Delivery of therapy-loaded nanoparticles (NP) via inhalation is an innovative technology shown to successfully reduce heart failure in mice, improving the efficiency of drug delivery, and reducing adverse side effects. However, how exactly therapeutic NP are distributed and absorbed by heart tissue remains poorly understood, and accelerating this technology to humans is a major challenge. To overcome this problem we developed an open-source finite element model of myocardial perfusion based on porous media, where perfused tissue is treated as a sponge-like continuum material, driven by a continuum model of cardiac contraction to simulate perfusion patterns. We use our novel particle-tracking based method that remains numerically stable under high Peclet number flow to study NP distribution.