New Algorithms for Macromolecular Simulation [electronic resource] /
Leimkuhler, Benedict.editor.
Chipot, Christophe.editor.
Elber, Ron.editor.
Laaksonen, Aatto.editor.
Mark, Alan.editor.
Schlick, Tamar.editor.
Schütte, Christoph.editor.
Skeel, Robert.editor.
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.
Description based upon print version of record.
Includes bibliographical references.
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.
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.
Computer simulation.
Biomathematics.
Mathematical physics.
Biomedical engineering.
Simulation and Modeling.
Mathematical and Computational Biology.
Theoretical, Mathematical and Computational Physics.
Biomedical Engineering and Bioengineering.