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 studied nuclear effects in $p$$+$Al and $p$$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV on charged hadron production at forward rapidity ($1.4<\eta<2.4$, $p$-going direction) and backward rapidity ($-2.2<\eta<-1.2$, $A$-going direction). Such effects are quantified by measuring nuclear modification factors as a function of transverse momentum and pseudorapidity in various collision multiplicity selections. In central $p$$+$Al and $p$$+$Au collisions, a suppression (enhancement) is observed at forward (backward) rapidity compared to the binary scaled yields in $p$+$p$ collisions. The magnitude of enhancement at backward rapidity is larger in $p$$+$Au collisions than in $p$$+$Al collisions, which have a smaller number of participating nucleons. However, the results at forward rapidity show a similar suppression within uncertainties. The results in the integrated centrality are compared with calculations using nuclear parton distribution functions, which show a reasonable agreement at the forward rapidity but fail to describe the backward rapidity enhancement.

The PHENIX Collaboration at the Relativistic Heavy Ion Collider has measured open heavy-flavor production in minimum bias Au$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV via the yields of electrons from semileptonic decays of charm and bottom hadrons. Previous heavy-flavor electron measurements indicated substantial modification in the momentum distribution of the parent heavy quarks due to the quark-gluon plasma created in these collisions. For the first time, using the PHENIX silicon vertex detector to measure precision displaced tracking, the relative contributions from charm and bottom hadrons to these electrons as a function of transverse momentum are measured in Au$+$Au collisions. We compare the fraction of electrons from bottom hadrons to previously published results extracted from electron-hadron correlations in $p$$+$$p$ collisions at $\sqrt{s_{_{NN}}}=200$ GeV and find the fractions to be similar within the large uncertainties on both measurements for $p_T>4$ GeV/$c$. We use the bottom electron fractions in Au$+$Au and $p$$+$$p$ along with the previously measured heavy flavor electron $R_{AA}$ to calculate the $R_{AA}$ for electrons from charm and bottom hadron decays separately. We find that electrons from bottom hadron decays are less suppressed than those from charm for the region $3<p_T<4$ GeV/$c$.

J/psi production has been measured in proton-proton collisions at sqrt(s)= 200 GeV over a wide rapidity and transverse momentum range by the PHENIX experiment at RHIC. Distributions of the rapidity and transverse momentum, along with measurements of the mean transverse momentum and total production cross section are presented and compared to available theoretical calculations. The total J/psi cross section is 3.99 +/- 0.61(stat) +/- 0.58(sys) +/- 0.40(abs) micro barns. The mean transverse momentum is 1.80 +/- 0.23(stat) +/- 0.16(sys) GeV/c.

A measurement of direct photons in p+p collisions at sqrt(s)=200 GeV is presented. A photon excess above background from pi^0 --> gamma+gamma, eta --> gamma+gamma, and other decays is observed in the transverse momentum range 5.5 < p_T < 7 GeV/c. The result is compared to a next-to-leading-order perturbative QCD calculation. Within errors, good agreement is found between the QCD calculation and the measured result.

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.

The PHENIX experiment at the Relativistic Heavy Ion Collider measured $\pi^0$ and $\eta$ mesons at midrapidity in U$+$U collisions at $\sqrt{s_{_{NN}}}=192$ GeV in a wide transverse momentum range. Measurements were performed in the $\pi^0(\eta)\rightarrow\gamma\gamma$ decay modes. A strong suppression of $\pi^0$ and $\eta$ meson production at high transverse momentum was observed in central U$+$U collisions relative to binary scaled $p$$+$$p$ results. Yields of $\pi^0$ and $\eta$ mesons measured in U$+$U collisions show similar suppression pattern to the ones measured in Au$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV for similar numbers of participant nucleons. The $\eta$/$\pi^0$ ratios do not show dependence on centrality or transverse momentum, and are consistent with previously measured values in hadron-hadron, hadron-nucleus, nucleus-nucleus, and $e^+e^-$ collisions.

We report on the yield of protons and anti-protons, as a function of centrality and transverse momentum, in Au+Au collisions at sqrt(s_NN) = 200 GeV measured at mid-rapidity by the PHENIX experiment at RHIC. In central collisions at intermediate transverse momenta (1.5 < p_T < 4.5 GeV/c) a significant fraction of all produced particles are protons and anti-protons. They show a centrality-scaling behavior different from that of pions. The p-bar/pion and p/pion ratios are enhanced compared to peripheral Au+Au, p+p, and electron+positron collisions. This enhancement is limited to p_T < 5 GeV/c as deduced from the ratio of charged hadrons to pi^0 measured in the range 1.5 < p_T < 9 GeV/c.

During 2015 the Relativistic Heavy Ion Collider (RHIC) provided collisions of transversely polarized protons with Au and Al nuclei for the first time, enabling the exploration of transverse-single-spin asymmetries with heavy nuclei. Large single-spin asymmetries in very forward neutron production have been previously observed in transversely polarized $p$$+$$p$ collisions at RHIC, and the existing theoretical framework that was successful in describing the single-spin asymmetry in $p$$+$$p$ collisions predicts only a moderate atomic-mass-number ($A$) dependence. In contrast, the asymmetries observed at RHIC in $p$$+$$A$ collisions showed a surprisingly strong $A$ dependence in inclusive forward neutron production. The observed asymmetry in $p$$+$Al collisions is much smaller, while the asymmetry in $p$$+$Au collisions is a factor of three larger in absolute value and of opposite sign. The interplay of different neutron production mechanisms is discussed as a possible explanation of the observed $A$ dependence.

The PHENIX experiment has measured $\phi$ meson production in $d$$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV using the dimuon and dielectron decay channels. The $\phi$ meson is measured in the forward (backward) $d$-going (Au-going) direction, $1.2<y<2.2$ ($-2.2<y<-1.2$) in the transverse-momentum ($p_T$) range from 1--7 GeV/$c$, and at midrapidity $|y|<0.35$ in the $p_T$ range below 7 GeV/$c$. The $\phi$ meson invariant yields and nuclear-modification factors as a function of $p_T$, rapidity, and centrality are reported. An enhancement of $\phi$ meson production is observed in the Au-going direction, while suppression is seen in the $d$-going direction, and no modification is observed at midrapidity relative to the yield in $p$$+$$p$ collisions scaled by the number of binary collisions. Similar behavior was previously observed for inclusive charged hadrons and open heavy flavor indicating similar cold-nuclear-matter effects.