This dissertation consists of two parts, treating significantly separated fields. Each part consists on several chapters, each treating a somewhat isolated topic from the rest. In each chapter, I present some of the work developed during my passage through the graduate program, which has mostly been published elsewhere. Part I – Cosmic Rays and Particle Physics Chapter 1: In this chapter we present an introduction to the topic of cosmic ray physics, with an special focus on the so-called ultra high energy cosmic rays: their potential origins, effects during their propagation between their sources and Earth, the different techniques used for their detection, and the use of cosmic rays to explore fundamental physics at energies unattainable...