The study of the fundamental theory of the strong interaction, Quantum Chromo Dynamics (QCD), under extreme conditions of temperature and density has captured an increasing interest due to its very rich dynamical content and its relation to the Early Universe physics. Heavy-Ion Collisions (HIC) at ultra-relativistic energy (above ~10 AGeV) provide the possibility to scrutiny the QCD phase diagram reaching energy densities high enough to cause a phase transition of the hadronic matter into a quark-gluon plasma (QGP). The experiments conducted at the Brookhaven National Laboratory have shown that such a state of matter behaves like a nearly perfect fluid with a very small shear viscosity, a very high opacity at high transverse momentum pT (>6 GeV) and manifesting evidences for a modification of the hadronization process at intermediate pT (2-6 GeV) . Interestingly and surprisingly enough, also in the heavy quark sector there are hints that viscosity is similarly small. Furthermore some evidence of a new phase of QCD, the color glass condensate (CGC), has been found while its relevance should increase in the upcoming LHC program at CERN. These are the main physics subjects that we deal with in our project.The main objective of the project is to determine the value of the shear viscosity to entropy ratio h/s of the perfect fluid and the implications of a possible primordial CGC phase on the dynamical evolution of the system. The research gains strength from a comprehensive study of the rich phenomenology including both inclusive and more exclusive observables (like the two-three particles correlations triggered by hadronic jets) and from the inclusion of hadronization effects. In addition the study will be conducted considering also the heavy flavor sector where a fluid behaviour similar to the light one is observed. The microscopic origin of such a similarity will be investigated together with its relation to the suppression/regeneration of quarkonia.