Clusters of galaxies are unique and powerful probes of cosmology and astrophysics, promising to provide new insights into the nature of dark energy and dark matter to the physics of galaxy formation. The study of galaxy clusters combines the richness of plasma physics with the predictive power of modern cosmological models to explain remarkable new observational results. In this talk, I will describe recent advances in theoretical and intensive numerical modeling of galaxy cluster formation to interpret recent X-ray and Sunyaev- Zel'dovich Effect cluster surveys. Finally, I will discuss outstanding issues and future directions in this area.