The course describes the interaction of photons and atoms in different fields of physics and the manipulation of ensemble of atoms with laser beams. It starts with a microscopic description of the interaction between a classical light field and a quantum atom and then it extends the description to ensemble of atoms thanks to the density matrix and Optical Bloch Equations (OBE). Applications of this microscopic description include the radiation pressure force and optical dipole potentials, laser cooling of atomic and molecular gases, slow light and Electromagnetically Induced Transparency (EIT). The course will proceed with the treatment of systems in contact with Markovian reservoirs and the derivation of the Master Equation from which OBEs are obtained. The alternative approach of the Monte-Carlo wave-function for dissipative processes will be presented as well. Finally the Bloch-Maxwell equations for the propagation of light in optically thick media will be introduced, along with applications (i.e. fast/slow light, photon echo or quantum memories).