New Algorithms for Macromolecular Simulation [E-Book] / edited by Benedict Leimkuhler, Christophe Chipot, Ron Elber, Aatto Laaksonen, Alan Mark, Tamar Schlick, Christoph Schütte, Robert Skeel.
Chipot, Christophe, (editor)
Elber, Ron, (editor) / Laaksonen, Aatto, (editor) / Leimkuhler, Benedict, (editor) / Mark, Alan, (editor) / Schlick, Tamar, (editor) / Schütte, Christoph, (editor) / Skeel, Robert, (editor)
Berlin, Heidelberg : Springer, 2006
XVI, 367 p. 85 illus., 8 illus. in color. online resource.
Lecture Notes in Computational Science and Engineering ; 49
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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.