This thesis concerns the interaction between matter and light, in particular the coherent manipulation and directed motion of cold atoms in a Hamiltonian system in the fully chaotic regime. The system under scrutiny is the cold atom realisation of the delta kicked rotor, a paradigm system for the study of quantum chaos in which ultra-cold caesium atoms are periodically 'kicked' by a symmetric (and in this case far-detuned) optical lattice. Experiments demonstrate quantum features such as dynamical localisation, and asymmetric diffusion is achieved as a result of mixed (chaotic and regular) classical dynamics. Further experiments make an exploration of phase space past the momentum boundary, a manifestation of finite-width kicks, and by reducing system symmetries it is shown that directed atomic motion in this Hamiltonian system can result from purely chaotic dynamics alone. The second part of this thesis describes the design and construction of a computer-controlled scanning-beam laser tweezers for the manipulation of dielectric microspheres and micron-sized protein-coated bubbles. Evidence for the three-dimensional trapping and the automated two-dimensional manipulation of these neutral particles in time-shared optical traps is presented. The preparation and plans for biological research applications is also detailed, the work of which marks the beginning of future biophysical collaborations.