In this thesis, we harness the power of modern scientic computing to explore the formation and evolution of cosmological structure in a wide variety of astrophysical scenarios. We explore the nonlinear dynamics associated with the interplay between cold dark matter (CDM), baryons, ionizing radiation, and cosmic neutrinos, within regimes where analytic calculations necessarily fail. We begin by providing an overview of structure formation and its connections to the fields of study considered here: the epoch of reionization, galactic substructure evolution, and cosmic neutrinos. We then present a rigorous numerical convergence study of cosmological hydrodynamics simulations post-possessed with radiative transfer to study the impact of small-scale absorption systems within the intergalactic medium (IGM) during the onset of reionization. We present converged statistics of the IGM on smaller scales and earlier times than previously considered. Moreover, we provide strict resolution limits for hydrodynamic simulations to properly resolve the unheated IGM. Next we study the infall and dynamical evolution of CDM halos in a galactic host. We find the behaviour of low-mass subhalos is qualitatively different than previously described for high-mass subhalos. In particular, the evolution of low-mass subhalos, with masses less than 0.1 per cent that of the host, is mainly driven by their concentration. This presents an opportunity to use concentration as a predictive indicator of substructure evolution. We finish this thesis with an investigation of a recently proposed method for constraining individual neutrino mass from cosmological observations. Such a detection depends on the ability to reconstruct the CDM-neutrino relative velocity, which we show can be accomplished using linear transformations of an observed galaxy field. Based on this, we perform the world's largest cosmological N-body simulation and present preliminary results for the observational prospects of cosmic neutrinos.