Massive stars play a crucial role in galactic chemical evolution, compact object formation, and stellar feedback. Computational models of massive stars and their explosions have progressed over the decades in concert with astrophysical observations to advance our theoretical understanding of stellar evolution and transient phenomena. Stellar models have been used to constrain supernova progenitor masses of observed explosions, estimate the age of globular clusters, and determine properties of the interior of the Sun. However, despite these advances, stellar models are subject to uncertainties that can qualitatively alter the outcome and often disagree with observation. Among the sources of uncertainties in stellar models are thermonuclear reaction rates, the treatment of mixing and heat transport via convection, and pre-supernova structure in core collapse supernova simulations. The consequences of these uncertainties directly impact theoretical models of massive stars and their explosions.In this Dissertation, I explore these areas of uncertainty and consider the implications they have on our theoretical understanding of massive stars and stellar transients. I begin by considering the impact of nuclear reaction rate uncertainties on the evolution of massive stars using 1D stellar evolution models. In this work, I sample 665 nuclear reaction rates according to their temperature-dependent uncertainties in a grid of 2000 stellar models to identify key reaction rates at five evolutionary epochs. Next, I present results of a 15 solar mass stellar model evolved in 2D and 3D for the final seven minutes prior to iron core collapse. In this work, I characterize the Si- and O-shell convective properties and compare them to predictions from 1D models. Following this, I present work considering 3D simulations of stellar Si- and O-shell convection in a 14-, 20-, and 25 solar mass model. These models are simulated for the final ten minutes prior to iron core collapse and represent the largest set of 3D pre-supernova models in the literature. Following this work, I consider the implications that models of 3D pre-supernova perturbations have on core-collapse supernova (CCSN) explosion properties. I present the results of 1-, 2-, and 3D neutrino-radiation-hydrodynamic CCSN simulations of a 15 solar mass using 2D/3D initial conditions. This work investigates the role that non-radial perturbations in the progenitor might have on multi-messenger signals produced in models of CCSNe. Lastly, I conclude with a brief discussion of MESA-Web: an online web interface to the stellar evolution toolkit, MESA. I discuss the current capabilities of this tool, the impact it has had over the past five years since its inception, and the future plans to continue to increase its utility as a scientific tool and resource for astronomy education. The data products as a result of this Dissertation are publicly available online.
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