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.