Understanding the detailed production and hadronization mechanisms for heavy quarkonia and their modification in a nuclear environment presents one of the major challenges in QCD. Calculations including nuclear-modified parton distribution functions
(nPDFs) and fitting of break-up cross sections (sigma_breakup) as parameters have been successful at describing many features of J/psi modification in proton(deuteron)-nucleus collisions. In this paper, we extend these calculations to explore different geometric dependencies of the modification and confront them with new experimental results from the PHENIX experiment. We find that no combination of nPDFs and sigma_breakup, regardless of the nPDF parameter set and the assumed geometric dependence, can simultaneously describe the entire rapidity and centrality dependence of J/psi modifications in d+Au collisions at sqrt(s_NN) = 200 GeV. We also compare the data with coherence calculations and find them unable to describe the full rapidity and centrality dependence as well. We discuss how these calculations might be extended and further tested, in addition to discussing other physics mechanisms including initial-state parton energy loss.
The hot nuclear matter created at the Relativistic Heavy Ion Collider (RHIC) has been characterized by near-perfect fluid behavior. We demonstrate that this stands in contradiction to the identification of QCD quasi-particles with the thermodynamic d
egrees of freedom in the early (fluid) stage of heavy ion collisions. The empirical observation of constituent quark ``$n_q$ scaling of elliptic flow is juxtaposed with the lack of such scaling behavior in hydrodynamic fluid calculations followed by Cooper-Frye freeze-out to hadrons. A ``quasi-particle transport time stage after viscous effects break down the hydrodynamic fluid stage, but prior to hadronization, is proposed to reconcile these apparent contradictions. However, without a detailed understanding of the transitions between these stages, the ``$n_q$ scaling is not a necessary consequence of this prescription. Also, if the duration of this stage is too short, it may not support well defined quasi-particles. By comparing and contrasting the coalescence of quarks into hadrons with the similar process of producing light nuclei from nucleons, it is shown that the observation of ``$n_{q}$ scaling in the final state does not necessarily imply that the constituent degrees of freedom were the relevant ones in the initial state.
