The goal of this project is to study equilibrium and non-equilibrium properties of mesoscopic ensembles (<1000 particles) of neutral atoms. These investigations will be made possible by the continued development of three quantum limited atom detection methods: integrated atom counting on the atom chip, fluorescence imaging with single atom detection in time of flight (ToF), and homodyne/heterodyne-like detection by interference with a strong local oscillator. We use these novel, atom chip based methods to analyse the quantum nature of mesoscopic many-body systems. Our experiments probe single systems and allow the study of full distribution functions of quantum variables. They are complementary to efforts in optical lattices, where in most cases ensemble averages are investigated. Spatially resolved single atom detection allows probing high order correlations. On-chip matter-wave interferometry gives access to the order parameter; the full statistics of the interference patterns reveals quantum coherence, quantum dynamics and the interplay of quantum and thermal noise. A central question will be to probe how decoherence proceeds in an isolated interacting many-body system, and how to control it. We will investigate the weakly interacting, the strongly correlated, and the isolated few atom regime in both ¿thermal¿ equilibrium, and the dynamics that leads to equilibrium. An interesting question to study are the scaling properties of atomic quantum systems, i.e. to map the boundary between thermodynamic limits and the behaviour of finite systems. Implementing optimal control schemes combined with exploiting atom-atom interactions in tight traps we will devise ways to create, measure and analyse multi-particle entanglement of atoms and macroscopic superposition states. Employing atom-light entanglement we will explore the possibilities to link atomic ensembles to photonic quantum information experiments. We will connect to the theoretical models and test mesoscopic ensembles as a candidate for quantum information science and quantum simulations.