PART I: The origin of Ultra-High-Energy Cosmic Rays (UHECRs) and the highest-energy astrophysical neutrinos remains as one of the most prominent unresolved questions in astrophysics. Part of my research can shed light on such phenomena employing a thorough bottom-up approach to understand the spectra of UHECRs, and neutrinos from Active Galactic Nucleus (AGN) jets. My frameworks account for i) particle injection, ii) particle acceleration, iii) spectra of UHECRs, iv) the effects of losses on UHECRs, v) the resulting neutrino spectral features, and vi) potentially lepton cooling and its ensuing radiation spectrum. I study these effects from the large structures of AGN jets employing magnetohydrodynamic (MHD) simulations to the kinetic scales of the plasma relevant for lepton acceleration using Particle-in-Cell (PIC) simulations. My results are backed by original theories that govern particle acceleration.I developed a framework—agnostic to particle acceleration mechanisms—where trajectories are integrated via standard PIC techniques in relativistic 3D MHD jet simulations to explore particle energization. I then enhanced this particle acceleration framework by including subgrid scattering (SGS) to characterize the role of small-scale magnetic irregularities that are not captured in MHD simulations. The results I obtain are consistent with current UHECR phenomenology in terms of spectral slope, chemical composition, and anisotropy. I then augment this framework with realistic photon field prescriptions to study the effects of losses on accelerated particles, and the expected spectrum of neutrinos produced by typical AGN jets. This enabled me to set constraints on the anisotropy and maximum expected neutrino flux from AGN jets. I also study the effect of relativistic asymmetric reconnection on particle energization in relativistic astrophysical systems, such as jets, analytically and with kinetic PIC simulations. In a nutshell, I present the first steps in understanding asymmetric reconnection in the relativistic plasma regime. PART II: I complement these studies by propagating particles employing similar methods in magnetic fields over distances normalized to the particle Larmor radii to examine the impact of the magnetic field and its coherence length on the delay incurred during propagation and deflection angles. While applying these methods to UHECR propagation, we find that the delay incurred by UHECRs on their way to Earth is comparable to AGN duty cycles, making correlation studies with AGNs challenging. These propagation considerations could potentially be important for galactic propagation as they have similar predictive powers for galactic cosmic rays. The confinement time of galactic CRs could also be measured in a more direct manner using CR isotope ratios. I have been heavily involved with theHigh Energy Light Isotope eXperiment (HELIX) to obtain an observationally motivated value for the confinement time of CRs in the galaxy. HELIX is a magnet spectrometer designed to make measurements of the composition of light CR isotopes. This NASA funded experiment is a set of high-precision particle detectors designed specifically to make measurements of significant isotopic abundance ratios such as Beryllium isotopes in the energy range ∼0.2 GeV/n to ∼10 GeV/n, a range that is not accessible to any current or planned instrument.