Proton beam therapy is an effective treatment option for deep-seated tumors. Although the behavior of protons as they travel through tissue is well understood, there are significant technological challenges involved in generating and optimizing a beam to effectively treat a specific tumor. Proton therapy Monte Carlo simulation packages require designated operating systems and software, thus making it difficult to study the effects of a proton beam in a non-clinical setting. Here we seek to (1) develop a model that captures the salient physics while simulating a proton beam entering the body given the beam energy and beam width, and (2) optimize these properties to effectively target a simulated tumor in three dimensions.