The level of 'anomalous' charmonium suppression in high-energy heavy-ion collisions and its interpretation as a signal of quark-gluon plasma formation requires a robust understanding of charmonium production and absorption in proton-nucleus collisions. In a previous study we have shown that, contrary to common belief, the so-called J/[psi] 'absorption cross section', [sigma]{sub abs}{sup J/[psi]}, is not a 'universal constant' but, rather, an effective parameter that depends very significantly on the charmonium rapidity and on the collision energy. Here we present ugraded Glauber calculations with the EPS09 parameterization of nuclear modifications of the parton densities. We confirm that the effective 'absorption cross section' depends on the J/{psi} kinematics and the collision energy. We also make further steps towards understanding the physics of the mechanisms behind the observed 'cold nuclear matter' effects.

The authors study medium modifications of J/[psi] production in cold nuclear media in deuterium-nucleus collisions. They discuss several parameterizations of the modifications of the parton densities in the nucleus, known as shadowing, an initial-state effect. They also include absorption of the produced J/[psi] by nucleons, a final-state effect. Both spatially homogeneous and inhomogeneous shadowing and absorption are considered. They use the number of binary nucleon-nucleon collisions as a centrality measure. Results are presented for d+Au collisions at √S{sub NN} = 200 GeV and for d+Pb collisions at √S{sub NN} = 6.2 TeV. To contrast the centrality dependence in pA and dA collisions, they also present pPb results at √S{sub NN} = 8.8 TeV.

J/psi and psi' produced in high-energy heavy-ion collisions are absorbed by their collisions with nucleons and produced soft particles, leading to two distinct absorption mechanisms. The signature of absorption by produced soft particles, as revealed by psi' production data, consists of a gap and a change of the slope in going from the pA line to the nucleus-nucleus line when we make a semi-log plot of the survival probability as a function of the path length. Using this signature, we find from the J/psi production data in pA, O-Cu, O-U, and S-U collisions that the degree of J/psi absorption by produced soft particles is small and cannot account for the J/psi data in Pb-Pb collisions. The anomalous suppression of J/psi production in Pb-Pb collisions can be explained as due to the occurrence of a new phase of strong J/psi absorption, which sets in when the local energy density exceeds about 3.4 GeV/fm3. To probe the chemical content of the new phase, we propose to study the abundance of open-charm mesons and charm hyperons which depends sensitively on the quark chemical potential.

J/psi and psi ̀produced in high-energy heavy-ion collisions are absorbed by their collisions with nucleons and produced soft particles, leading to two distinct absorption mechanisms. The signature of absorption by produced soft particles, as revealed by psi ̀production data, consists of a gap and a change of the slope in going from the pA line to the nucleus-nucleus line when we make a semi-log plot of the survival probability as a function of the path length. Using this signature, we find from the J/psi production data in pA, O-Cu, O-U, and S-U collisions that the degree of J/psi absorption by produced soft particles is small and cannot account for the J/psi data in Pb-Pb collisions. The anomalous suppression of J/psi production in Pb-Pb collisions can be explained as due to the occurrence of a new phase of strong J/psi absorption, which sets in when the local energy density exceeds about 3.4 GeV/fm3. To probe the chemical content of the new phase, we propose to study the abundance of open-charm mesons and charm hyperons which depends sensitively on the quark chemical potential.

We have carried out a wide study of Cold Nuclear Matter (CNM) effects on J/[Psi] = production in dAu, CuCu and AuAu collisions at √s{sub NN} = 200 GeV. We have studied the effects of three different gluon-shadowing parameterizations, using the usual simplified kinematics for which the momentum of the gluon recoiling against the J/[Psi] is neglected as well as an exact kinematics for a 2 → 2 process, namely g + g → J/[psi] + g as expected from LO pQCD. We have shown that the rapidity distribution of the nuclear modification factor R{sub dAu}, and particularly its anti-shadowing peak, is systematically shifted toward larger rapidities in the 2 → 2 kinematics, irrespective of which shadowing parameterization is used. In turn, we have noted differences in the effective final-state nuclear absorption needed to fit the PHENIX dAu data. Taking advantage of our implementation of a 2 → 2 kinematics, we have also computed the transverse momentum dependence of the nuclear modification factor, which cannot be predicted with the usual simplified kinematics. All the corresponding observables have been computed for CuCu and AuAu collisions and compared to the PHENIX and STAR data. Finally, we have extracted the effective nuclear absorption from the recent measurements of RCP in dAu collisions by the PHENIX collaboration.

This thesis presents the first J/psi production analysis of Au+Au reactions at forward rapidity at [square root]sNN = 200 GeV. In the second year of RHIC running, design energy was achieved in the collisions of both Au+Au ions and proton+proton reactions. The production of the J/psi is measured by the PHENIX experiment in Au+Au collisions as well as in proton-proton collisions. The scientific goal is to investigate the nature of hot, dense nuclear matter capitalizing on the unique properties of the J/psi as a probe of this matter. Recent experimental results by the NA50 collaboration at CERN strongly deviate from the conventional picture that successfully describes data at lower energies. The importance of such a measurement is demonstrated by the wide spectrum of theoretical explanations concerning the existing data. The merits of these models will be explored in a systematic and comprehensive study of the J/psi and open charm in collisions of a variety of species and energy. A survey of the theoretical models is presented and the relevant open charm and J/psi PHENIX measurements are compared.