Alex Mahalov Arizona State University Multi-scale modeling and high resolution three-dimensional simulations of limited area atmospheric environments are major frontiers in the field of space sciences. The latest developments in fast computational algorithms and novel numerical methods have advanced reliable forecasting of the upper troposphere and lower stratosphere (UTLS), and ionospheric environments at fine scales. These new capabilities include improved physics-based predictive modeling, nesting and implicit relaxation techniques that are designed to integrate models of disparate scales. A range of scales, from mesoscale to microscale, are included in a 3D modeling framework. In the first part, the computational results for shear-stratified turbulence in the UTLS are validated with data from recent observational campaigns designed to study mountain waves, jetstream and non-equilibrium layer dynamics near the tropopause. In the second part, analyses and simulations of primary and secondary Rayleigh-Taylor instabilities in the equatorial spread F (ESF), the response of the plasma density to the neutral turbulent dynamics, and wave breaking in the lower region of the ionosphere and non-equilibrium layer dynamics at fine scales are presented for coupled systems (ions, electrons and neutral winds), thus enabling studies of mesoscale/microscale dynamics for a range of altitudes that encompass the ionospheric E and F layers.