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/$c$.

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.

Asymmetric nuclear collisions of $p$$+$Al, $p$$+$Au, $d$$+$Au, and $^{3}$He$+$Au at $\sqrt{s_{_{NN}}}=200$ GeV provide an excellent laboratory for understanding particle production, as well as exploring interactions among these particles after their initial creation in the collision. We present measurements of charged hadron production $dN_{\rm ch}/d\eta$ in all such collision systems over a broad pseudorapidity range and as a function of collision multiplicity. A simple wounded quark model is remarkably successful at describing the full data set. We also measure the elliptic flow $v_{2}$ over a similarly broad pseudorapidity range. These measurements provide key constraints on models of particle emission and their translation into flow.

Polarized proton-proton collisions provide leading-order access to gluons, presenting an opportunity to constrain gluon spin-momentum correlations within transversely polarized protons and enhance our understanding of the three-dimensional structure of the proton. Midrapidity open-heavy-flavor production at $\sqrt{s}=200$ GeV is dominated by gluon-gluon fusion, providing heightened sensitivity to gluon dynamics relative to other production channels. Transverse single-spin asymmetries of positrons and electrons from heavy-flavor hadron decays are measured at midrapidity using the PHENIX detector at the Relativistic Heavy Ion Collider. These charge-separated measurements are sensitive to gluon correlators that can in principle be related to gluon orbital angular momentum via model calculations. Explicit constraints on gluon correlators are extracted for two separate models, one of which had not been constrained previously.

Production of $\pi^0$ and $\eta$ mesons has been measured at midrapidity in Cu$+$Au collisions at $\sqrt{s_{_{NN}}}$=200 GeV. Measurements were performed in $\pi^0(\eta)\rightarrow\gamma\gamma$ decay channel in the 1(2)-20 GeV/$c$ transverse momentum range. A strong suppression is observed for $\pi^0$ and $\eta$ meson production at high transverse momentum in central Cu$+$Au collisions relative to the $p$$+$$p$ results scaled by the number of nucleon-nucleon collisions. In central collisions the suppression is similar to Au$+$Au with comparable nuclear overlap. The $\eta/\pi^0$ ratio measured as a function of transverse momentum is consistent with $m_T$-scaling parameterization down to $p_T=$2 GeV/$c$, its asymptotic value is constant and consistent with Au$+$Au and $p$$+$$p$ and does not show any significant dependence on collision centrality. Similar results were obtained in hadron-hadron, hadron-nucleus, and nucleus-nucleus collisions as well as in $e^+e^-$ collisions in a range of collision energies $\sqrt{s_{_{NN}}}=$3--1800 GeV. This suggests that the quark-gluon-plasma medium produced in Cu$+$Cu collisions either does not affect the jet fragmentation into light mesons or it affects the $\pi^0$ and $\eta$ the same way.

The cross section of bottom quark-antiquark ($b\bar{b}$) production in $p$+$p$ collisions at $\sqrt{s}=510$ GeV is measured with the PHENIX detector at the Relativistic Heavy Ion Collider. The results are based on the yield of high mass, like-sign muon pairs measured within the PHENIX muon arm acceptance ($1.2<|y|<2.2$). The $b\bar{b}$ signal is extracted from like-sign dimuons by utilizing the unique properties of neutral $B$ meson oscillation. We report a differential cross section of $d\sigma_{b\bar{b}\rightarrow \mu^\pm\mu^\pm}/dy = 0.16 \pm 0.01~(\mbox{stat}) \pm 0.02~(\mbox{syst}) \pm 0.02~(\mbox{global})$ nb for like-sign muons in the rapidity and $p_T$ ranges $1.2<|y|<2.2$ and $p_T>1$ GeV/$c$, and dimuon mass of 5--10 GeV/$c^2$. The extrapolated total cross section at this energy for $b\bar{b}$ production is $13.1 \pm 0.6~(\mbox{stat}) \pm 1.5~(\mbox{syst}) \pm 2.7~(\mbox{global})~\mu$b. The total cross section is compared to a perturbative quantum chromodynamics calculation and is consistent within uncertainties. The azimuthal opening angle between muon pairs from $b\bar{b}$ decays and their $p_T$ distributions are compared to distributions generated using {\sc ps pythia 6}, which includes next-to-leading order processes. The azimuthal correlations and pair $p_T$ distribution are not very well described by {\sc pythia} calculations, but are still consistent within uncertainties. Flavor creation and flavor excitation subprocesses are favored over gluon splitting.

We present measurements from the PHENIX experiment of large parity-violating single spin asymmetries of high transverse momentum electrons and positrons from $W^\pm/Z$ decays, produced in longitudinally polarized $p$$+$$p$ collisions at center of mass energies of $\sqrt{s}$=500 and 510~GeV. These asymmetries allow direct access to the anti-quark polarized parton distribution functions due to the parity-violating nature of the $W$-boson coupling to quarks and anti-quarks. The results presented are based on data collected in 2011, 2012, and 2013 with an integrated luminosity of 240 pb$^{-1}$, which exceeds previous PHENIX published results by a factor of more than 27. These high $Q^2$ data provide an important addition to our understanding of anti-quark parton helicity distribution functions.

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.