In recent years, the evidence for a correlation between lower atmospheric behaviour and changes in solar activity has increased. This correlation is thought to be associated with complex coupling mechanisms that link the upper and lower regions of the atmosphere. Dynamical processes are believed to play an important role via the influence of large- and small-scale waves that can lead to the transport of energy, momentum and chemical constituents. Compositional and energetic changes that occur as a direct result of changes in solar energy flux are also thought to contribute to the coupling of atmospheric regions. The production and transport of odd nitrogen species is thought to be particularly important, especially following periods of enhanced geomagnetic activity. The UCL Coupled Middle Atmosphere - Thermosphere (CMAT) general circulation model was developed in order to provide a tool to investigate two-way coupling between the Earth's lower and upper atmosphere. This model has been updated to include high-resolution empirical solar flux data and current photoabsorption and ionisation cross sections. Improvements have been made to the chemical scheme, and a new spectral gravity wave parameterisation has been implemented Factors influencing production and loss of odd nitrogen species in the lower thermosphere have been investigated. The representation of nitric oxide in the CMAT model is presented and compared with empirical data. Studies have been carried out to investigate the global production, transport and impact of nitric oxide in the MLT (mesosphere lower thermosphere) region during and following periods of enhanced solar and geomagnetic activity, including a simulation of the 2003 'Halloween super storm'. The effect of the new gravity wave parameterisation on the zonal and meridional wind structure is also investigated along with its effect on the equatorial local diurnal maximum of atomic oxygen and associated OS) 557.7nm green line volume emission rates.