The thesis is divided into two parts. In the first part, we show that the cascade limit on ultra high energy cosmic neutrino (UHEC) flux imposes alower bound on the neutrino mass provided that super-GZK events of ultra high energy cosmic rays (UHECRs) are produced from Z-bursts. Based on the data from HiRes and AGASA, the obtainedneutrino mass lower bound violates its existing cosmological upper bound. We conclude that the Z-burst cannot be the dominant source for the observed super-GZK UHECR events. This is consistent with the recent ANITA-lite data. In the second part, We investigate the possible in-prints of ion-acoustic oscillations on the large-scale structure formation during the reinonization epoch. In order to trace the plasma electromagnetic interactions during the reionization epoch, we generalize the conventional Einstein-Boltzmann equation into a Maxwell-Einstein-Boltzmann equation in the Newtonian limit. We found that when the collective plasma interaction is included in the analysis, the ion-acoustic oscillations causes the Jean's scale to increase by » 60% while the Jean's mass by about a factor 2, from the conventional calculations where only the gravitational interaction was invoked. Such a modi‾cation should impact the evolution of the large scale structure.