The Hong-Ou-Mandel effect is studied in the context of twophoton transport in a one-dimensional waveguide with a single scatterer. We numerically investigate the scattering problem within a time-dependent, wave-function-based framework. Depending on the realization of the scatterer and its properties, we calculate the joint probability of finding both photons on either side of the waveguide after scattering. We specifically point out how Hong-Ou-Mandel interferometry techniques could be

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... d to identify effective photon-photon interactions which are mediated by the scatterer. The Hong-Ou-Mandel dip is discussed in detail for the case of a single two-level atom embedded in the waveguide, and dissipation and dephasing are taken into account by means of a quantum jump approach.