$J/\psi$ $R_{CP}$ for 0-20%, 20-40%, and 40-60% (central) relative to 60-86% (peripheral) Au+Au collisions at 62.4 GeV. Type A errors are point-to-point uncorrelated, Type B errors are point-to-point correlated, and Type C are global systematic from the uncertainty in the peripheral $<N_{coll}>$ value.

$J/\psi$ $R_{CP}$ for 0-40% (central) relative to 40-86% (peripheral) Au+Au collisions at 39 GeV. Type A errors are point-to-point uncorrelated, Type B errors are point-to-point correlated, and Type C are global systematic from the uncertainty in the peripheral $<N_{coll}>$ value.

$J/\psi$ $R_{AA}$ at $\sqrt{s_{NN}}$ = 39 and 62.4 GeV. Type A errors are point-to-point uncorrelated, Type B errors are point-to-point correlated, and Type C are global systematic from the uncertainty in the peripheral $<N_{coll}>$ value.

$J/\psi$ $R_{AA}$ at $\sqrt{s_{NN}}$ = 39 and 62.4 GeV.

c$\bar{c}$ production cross section as a function of rapidity in $p$+$p$ collisions, measured using semileptonic decay to electrons (closed square) and to muons (closed circle).

Transverse momentum distribution of $R_{AA}$ for negative muons from heavy-flavor mesons decay in Cu+Cu collisions in the following centrality classes: 40-94% (top panel), 20-40% (middle panel) and 0-20% (bottom panel). Also shown in the bottom panel is a theoretical calculation from [39,40], discussed in Section V.

Comparison of $R_{AA}$ as a function of $N_{part}$ between heavy-flavor muons reconstructed at forward rapidity ($1.4<y<1.9$) and $p_T >$ 2 GeV in Cu+Cu collisions (red squares) and nonphotonic electrons reconstructed at midrapidity and $p_T>$ 3 GeV in Au+Au collisions (blue circles).

Comparison of $R_{AA}$ as a function of $N_{part}$ between heavy-flavor muons reconstructed at forward rapidity ($1.4<y<1.9$) and $p_T >$ 2 GeV in Cu+Cu collisions (red squares) and nonphotonic electrons reconstructed at midrapidity and $p_T>$ 3 GeV in Au+Au collisions (blue circles).

$J_{dA}$ versus $x^{frag}_{Au}$ for $d$+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV for different centrality classes.

$J_{dA}$ versus $x^{frag}_{Au}$ for $d$+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV for different centrality classes.

$J_{dA}$ versus $x^{frag}_{Au}$ for $d$+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV for different centrality classes.

$p_T$ versus $R_{dA}$ for $\pi^0$ and range of 3.0 < $\eta$ < 3.8.

PHENIX $\pi^0$ invariant cross-section for $p$+$p$ collisions for range 3.0 < $\eta$ < 3.8.

Invariant transverse momentum spectra of $\omega$ production in $p$+$p$ and $d$+Au collisions at $\sqrt{s}$=200 GeV.

Invariant transverse momentum spectra of $\omega$ production in $p$+$p$ and $d$+Au collisions at $\sqrt{s}$=200 GeV.

Invariant transverse momentum spectra of $\omega$ production in Cu+Cu (left) and Au+Au (right) collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel for three centrality bins and minimum bias.

Invariant transverse momentum spectra of $\omega$ production in Cu+Cu (left) and Au+Au (right) collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel for three centrality bins and minimum bias.

Invariant transverse momentum spectra of $\omega$ production in Cu+Cu (left) and Au+Au (right) collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel for three centrality bins and minimum bias.

Invariant transverse momentum spectra of $\omega$ production in Cu+Cu (left) and Au+Au (right) collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel for three centrality bins and minimum bias.

Invariant transverse momentum spectra of $\omega$ production in Cu+Cu (left) and Au+Au (right) collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel for three centrality bins and minimum bias.

Invariant transverse momentum spectra of $\omega$ production in Cu+Cu (left) and Au+Au (right) collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel for three centrality bins and minimum bias.

Measured ${\omega}/{\pi}$ ratio as a function of $p_T$ in $p$ + $p$ collisions at $\sqrt{s}$=200 GeV.

Measured ${\omega}/{\pi}$ ratio as a function of $p_T$ in $p$ + $p$ collisions at $\sqrt{s}$=200 GeV.

Measured ${\omega}/{\pi}$ ratio as a function of $p_T$ in $p$ + $p$ collisions at $\sqrt{s}$=200 GeV.

${\omega}/{\pi}$ ratio versus transverse momentum in $d$+Au (0–88%) for $\omega \rightarrow {e}^{+}{e}^{-}$.

${\omega}/{\pi}$ ratio versus transverse momentum in $d$+Au (0–88%) for $\omega \rightarrow {\pi}^{+}{\pi}^{-}\pi^0$.

