This special topics issue offers a broad perspective on the recent developments and reviews of state-of-the-art particle methods in science and engineering applications. This issue grew out of contributions delivered during the closing conference of the Collaborative Research Centre (CRC) 716 that for the last twelve years was contributing important works to the area of "dynamical simulations of systems with large particle numbers". Since particle methods are present in many fields of science and engineering, the papers collected here span a considerable range of subjects and questions, but they also illustrate numerous connections to both fundamental science and technological/industrial applications. In addition reviews display the current state of three software packages that have been developed in this CRC in the area of simulations and visualization.Computer simulations are by now an established scientific field that is used to bridge the gap between experimental data and a purely theoretical analytical explanation. Especially useful are particle-based molecular dynamics (MD) simulations since from an accurate description of the pair interactions of microscopic particles it is possible to deduce the macroscopic material behavior if a sufficiently large ensemble can be simulated for long enough times to deduce equilibrium properties without finite-size effects.The notion of a particle can be manifold. A particle can denote a pseudo-particle in electronic structure theory, an atom, a molecule, or the monomer of a polymer. In even more coarse-grained (CG) approaches they can also represent an effective aggloma