Benedict Leimkuhler / Christophe Chipot / Ron Elber / Aatto Laaksonen / Alan Mark / Tamar Schlick / Christoph Schütte / Robert Skeel (eds.)

New Algorithms for Macromolecular Simulation

Herausgegeben:Chipot, Christophe; Elber, Ron; Laaksonen, Aatto

• Broschiertes Buch

Produktbeschreibung

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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Produktdetails

• Lecture Notes in Computational Science and Engineering 49
• Verlag: Springer / Springer Berlin Heidelberg / Springer, Berlin
• Artikelnr. des Verlages: 11360575, 978-3-540-25542-0
• 2006
• Seitenzahl: 384
• Erscheinungstermin: 20. Dezember 2005
• Englisch
• Abmessung: 235mm x 155mm x 24mm
• Gewicht: 546g
• ISBN-13: 9783540255420
• ISBN-10: 3540255427
• Artikelnr.: 14983410

Autorenporträt

Benedict Leimkuhler, University of Leicester, United Kingdom / Christophe Chipot, Université Henri Poincaré, Vandoeuvre-lès-Nancy, France / Ron Elber, Cornell University, Ithaca, NY, USA / Aatto Laaksonen, Stockholm University, Sweden / Alan Mark, University of Groningen, The Netherlands / Tamar Schlick, New York University, NY, USA / Christoph Schütte, Freie Universität Berlin, Germany / Robert Skeel, Purdue University, West Lafayette, IN, USA

Inhaltsangabe

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.