New Algorithms for Macromolecular Simulation

• Corporate Author: SpringerLink (Online service)
• Other Authors: Leimkuhler, Benedict (Editor), Chipot, Christophe (Editor), Elber, Ron (Editor), Laaksonen, Aatto (Editor), Mark, Alan (Editor), Schlick, Tamar (Editor), Schütte, Christoph (Editor), Skeel, Robert (Editor)
• Format: Electronic eBook
• Language: English
• Published: Berlin, Heidelberg : Springer Berlin Heidelberg, 2006.
• Series: Lecture Notes in Computational Science and Engineering, 49
• Subjects: Computer science.; Computer simulation.; Biomathematics.; Physics.; Biomedical engineering.; Computer Science.; Simulation and Modeling.; Mathematical and Computational Biology.; Theoretical, Mathematical and Computational Physics.; Biomedical Engineering.

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...

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.