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We present the work of an international team at the International Space Science Institute (ISSI) in Bern that worked together to review the current observational and theoretical status of the non-virialised X-ray emission components in clusters of galaxies. The subject is important for the study of large-scale hierarchical structure formation and to shed light on the "missing baryon" problem. The topics of the team work include thermal emission and absorption from the warm-hot intergalactic medium, non-thermal X-ray emission in clusters of galaxies, physical processes and chemical enrichment of this medium and clusters of galaxies, and the relationship between all these processes. One of the main goals of the team is to write and discuss a series of review papers on this subject. These reviews are intended as introductory text and reference for scientists wishing to work actively in this field. The team consists of sixteen experts in observations, theory and numerical simulations., Comment: 6 pages, 1 figure, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 1; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeker

Galaxy clusters grow by gas accretion, mostly from mergers of substructures, which release powerful shock waves into cosmic plasmas and convert a fraction of kinetic energy into thermal energy, amplification of magnetic fields and into the acceleration of energetic particles. The modeling of the radio signature of cosmic shocks, combined with the lack of detected gamma-rays from cosmic ray (CR) protons, poses challenges to our understanding of how cosmic rays get accelerated and stored in the intracluster medium. Here we review the injection of CRs by cosmic shocks of different strengths, combining the detailed "microscopic" view of collisionless processes governing the creation of non-thermal distributions of electrons and protons in cluster shocks (based on analytic theory and particle-in-cell simulations), with the "macroscopic" view of the large-scale distribution of cosmic rays, suggested by modern cosmological simulations. We discuss time dependent non-linear kinetic models of particle acceleration by multiple internal shocks with large scale compressible motions of plasma. The models produce soft CR spectra containing a noticeable energy density in the super-thermal protons of energies below a few GeV which are difficult to constrain by Fermi observations. We consider the effect of plasma composition on CR injection and super-thermal particle population in the hot intracluster matter which can be constrained by fine high resolution X-ray spectroscopy of Fe ions., Comment: Space Science Reviews, in print