New theoretical, algorithmic, and computational tools are needed to overcome the space and time scale challenges presented by genomics-based materials design and manufacturing. I will discuss several approaches to the coarse-graining of space and time needed to achieve the predictive and efficient simulation of materials with optimized properties — accelerated dynamics, atomistic-to-continuum coupling, and microstructure coarse-graining. I will also present the need for theory-driven method verification and benchmarking with some examples.