Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1

Introduction: Condensed Matter Theory by Computer Simulation.- Transition Path Sampling Methods.- Sampling Kinetic Protein Folding Pathways using All-Atom Models.- Calculation of Classical Trajectories with Boundary Value Formulation.- Transition Path Theory.- Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States.- Transport Coefficients of Quantum-Classical Systems.- Linearized Path Integral Methods for Quantum Time Correlation Functions.- Ensemble Optimization Techniques for Classical and Quantum Systems.- The Coupled Electron-Ion Monte Carlo Method.- Path Resummations and the Fermion Sign Problem.- to Cluster Monte Carlo Algorithms.- Generic Sampling Strategies for Monte Carlo Simulation of Phase Behaviour.- Simulation Techniques for Calculating Free Energies.- Waste-Recycling Monte Carlo.- Equilibrium Statistical Mechanics, Non-Hamiltonian Molecular Dynamics, and Novel Applications from Resonance-Free Timesteps to Adiabatic Free Energy Dynamics.- Simulating Charged Systems with ESPResSo.- Density Functional Theory Based Ab Initio Molecular Dynamics Using the Car-Parrinello Approach.- Large Scale Condensed Matter Calculations using the Gaussian and Augmented Plane Waves Method.- Computing Free Energies and Accelerating Rare Events with Metadynamics.