I review physics-based predictive modeling and novel multi-nesting computational techniques developed to characterize propagation through strongly inhomogeneous non-Kolmogorov ionospheric media. Nested numerical simulations of ionospheric plasma density structures associated with nonlinear evolution of the Rayleigh-Taylor (RT) instabilities in Equatorial Spread F (ESF) are presented. The high resolution in targeted regions offered by the nested model is able to resolve scintillation producing ionospheric irregularities associated with secondary RT instabilities characterized by sharp gradients of the refractive index at the edges of mixed regions. The refractive index is decomposed into strongly inhomogeneous deterministic and stochastic components. The scintillation effects induced by trapping of electromagnetic (EM) waves in parabolic cavities created by the refractive index gradients along propagation paths are analyzed for solutions of the stochastic Maxwell equation.