${\omega}/{\pi}$ ratio versus transverse momentum in $d$+Au (0–88%) for $\omega \rightarrow {\pi}^{0}\gamma$.

${\omega}/{\pi}$ ratio versus transverse momentum in Cu+Cu (0–94%) for $\omega \rightarrow {\pi}^{0}\gamma$.

${\omega}/{\pi}$ ratio versus transverse momentum in Au+Au (0–92%) for $\omega \rightarrow {\pi}^{0}\gamma$.

${\omega}/{\pi}$ ratio versus transverse momentum in Au+Au (0–92%) for $\omega \rightarrow {\pi}^{0}\gamma$.

Nuclear modification factor, RdAu, measured for the ${R}_{dAu}$ in 0–88, 0–20, 20-40, and 40-60% centrality bins in $d$+Au collisions at $\sqrt{s}$=200 GeV.

Nuclear modification factor, RdAu, measured for the ${R}_{dAu}$ in 60–88% centrality bins in $d$+Au collisions at $\sqrt{s}$=200 GeV.

Nuclear modification factor, RdAu, measured for the ${R}_{dAu}$ in 0–88, 20-40, and 40–60% centrality bins in $d$+Au collisions at $\sqrt{s}$=200 GeV.

Nuclear modification factor, RdAu, measured for the ${R}_{dAu}$ in 0–20 and 60–88% centrality bins in $d$+Au collisions at $\sqrt{s}$=200 GeV.

Nuclear modification factor, RdAu, measured for the ${R}_{dAu}$ in 0–88, 0–20, 20-40, 40-60, and 60–88% centrality bins in $d$+Au collisions at $\sqrt{s}$=200 GeV.

$R_{AA}$ of the $\omega$ in Cu+Cu collisions from the $\omega \rightarrow \pi^0\gamma$ decay channel.

$R_{AA}$ of the $\omega$ in Au+Au collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel.

$R_{AA}$ of the $\omega$ in Au+Au collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel.

$R_{AA}$ of the $\omega$ in Au+Au collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel.

$R_{AA}$ of the $\omega$ in Au+Au collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel.

$R_{AA}$ of the $\omega$ in and Au+Au collisions from the $\omega \rightarrow \pi^0 \gamma$ decay channel.

($R_{AA}$) of the $\omega \rightarrow \pi^+\pi^-\pi^0$ collision for the $\omega$ meson integrated over the range $p_T$ > 7 $\mathrm{GeV}$/$c$ as a function of the number participating nucleons ($N_{part}$).

($R_{AA}$) of the $\omega \rightarrow \pi^0 \gamma$ collision for the $\omega$ meson integrated over the range $p_T$ > 7 $\mathrm{GeV}$/$c$ as a function of the number participating nucleons ($N_{part}$).

$R_{AA}$ of the $\omega \rightarrow \pi^0 \gamma$ collision for the $\omega$ meson integrated over the range $p_T$ > 7 $\mathrm{GeV}$/$c$ as a function of the number participating nucleons ($N_{part}$).

$\psi^{\prime}(J/\psi)$ dielectron yield ratio measured at $|y|$ < 0.35 followed by point-to-point uncorrelated (uncorr.) (statistical and uncorrelated systematic uncertainties) and correlated systematic (corr.) uncertainties.

$J/\psi$ counts obtained from the dimuon decay analysis of four different data sets, determined using the fit function. The S and N following 2006 and 2008 indicate the data sets for the south and north forward arms.

$J/\psi$ counts obtained from the dimuon decay analysis of four different data sets, determined using the fit function. The S and N following 2006 and 2008 indicate the data sets for the south and north forward arms.

Transverse momentum dependence of $J/\psi$ and $\psi^{\prime}$ yields in $|y|$ < 0.35, and ${\psi^{\prime}}/{J/\psi}$ ratio together with ratios obtained in other experiments. Uncertainties are point-to-point uncorrelated (uncorr.) (statistical and uncorrelated systematic uncertainties) and correlated systematic (corr.) uncertainties. The global uncertainty is 10%.

Transverse momentum dependence of $J/\psi$ and $\psi^{\prime}$ yields in $|y|$ < 0.35, and ${\psi^{\prime}}/{J/\psi}$ ratio together with ratios obtained in other experiments. Uncertainties are point-to-point uncorrelated (uncorr.) (statistical and uncorrelated systematic uncertainties) and correlated systematic (corr.) uncertainties. The global uncertainty is 10%.

Transverse momentum dependence of $J/\psi$ and $\psi^{\prime}$ yields in $|y|$ < 0.35, and ${\psi^{\prime}}/{J/\psi}$ ratio together with ratios obtained in other experiments. Uncertainties are point-to-point uncorrelated (uncorr.) (statistical and uncorrelated systematic uncertainties) and correlated systematic (corr.) uncertainties. The global uncertainty is 10%.

