First principle calculations and computational chemistry not only benefits from the advancements in computer technologies but also from the improvements in the theory itself to enhance performance. For example, recently developed Joint Density-Functional Theory (JDFT) provides us with the tools to study solvated systems efficiently, removing the need for sampling the phase space of the fluid. It enables the calculation of thermodynamic averages with little computational overhead and without sacrificing the rigor of ab initio physics. This thesis starts with a brief summary of the theory that sets the basis of electronic structure calculations. We follow by the application targeting two physical systems of technological importance: Rechargeable batteries in the context of preventing dendritic growth upon charging and Nb3Sn superconducting radio frequency cavities focusing on the microscopic mechanisms by which niobium transforms into niobium-tin during the coating process. For the first, we develop a macroscopic model to analyze the stability of a surface growing via electrodeposition (a charging battery electrode fits this description) and we calculate material specific parameters that appear in the model for various compounds found in battery systems. For the second, we present various defect energies and two possible transformation pathways from body-centered cubic structure (niobium bulk) to A15 structure (niobium-tin). We continue with a proof of concept and describe why combining molecular dynamics with Joint Density-Functional Theory should reproduce the correct rates of rare events. As a test system, we choose OH− moving in water via proton hopping (Grotthuss mechanism) and our initial results show that JDFT dynamics is a promising new way to estimate rare event rates in fluid environments.