This research uses three-dimensional numerical simulations of plasma instabilities in the polar cap to investigate mesoscale irregularities associated with patches of plasma that exist there. The first goal is to develop a parameterization of the spectra of mesoscale structuring as a function of drift velocity, and to using the results to calculate a scintillation index for ultimate verification by Global Positioning System (GPS) receiver response. While previous work used the gradient drift as the primary mechanism followed by secondary and tertiary instabilities, this approach doesn't adequately describe observed regions of strong shear flow. Thus, a second research goal incorporates gradient drift and Kelvin- Helmholtz instabilities to model strong shear conditions. Previous patch modeling involved two types of simulations, large-scale ionospheric models to explain the larger scale patch features, and instability simulations to study the irregularities imbedded in and around the patches. As a third task, this research studies the interface between these two views by asking what role the Kelvin-Helmholtz instability and the collisional Rayleigh-Taylor instability plays in the formation of large scale (300-400 km) patch structure. The final task investigates the role of instabilities in atmospheric heating in the polar cap. The role of simulated irregularities in both Ohmic and viscous heating is quantified by integration of micro scale irregularity physics into the mesoscale heat budget. These studies should synergistically stimulate observations of heating within patches and help clarify the role of the ionosphere in magnetosphere-ionosphere coupling within the polar cap.