The steady-state transmission spectrum of a cavity with two modes of orthogonal polarization strongly coupled to a single atom with multiple Zeeman states is computed. Effects due to cavity birefringence and atomic ac-Stark shifts are included. The transmission spectrum is compared to experimental results for a single Cesium atom trapped via an intracavity FORT in a Fabry-Perot cavity. The excellent agreement of the theory with the data is used to infer the distribution of the position of the trapped atom.; The intensity correlation function of this system is also calculated, and found to be strongly antibunched and sub-Poissonian. This effect is explained in terms of photon blockade, based on the structure of the lowest energy eigenvalues. Experimental results confirm the strong nonlinearity at the single-photon level.; We present theoretical predictions of the weak field spectra of microtoroid and photonic bandgap cavities strongly coupled to the D2 transition of single Cesium atoms. These calculations include all hyperfine and Zeeman states of the transition and model the cavity as a single-mode, linearly polarized resonator.; Finally, we outline a technique for using multiple hyperfine and Zeeman levels of a single atom in a strongly coupled atom-cavity system to generate polarized single photons on demand in a well-defined temporal mode via adiabatic passage. The technique is insensitive to cavity birefringence and only weakly sensitive to atomic position. Variations of this technique for generating entanglement of photon polarization and atomic Zeeman state are also discussed.
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