The formation of large scale structure includes objects on a wide range of physical scales. Groups and clusters of galaxies, as well as filaments and sheets exist on scales from hundreds of kiloparsecs to hundreds of megaparsecs. Shocks are common, exist in a complex web which links the structure across all these scales, and can be used to trace the process of structure formation. We use numerical cosmological simulations to study the distribution of complex flows in large scale structure. We also study the role of large scale shocks in cosmic ray acceleration. Synthetic observations of the collapsed structures are used to determine how best to observe these flows to determine the dynamical state of the gas.