.- Membrane Protein Simulations: Modelling a Complex Environment.- Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes.- Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach.- Learning to Align Sequences: A Maximum-Margin Approach.- Minimization of Complex Molecular Landscapes.- Overcoming Energetic and Time Scale Barriers Using the Potential Energy Surface.- The Protein Folding Problem.- Dynamical and Stochastic-Dynamical Foundations for Macromolecular Modelling.- Biomolecular Sampling: Algorithms, Test Molecules, and Metrics.- Approach to Thermal Equilibrium in Biomolecular Simulation.- The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method.- The Langevin Equation for Generalized Coordinates.- Metastability and Dominant Eigenvalues of Transfer Operators.- Computation of the Free Energy.- Free Energy Calculations in Biological Systems. How Useful Are They in Practice?.- Numerical Methods for Calculating the Potential of Mean Force.- Replica-Exchange-Based Free-Energy Methods.- Fast Electrostatics and Enhanced Solvation Models.- Implicit Solvent Electrostatics in Biomolecular Simulation.- New Distributed Multipole Metdhods for Accurate Electrostatics in Large-Scale Biomolecular Simulations.- Quantum-Chemical Models for Macromolecular Simulation.- Towards Fast and Reliable Quantum Chemical Modelling of Macromolecules.- Quantum Chemistry Simulations of Glycopeptide Antibiotics.- Panel Discussion.