The aim of this thesis is to supply a theoretical study of the interaction mechanisms between quantum dots beyond the simple picture of macroatoms. Coulomb interaction between excitons, exciton-phonon interaction as well as radiative interaction are, in particular, considered. These mechanisms can be exploited to coherently couple quantum dots, thus being the physical tool enabling quantum information processing using quantum-dot-based logic gates. On the other hand, the same mechanisms are responsible for the decoherence of the quantum-state that prevent the storing of the quantum information. Already if considered as simple two-level systems, quantum dots are subject to mutual interaction. Quantum dots in the excited state can be considered as dipoles, and are thus coupled with each other via the dipole-dipole electrostatic interaction. This results in excitation transfer between dots over distances of a few tens of nanometers. In Chapter 2 we show that taking into account the retarded nature of the electromagnetic field results in a correction to this effect, that become a leading contribution at large distances, effectively coupling quantum dots over distances of a few hundreds of nanometers. Strong exciton-phonon-coupling in quantum dots results in a very efficient decoherence mechanism. The strongly localized polarization in an excited quantum dot can induce virtual phonon emission and reabsorption processes which act as a phase-destroying mechanism. In quantum dot molecules the decay rate of the interband polarization is almost one order of magnitude larger than in the single quantum dot case, and depends on the interdot distance. The description of this coupling mechanism is possible only beyond the marcoatom picture. In Chapter 3 we develop a model that describes the phonon-mediated interaction between quantum dots in a dot molecule, explaining the strong distance dependence of the exciton dephasing rates in terms of a matching condition between the phonon wavelength and the interdot distance, which enhances the phonon-assisted scattering from bright to dark states. The heterodyne spectral interferometry is a novel implementation of transient nonlinear spectroscopy that enables to study the transient nonlinear polarization emitted from individual localized electronic transitions, in both intensity and phase. Two-dimensional spectra obtained by means of this technique display signals that can be associated to the coherent coupling between different resonances of the system under study. This technique is theoretically modeled for the first time in Chapter 4, where a very satisfactory description of the measured spectra is provided, showing that coherent coupling between different optical transitions of a quantum system result in off-diagonal peaks of the two-dimensional excitation spectrum. Furthermore, we show that in the low intensity regime, each spectral signal can be associated to a specific pair of coupled resonances as long as the level structure of the system under study is known.