We study different phenomena associated with single-photon propagation in optical cavities coupled through optical fibers. We first address the issue of storing and delaying single-photon wavepackets in an array of microcavities. This has possible applications in developing reliable and efficient quantum repeaters that will be utilized in building long distance quantum networks. Second, we investigate a Hong-Ou-Mandel (HOM) type of interference between two photons that are produced in two coupled atom-cavity systems. The HOM effect in this setup can test the degree of indistinguishability between photons when they are stored inside cavities. This part of the dissertation also includes the study of entanglement between atoms, cavities and atom-cavity systems induced by the photons. Finally, we focus on single-photon interactions with a tiny movable mirror in the context of quantum optomechanics. We investigate how the mechanical motion of the mirror leaves its imprints on the optical spectrum of the photon This dissertation includes previously published and unpublished co-authored material. / 10000-01-01

"Photonic crystals have recently been the subject of studies for use in optical signal processing. In particular, a Coupled Resonator Optical Waveguide (CROW) structure has been considered by M. F. Yanik and S. Fan in “Stopping Light All Optically” for use in a time-varying optical system for the storage of light in order to mitigate the effects of waveguide dispersion. In this thesis, the effects of the thermal field on the state stored in such a structure is studied. Through simulation, this thesis finds that when this structure is constructed of gallium arsenide cylinders in air, loss of the signal was found to be caused by free-carrier absorption, and the decay of the signal dominates over thermal spreading of the optical signal’s spectrum."