This document is a doctoral thesis submitted by Dimitrios Bisias to MIT's Sloan School of Management. The thesis contains four essays on applications of optimal portfolio theory. The first essay studies optimal trading of arbitrage opportunities under value-at-risk and collateral constraints. The second essay extends this to consider the impact of model misspecification. The third essay applies portfolio theory to analyze biomedical funding allocation at the National Institutes of Health. The fourth essay investigates how risk constraints and model misspecification affect market statistics. The thesis was certified by Andrew Lo and accepted in partial fulfillment of the requirements for a PhD in Operations Research.