Sections focus on transition path sampling and diffusive barrier crossing to simulate rare events, dissipative particle dynamic as a course-grained simulation technique, novel schemes to compute the long-ranged forces, Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations, Multiple-time step algorithms as an alternative for constraints, and more. Additional sections cover Defects in solids, The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules, Parallel tempering for glassy Hamiltonians, Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web.