Characterizing the physical behavior of complex heterogeneous systems is not straightforward, especially when the constituent components are micrometer to nanometer in size. Analytical models, while useful, are restricted by their simplifying assumptions. Experimental measurements of physical properties and behavior likewise are subject to interpretation, especially at small length scales, and are fraught with experimental uncertainties. Mesoscale computer simulations provide an alternative stratagem for predicting physical properties and behavior of complex heterogeneous systems at the small scale. Several examples are given to illustrate this approach. They range from near- zero thermal expansion ceramic composites for use in precision optical devices (e.g., extreme ultraviolet nano-lithography), but which can self-destruct due to high internal stresses, to optically activated gold-shell nanoparticles for use in tumor ablation, while leaving the surrounding healthy tissue intact.