The most energetic part of the Sun, its interior, due to its plasma parameters is hidden below the solar surface and invisible to the observer. Nevertheless, the solar interior generates the energy and provokes atmospheric magnetic activity. Despite great progress in both observational and simulational methods, the mechanism of energy transport from the solar convection zone into the upper atmosphere, and the upper-atmospheric heating mechanism remain the main unresolved problems in solar and stellar structure. In this presentation, we analyse the role of non-ideal plasma effects and partial ionization in the solar atmospheric energy transport and chromospheric heating. Using numerical magneto-hydrodynamic modelling we create detailed models of magnetic flux tubes and realistic simulations of the coupled solar interior and atmosphere with different levels of magnetic activity, which take into account the effects of partial ionisation and ion-neutral interaction in the solar atmospheric plasma. We show that compressible and incompressible oscillations in solar magnetic fields, indeed, are able to provide sufficient energy to compensate chromospheric radiative losses. Detailed radiative diagnostics of the simulated models is carried out to create a link between the simulations and observational data. This gives an opportunity to directly compare the simulation results with modern solar observations.