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This thesis makes significant advances in the quantitative understanding of two intrinsically linked yet technically very different phenomena in quantum chromodynamics (QCD). Firstly, the thesis investigates the soft probe of strong interaction topological fluctuations in the quark-gluon plasma (QGP) which is made possible via the anomalous chiral transport effects induced by such fluctuations. Here, the author makes contributions towards establishing the first comprehensive tool for quantitative prediction of the chiral magnetic effect in the QGP that is produced in heavy ion collision experiments. Secondly, the thesis deals with the hard probe of strongly coupled QGP created in heavy-ion collisions. In particular, this study addresses the basic question related to the nonperturbative color structure in the QGP via jet energy loss observables. The author further develops the CUJET computational model for jet quenching and uses it to analyze the topological degrees of freedom in quark-gluon plasma. The contributions this thesis makes towards these highly-challenging problems have already generated widespread impacts in the field of quark-gluon plasma and high-energy nuclear collisions.
Hadrons carrying heavy quarks, i.e. charm or bottom, are important probes of the hot and dense medium created in relativistic heavy ion collisions. Heavy quark-antiquark pairs are mainly produced in initial hard scattering processes of partons. While some of the produced pairs form bound quarkonia, the vast majority hadronize into particles carrying open heavy flavor. Heavy quark production has been studied by the PHENIX experiment at RHIC via measurements of single leptons from semi-leptonic decays in both the electron channel at mid-rapidity and in the muon channel at forward rapidity. A large suppression and azimuthal anisotropy of single electrons have been observed in Au + Au collisions at 200 GeV. These results suggest a large energy loss and flow of heavy quarks in the hot, dense matter. The PHENIX experiment has also measured J/[psi] production at 200 GeV in p + p, d + Au, Cu + Cu and Au + Au collisions, both at mid- and forward-rapidities, and additionally Cu + Au and U + U at forward-rapidities. In the most energetic collisions, more suppression is observed at forward rapidity than at central rapidity. This can be interpreted either as a sign of quark recombination, or as a hint of additional cold nuclear matter effects. The centrality dependence of nuclear modification factor, RAA(pT), for J/[psi] in U + U collisions at √sNN = 193 GeV shows a similar trend to the lighter systems, Au + Au and Cu + Cu, at similar energy 200 GeV.