Magnetic flux emergence into the outer layers of the Sun is a fundamental mechanism for releasing energy into the chromosphere and the corona. In this paper, we study the emergence of granular-sized flux concentrations and the structuring of the corresponding physical parameters and atmospheric diagnostics in the upper photo- sphere and in the chromosphere. We make use of a realistic 3D MHD simulation of the outer layers of the Sun to study the formation of the Ca II 8542 line. We also derive semi-empirical 3D models from non-LTE inversions of our observations. These models contain depth-dependent information of the temperature and line-of-sight stratification. Our analysis explains the peculiar Ca II 8542 profiles observed in the flux-emerging region. In addition, we derive detailed temperature and velocity maps describing the ascent of magnetic bubbles from the photosphere to the chromosphere. The inversions suggest that, in active regions, granular-sized bubbles emerge up to the lower chromosphere where the existing large-scale field hinders their ascent. We report hints of heating when the field reaches the chromosphere.
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