This thesis concentrates on generating and measuring non-classical states of mechanical oscillators by coupling them to atomic and molecular quantum systems. We start with a discussion of what novel physics can be explored by mechanical systems operating in the quantum regime. We then discuss one technique making it a possibility- cavity optomechanics, particularly optomechanical cooling. We investigate the limits of optomechanical cooling and review how the coupling of mechanical oscillators to external heat baths limits the minimum attainable phonon occupation number. As a possible alternative for circumventing clamping losses, we consider an all-optical approach where the mechanical element (in this case, a Bragg mirror) is suspended via optical forces, and discuss some limitations of this approach. We explore several schemes aimed at the generation of quantum states in mechanical oscillators. We consider specifically two examples: one in which the mechanical oscillator is coupled to polar molecules via dipole-dipole interaction, and another where it is magnetically coupled to a Bose condensate. The first example emphasizes that such an interaction can generate parametric squeezing and entanglement. The second scheme demonstrates that the back action of BEC spin measurements can be used to generate quantum states of motion of a mechanical oscillator. We then discuss possible methods for measuring the entire density matrix of a mechanical oscillator. The first method achieves the tomographic reconstruction of the mechanical Wigner function by coupling it simultaneously to a classical optical oscillator and a qubit. The second approach involves a state transfer scheme between momentum excitations of a bose-condensate in a cavity and a moving mirror of the cavity that is entirely mediated by the light field. We conclude with a discussion of the broader implications of this work, and some future research directions.
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