Charmonium is a valuable probe in heavy-ion collisions to study the properties of the quark gluon plasma, and is also an interesting probe in small collision systems to study cold nuclear matter effects, which are also present in large collision systems. With the recent observations of collective behavior of produced particles in small system collisions, measurements of the modification of charmonium in small systems have become increasingly relevant. We present the results of J/ψ measurements at forward and backward rapidity in various small collision systems, p+p, p+Al, p+Au and 3He+Au, at √sNN =200 GeV. The results are presented in the form of the observable RAB, the nuclear modification factor, a measure of the ratio of the J/ψ invariant yield compared to the scaled yield in p+p collisions. We examine the rapidity, transverse momentum, and collision centrality dependence of nuclear effects on J/ψ production with different projectile sizes p and 3He, and different target sizes Al and Au. The modification is found to be strongly dependent on the target size, but to be very similar for p+Au and 3He+Au. However, for 0%–20% central collisions at backward rapidity, the modification for 3He+Au is found to be smaller than that for p+Au, with a mean fit to the ratio of 0.89±0.03(stat)±0.08(syst), possibly indicating final state effects due to the larger projectile size.

The PHENIX experiment has measured mid-rapidity transverse momentum spectra (0.4 < p_T < 5.0 GeV/c) of electrons as a function of centrality in Au+Au collisions at sqrt(s_NN)=200 GeV. Contributions from photon conversions and from light hadron decays, mainly Dalitz decays of pi^0 and eta mesons, were removed. The resulting non-photonic electron spectra are primarily due to the semi-leptonic decays of hadrons carrying heavy quarks. Nuclear modification factors were determined by comparison to non-photonic electrons in p+p collisions. A significant suppression of electrons at high p_T is observed in central Au+Au collisions, indicating substantial energy loss of heavy quarks.

Suppression of the $J/\psi$ nuclear-modification factor has been seen as a trademark signature of final-state effects in large collision systems for decades. In small systems, the nuclear modification was attributed to cold-nuclear-matter effects until the observation of strong differential suppression of the $\psi(2S)$ state in $p/d$ $+$ $A$ collisions suggested the presence of final-state effects. Results of $J/\psi$ and $\psi(2S)$ measurements in the dimuon decay channel are presented here for $p$ $+$ $p$, $p$ $+$Al, and $p$ $+$Au collision systems at $\sqrt{s_{_{NN}}}=200$ GeV. The results are predominantly shown in the form of the nuclear-modification factor, $R_{pA}$, the ratio of the $\psi(2S)$ invariant yield per nucleon-nucleon collision in collisions of proton on target nucleus to that in $p$ $+$ $p$ collisions. Measurements of the $J/\psi$ and $\psi(2S)$ nuclear-modification factor are compared with shadowing and transport-model predictions, as well as to complementary measurements at Large-Hadron-Collider energies.

Muon production at forward rapidity (1.5 < |\eta| < 1.8) has been measured by the PHENIX experiment over the transverse momentum range 1 < p_T \le 3 GeV/c in sqrt(s) = 200 GeV p+p collisions at the Relativistic Heavy Ion Collider. After statistically subtracting contributions from light hadron decays an excess remains which is attributed to the semileptonic decays of hadrons carrying heavy flavor, i.e. charm quarks or, at high p_T, bottom quarks. The resulting muon spectrum from heavy flavor decays is compared to PYTHIA and a next-to-leading order perturbative QCD calculation. PYTHIA is used to determine the charm quark spectrum that would produce the observed muon excess. The corresponding differential cross section for charm quark production at forward rapidity is determined to be d\sigmac c^bar)/dy|_(y=1.6)=0.243 +/- 0.013 (stat.) +/- 0.105 (data syst.) ^(+0.049(-0.087) (PYTHIA syst.) mb.

We present the midrapidity charged pion invariant cross sections and the ratio of $\pi^-$-to-$\pi^+$ production ($5<p_T<13$ GeV/$c$), together with the double-helicity asymmetries ($5<p_T<12$ GeV/$c$) in polarized $p$$+$$p$ collisions at $\sqrt{s} = 200$ GeV. The cross section measurements are consistent with perturbative calculations in quantum chromodynamics within large uncertainties in the calculation due to the choice of factorization, renormalization, and fragmentation scales. However, the theoretical calculation of the ratio of $\pi^-$-to-$\pi^+$ production when considering these scale uncertainties overestimates the measured value, suggesting further investigation of the uncertainties on the charge-separated pion fragmentation functions is needed. Due to cancellations of uncertainties in the charge ratio, direct inclusion of these ratio data in future parameterizations should improve constraints on the flavor dependence of quark fragmentation functions to pions. By measuring charge-separated pion asymmetries, one can gain sensitivity to the sign of $\Delta G$ through the opposite sign of the up and down quark helicity distributions in conjunction with preferential fragmentation of positive pions from up quarks and negative pions from down quarks. The double-helicity asymmetries presented are sensitive to the gluon helicity distribution over an $x$ range of $\sim$0.03--0.16.

