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.
Inhaltsverzeichnis
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.