Transverse momentum dependence of the $J/\psi$ dimuon differential cross section obtained in the muon arms in 2006 and 2008 Runs. Uncertainties are point-to-point uncorrelated (uncorr.) (statistical and uncorrelated systematic uncertainties) and correlated systematic (corr.) uncertainties. The global uncertainty is 10%.

Rapidity dependence of the $J/\psi$ yield combining dielectron ($|y|$ < 0.35 - full squares) with dimuon channels (1.2 < $|y|$ < 2.4 - full circles) along with the fits used to estimate the total cross section. Uncertainties are point-to-point uncorrelated (uncorr.) (statistical and uncorrelated systematic uncertainties) and correlated systematic (corr.) uncertainties. The global uncertainty is 10%.

Differential invariant yield of electrons (($N_{e^+}$+$N_{e^-}$)/2) from heavy-flavor decays for different centrality classes.

Differential invariant yield of electrons (($N_{e^+}$+$N_{e^-}$)/2) from heavy-flavor decays for different centrality classes.

Differential invariant yield of electrons (($N_{e^+}$+$N_{e^-}$)/2) from heavy-flavor decays for different centrality classes.

Differential invariant yield of electrons (($N_{e^+}$+$N_{e^-}$)/2) from heavy-flavor decays for different centrality classes.

$R_{AuAu}(p^e_T)$ for different centrality classes.

$R_{AuAu}(p^e_T)$ for different centrality classes.

$R_{AuAu}(p^e_T)$ for different centrality classes.

$p^e_T$-integrated nuclear modification factors $R_{AuAu}$.

Nonphotonic electron $v_2$ as a function of $p_T$ in Au+Au collisions at $\sqrt{s_{NN}}$ = 200 GeV.

Parameters of the Tsallis fit with parameter $n$ constrained to a fixed linear dependence on mass (for mesons). Cross sections are in $\mu$b for $J/\psi$ and $\psi^{\prime}$ and in mb for all other particles.

Constant and linear fits to the Tsallis parameter $T$ of mesons with fixed parameter $n$. The last column (Prob.) gives the probability estimated by the $\chi^2$/$n.d.f.$ of the fit.

Parameters of the Tsallis fit with Eq. 8 in the paper with parameters $n$ and $T$ constrained to have a fixed linear dependence on mass (for mesons). Cross sections are in $\mu$b for $J/\psi$ and $\psi^{\prime}$ and in mb for all other particles.

Cross sections in mb and $<p_T>$ in GeV/$c$ of different particles in $p$+$p$ collisions at $\sqrt{s}$ = 200 GeV. PHENIX columns show the values obtained by fits to the experiment spectra with the Tsallis functional form as described in the text. One should state explicitly that these values do not supersede values given in the ”Published” column by the experiments, in their publications listed in the last column, or elsewhere. An additional 9.7% systematic uncertainty should be added to all $d\sigma$/$dy$ values listed in the column “PHENIX” to account for the trigger uncertainties. Values in the column “Published” are also given without these systematic uncertainties. The column “S.M.” is the prediction of the statistical model discussed in the text. The characteristic widths of the particle spectra are $\langle p_T \rangle$ for all species except for $J/\psi$ and $\psi^{\prime}$ for which the values given in the Table are $\langle p_T^2 \rangle$. For $\psi^{\prime}$ the integration is done in the $p_T$ regionbelow 5 GeV/$c$. All errors are the combined statistical and systematic uncertainties.

Cross sections in mb and $<p_T>$ in GeV/$c$ of different particles in $p$+$p$ collisions at $\sqrt{s}$ = 200 GeV. PHENIX columns show the values obtained by fits to the experiment spectra with the Tsallis functional form as described in the text. One should state explicitly that these values do not supersede values given in the ”Published” column by the experiments, in their publications listed in the last column, or elsewhere. An additional 9.7% systematic uncertainty should be added to all $d\sigma$/$dy$ values listed in the column “PHENIX” to account for the trigger uncertainties. Values in the column “Published” are also given without these systematic uncertainties. The column “S.M.” is the prediction of the statistical model discussed in the text. The characteristic widths of the particle spectra are $\langle p_T \rangle$ for all species except for $J/\psi$ and $\psi^{\prime}$ for which the values given in the Table are $\langle p_T^2 \rangle$. For $\psi^{\prime}$ the integration is done in the $p_T$ regionbelow 5 GeV/$c$. All errors are the combined statistical and systematic uncertainties.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.

The invariant differential cross section ${d^2 \sigma}$/${2\pi p_T dy p_T}$ of $\omega$ meson production measured in the indicated decay channel. Type A uncertainties are $p_T$ independent. Type C & B systematic uncertainties are residual with Type B having an unknown $p_T$ dependence. For each $y$-coordinate in each $p_T$ bin was varied by the same amount according to the uncertainty Type C.