We present a measurement of the cross section and transverse single-spin asymmetry ($A_N$) for $\eta$ mesons at large pseudorapidity from $\sqrt{s}=200$~GeV $p^{\uparrow}+p$ collisions. The measured cross section for $0.5<p_T<5.0$~GeV/$c$ and $3.0<|\eta|<3.8$ is well described by a next-to-leading-order perturbative-quantum-chromodynamics calculation. The asymmetries $A_N$ have been measured as a function of Feynman-$x$ ($x_F$) from $0.2<|x_{F}|<0.7$, as well as transverse momentum ($p_T$) from $1.0<p_T<4.5$~GeV/$c$. The asymmetry averaged over positive $x_F$ is $\langle{A_{N}}\rangle=0.061{\pm}0.014$. The results are consistent with prior transverse single-spin measurements of forward $\eta$ and $\pi^{0}$ mesons at various energies in overlapping $x_F$ ranges. Comparison of different particle species can help to determine the origin of the large observed asymmetries in $p^{\uparrow}+p$ collisions.

The PHENIX experiment has measured mid-rapidity transverse momentum spectra (0.4 < p_T < 4.0 GeV/c) of single electrons as a function of centrality in Au+Au collisions at sqrt(s_NN) = 200 GeV. Contributions to the raw spectra from photon conversions and Dalitz decays of light neutral mesons are measured by introducing a thin (1.7% X_0) converter into the PHENIX acceptance and are statistically removed. The subtracted ``non-photonic'' electron spectra are primarily due to the semi-leptonic decays of hadrons containing heavy quarks (charm and bottom). For all centralities, charm production is found to scale with the nuclear overlap function, T_AA. For minimum-bias collisions the charm cross section per binary collision is N_cc^bar/T_AA = 622 +/- 57 (stat.) +/- 160 (sys.) microbarns.

First results on charm quarkonia production in heavy ion collisions at the Relativistic Heavy Ion Collider (RHIC) are presented. The yield of J/Psi's measured in the PHENIX experiment via electron-positron decay pairs at mid-rapidity for Au-Au reactions at sqrt(s_NN) = 200 GeV are analyzed as a function of collision centrality. For this analysis we have studied 49.3 million minimum bias Au-Au reactions. We present the J/Psi invariant yield dN/dy for peripheral and mid-central reactions. For the most central collisions where we observe no signal above background, we quote 90% confidence level upper limits. We compare these results with our J/Psi measurement from proton-proton reactions at the same energy. We find that our measurements are not consistent with models that predict strong enhancement relative to binary collision scaling.

The momentum distribution of electrons from semi-leptonic decays of charm and bottom for mid-rapidity |y|<0.35 in p+p collisions at sqrt(s)=200 GeV is measured by the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC) over the transverse momentum range 2 < p_T < 7 GeV/c. The ratio of the yield of electrons from bottom to that from charm is presented. The ratio is determined using partial D/D^bar --> e^{+/-} K^{-/+} X (K unidentified) reconstruction. It is found that the yield of electrons from bottom becomes significant above 4 GeV/c in p_T. A fixed-order-plus-next-to-leading-log (FONLL) perturbative quantum chromodynamics (pQCD) calculation agrees with the data within the theoretical and experimental uncertainties. The extracted total bottom production cross section at this energy is \sigma_{b\b^bar}= 3.2 ^{+1.2}_{-1.1}(stat) ^{+1.4}_{-1.3}(syst) micro b.

We present the first measurement of photoproduction of J/psi and of two-photon production of high-mass e+e- pairs in electromagnetic (or ultra-peripheral) nucleus-nucleus interactions, using Au+Au data at sqrt(s_NN) = 200 GeV. The events are tagged with forward neutrons emitted following Coulomb excitation of one or both Au^{star} nuclei. The event sample consists of 28 events with m_{e+e-} > 2 GeV/c^2 with zero like-sign background. The measured cross sections at midrapidity of d\sigma / dy (J/psi + Xn, y=0) = 76 +/- 33 (stat) +/- 11 (syst) micro b and d^2\sigma/dm dy (e^+e^- + Xn, y=0) = 86 +/- 23 (stat) +/- 16 (syst) micro b/(GeV/c^2) for m_{e+e-} \in [2.0,2.8] GeV/c^2 are consistent with various theoretical predictions.