In this talk we present two intimately related approaches in speeding-up molecular simulations via Monte Carlo simulations. First, we discuss coarse-graining algorithms for systems with complex, and often competing particle interactions, both in the equilibrium and non-equilibrium settings, which rely on multilevel sampling and communication. Second, we address mathematical, numerical and algorithmic issues arising in the parallelization of spatially distributed Kinetic Monte Carlo simulations, by developing a new hierarchical operator splitting of the underlying high-dimensional generator, as means of decomposing efficiently and systematically the computational load and communication between multiple processors. The common theme in both methods is the desire to identify and decompose the particle system in components that communicate minimally and thus local information can be either described by suitable coarse-variables (coarse-graining), or computed locally on a individual processors within a parallel architecture.