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.

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.