New Algorithms for Macromolecular Simulation
by
Leimkuhler, Benedict. editor.
Title
:
New Algorithms for Macromolecular Simulation
Author
:
Leimkuhler, Benedict. editor.
ISBN
:
9783540316183
Physical Description
:
XVI, 367 p. 85 illus., 8 illus. in color. online resource.
Series
:
Lecture Notes in Computational Science and Engineering, 49
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.
Abstract
:
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.
Subject Term
:
Computer science.
Computer simulation.
Biology -- Mathematics.
Mathematical physics.
Biomedical engineering.
Simulation and Modeling.
Mathematical Biology in General.
Mathematical and Computational Physics.
Added Author
:
Leimkuhler, Benedict.
Chipot, Christophe.
Elber, Ron.
Laaksonen, Aatto.
Mark, Alan.
Schlick, Tamar.
Schütte, Christoph.
Skeel, Robert.
Added Corporate Author
:
SpringerLink (Online service)
Electronic Access
:
Library | Material Type | Item Barcode | Shelf Number | Status |
---|
IYTE Library | E-Book | 510090-1001 | QA76.9 .C65 | Online Springer |