  The atmosphere of the Sun is highly structured and dynamic in nature. From
the photosphere and chromosphere into the transition region and the corona
plasma-$\beta$ changes from above to below one, i.e. while in the lower
atmosphere the energy density of the plasma dominates, in the upper atmosphere
the magnetic field plays the governing role -- one might speak of a ``magnetic
transition''. Therefore the dynamics of the overshooting convection in the
photosphere, the granulation, is shuffling the magnetic field around in the
photosphere. This leads not only to a (re-)structuring of the magnetic field in
the upper atmosphere, but induces also the dynamic reaction of the coronal
plasma e.g. due to reconnection events. Therefore the (complex) structure and
the interaction of various magnetic patches is crucial to understand the
structure, dynamics and heating of coronal plasma as well as its acceleration
into the solar wind.
  The present article will emphasize the need for three-dimensional modeling
accounting for the complexity of the solar atmosphere to understand these
processes. Some advances on 3D modeling of the upper solar atmosphere in
magnetically closed as well as open regions will be presented together with
diagnostic tools to compare these models to observations. This highlights the
recent success of these models which in many respects closely match the
observations.
