The PHENIX experiment at the BNL Relativistic Heavy Ion Collider (RHIC) has measured $J/\psi$ production for rapidities $-2.2<y<2.2$ in $\mathrm{Au}+\mathrm{Au}$ collisions at $\sqrt{s_{NN}}=200\mathrm{GeV}$. The $J/\psi$ invariant yield and nuclear modification factor $R_{AA}$ as a function of centrality, transverse momentum, and rapidity are reported. A suppression of $J/\psi$ relative to binary collision scaling of proton-proton reaction yields is observed. Models which describe the lower energy $J/\psi$ data at the CERN Super Proton Synchrotron invoking only $J/\psi$ destruction based on the local medium density predict a significantly larger suppression at RHIC and more suppression at midrapidity than at forward rapidity. Both trends are contradicted by our data.

The production of $e^{+}{e}^{-}$ pairs for $m_{e^{+}{e}^{-}}<0.3\mathrm{GeV}/c^2$ and $1<p_T<5\mathrm{GeV}/c$ is measured in $p+p$ and $\mathrm{Au}+\mathrm{Au}$ collisions at $\sqrt{s_{NN}}=200\mathrm{GeV}$. An enhanced yield above hadronic sources is observed. Treating the excess as photon internal conversions, the invariant yield of direct photons is deduced. In central $\mathrm{Au}+\mathrm{Au}$ collisions, the excess of the direct photon yield over $p+p$ is exponential in transverse momentum, with an inverse slope $T=221\pm {19}^{\mathrm{stat}}\pm {19}^{\mathrm{syst}}\mathrm{MeV}$. Hydrodynamical models with initial temperatures ranging from $T_{\mathrm{init}}\sim 300–600\mathrm{MeV}$ at times of $\sim 0.6–0.15\mathrm{fm}/c$ after the collision are in qualitative agreement with the data. Lattice QCD predicts a phase transition to quark gluon plasma at $\sim 170\mathrm{MeV}$.

Differential measurements of elliptic flow ($v_2$) for $\mathrm{Au}+\mathrm{Au}$ and $\mathrm{Cu}+\mathrm{Cu}$ collisions at $\sqrt{s_{\mathrm{NN}}}=200\mathrm{GeV}$ are used to test and validate predictions from perfect fluid hydrodynamics for scaling of $v_2$ with eccentricity, system size, and transverse kinetic energy (${\mathrm{KE}}_T$). For ${\mathrm{KE}}_T\equiv m_T-m$ up to $\sim 1\mathrm{GeV}$ the scaling is compatible with hydrodynamic expansion of a thermalized fluid. For large values of ${\mathrm{KE}}_T$ mesons and baryons scale separately. Quark number scaling reveals a universal scaling of $v_2$ for both mesons and baryons over the full ${\mathrm{KE}}_T$ range for $\mathrm{Au}+\mathrm{Au}$. For $\mathrm{Au}+\mathrm{Au}$ and $\mathrm{Cu}+\mathrm{Cu}$ the scaling is more pronounced in terms of ${\mathrm{KE}}_T$, rather than transverse momentum.

Flow coefficients $v_n$ for $n=2$, 3, 4, characterizing the anisotropic collective flow in $\mathrm{Au}+\mathrm{Au}$ collisions at $\sqrt{s_{NN}}=200\mathrm{GeV}$, are measured relative to event planes ${\Psi }_n$, determined at large rapidity. We report $v_n$ as a function of transverse momentum and collision centrality, and study the correlations among the event planes of different order $n$. The $v_n$ are well described by hydrodynamic models which employ a Glauber Monte Carlo initial state geometry with fluctuations, providing additional constraining power on the interplay between initial conditions and the effects of viscosity as the system evolves. This new constraint can serve to improve the precision of the extracted shear viscosity to entropy density ratio $\eta /s$.

Transverse momentum spectra of electrons ($p_T^e$) from semileptonic weak decays of heavy-flavor mesons in the range of $0.3<p_T^e<9.0$ GeV/$c$ have been measured at midrapidity ($\left|y\right|<0.35$) by the PHENIX experiment at the Relativistic Heavy Ion Collider in $p+p$ and $\mathrm{Au}+\mathrm{Au}$ collisions at $\sqrt{s_{\mathrm{NN}}}=200$ GeV. In addition, the azimuthal anisotropy parameter $v_2$ has been measured for $0.3<p_T^e<5.0$ GeV/$c$ in $\mathrm{Au}+\mathrm{Au}$ collisions. The substantial modification in the $p_T^e$ spectra in $\mathrm{Au}+\mathrm{Au}$ compared with $p+p$ collisions as well as the nonzero $v_2$ indicate substantial interactions and flow of heavy quarks in traversing the produced medium. Comparisons of these observables with detailed theoretical calculations can be used to identify the nature of these interactions and to quantify their extent.