The cores of Arp 220, the closest ultra-luminous infrared starburst galaxy, provide an opportunity to study interactions of cosmic rays under extreme conditions. In this paper, we model the populations of cosmic rays produced by supernovae in the central molecular zones of both starburst nuclei. We find that ~65 - 100% of cosmic rays are absorbed in these regions due to their huge molecular gas contents, and thus, the nuclei of Arp 220 nearly complete proton calorimeters. As the cosmic ray protons collide with the interstellar medium, they produce secondary electrons that are also contained within the system and radiate synchrotron emission. Using results from chi-squared tests between the model and the observed radio spectral energy distribution, we predict the emergent gamma-ray and high-energy neutrino spectra and find the magnetic field to be at milligauss levels. Because of the extremely intense far-infrared radiation fields, the gamma-ray spectrum steepens significantly at TeV energies due to gamma-gamma absorption.
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