Abstract
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 the fitting of breakup cross sections (${\ensuremath{\sigma}}_{br}$) as parameters have been successful at describing many features of $J/\ensuremath{\psi}$ modifications in proton (deuteron)-nucleus collisions. In this paper, we extend these calculations to explore different geometric dependencies of the modifications and confront them with new experimental results from the PHENIX experiment. We find that no combination of nPDFs and ${\ensuremath{\sigma}}_{br}$, regardless of the nPDF parameter set and the assumed geometric dependence, can simultaneously describe the entire rapidity and centrality dependence of $J/\ensuremath{\psi}$ modifications in $d+\mathrm{Au}$ collisions at $\sqrt{{s}_{{}_{NN}}}=200$ GeV. We extend these calculations to incorporate initial-state parton energy loss, which results in an improved description of the experimental data. Finally, we compare the data with previously published calculations, including coherence effects, and find them unable to describe the full rapidity and centrality dependence.
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