Collective flow has historically been an indicator that nuclear matter created in heavy ion collisions has undergone a phase change to a novel state where its constituent particles are deconfined. This phase, called a \textit{Quark-Gluon Plasma} (QGP), has many characteristics that are signature of its creation. Chief among these is the collective behavior of the nuclear matter indicated by its anisotropic flow, as well as high $p_T$ particle suppression, baryon enhancement at mid-$p_T$, and the enhancement of strange quark containing particles above binary scaling expectations. Recent results from the Large Hadron Collider (LHC) show evidence of collective flow in the simpler p+Pb system, implying that a QGP may be formed in smaller systems than previously thought. An elliptic flow measurement with identified particles in d+Au collisions could reveal more about the nuclear matter created in these simpler systems. The Pioneering High Energy Nuclear Ion Experiment, or PHENIX, Time of Flight detector used in conjunction with its Aerogel Cherenkov Counter can provide particle identification with good proton/kaon/pion separation for $p_T<7$ GeV/c. Measurements of particle identified elliptic flow using these detectors are presented and could help to elucidate the underlying physics of the baryon excess and strangeness enhancement anomalies that may be evidence of new physics in the d+Au system.

The Quark-Gluon Plasma (QGP), a new hot dense matter created by melting the protons and neutrons in nucleus, was discovered at RHIC (Relativistic Heavy Ion Collider). The Universe passed through a QGP stage about 10 µs after the Big Bang before condensing into the familiar particles - primarily protons or neutrons. Experiments have shown thatthe QGP behaves like a strongly coupled liquid instead of a weakly couple gas - which was the original expectation. One key to understanding the QGP is the initial state. Experiments at HERA (Hadron Electron Ring Accelerator) suggest that protons and neutrons are dominated by gluons if we probe at small x (longitudinal momentum fraction). This effect should be more substantial in nuclei due to the large number of nucleons. One theory called Color Glass Condensate (CGC) proposed the gluon is saturated in nuclei if we probe below the saturation scale. We can use a dilute system (deuteron) to probe a dense system (gold) to investigate the saturation. Experiments have seen signs of saturation in the d+Au collisions, though these effects are subject to interpretation. In this thesis, using the MPCEX (Muon Piston Calorimeter Extension) in the PHENIX experiment at RHIC, I explore saturation effects in d+Au collision in the forward direction and present the suppression of neutral pions.

Dielectrons are a very important probe used for studying the properties of hot dense nuclear matter created in heavy ion collisions. Since dielectrons are color neutral and produced during all stages of the collision, they provide access to an abundance of information not readily available from other sources. These include thermal sources, vector meson resonances, heavy charm and bottom decay, and Drell-Yan processes. Previous measurements of the dielectron continuum in PHENIX have indicated an unexpectedly large enhancement in Au+Au collisions in the low mass region (0.3 - 0.8GeV/c^2), a possible signal of chiral symmetry restoration, but these measurements were limited by large systematic uncertainties primarily from a poor signal to background ratio. In 2009 the PHENIX experiment was upgraded with the addition of the Hadron Blind Detector which improves the background rejection by detecting partially reconstructed Dalitz decays and gamma conversion pairs. In this thesis, I will review the status of electromagnetic probes measured from the collision of heavy nuclei and present and compare the results obtained from 2009 data in p + p at 200 GeV using the HBD which will serve as a baseline for Au+Au results obtained in 2010.

Anisotropic flow in heavy-ion collisions describes the collective motion of participants and products of the collisions, most commonly in the plane transverse to the axis of the colliding beams. Mathematically, flow is decomposed into a Fourier series of simple shapes which contribute to the overall motion, with the coefficients ($v_n$) describing the magnitude each shape contributes on average. The third harmonic in the series is known as triangular flow ($v_3$) and has previously been shown to develop due to event-by-event fluctuations that randomly produce triangular shapes in the initial collision geometry. This dissertation describes the first study of $v_3$ using the STAR detector at the five lowest center of mass collision energies of gold nuclei in the second stage Beam Energy Scan program at the Relativistic Heavy Ion Collider. A form of $v_3$ which does not develop from fluctuations ($v_3\{\Psi_1\}$) was found and measured at the lowest energy of $\sqrt{s_{NN}}=3.0$ GeV. The source of this $v_3\{\Psi_1\}$ was investigated for the first time using simulated collisions and was found to arise due to two crucial components: geometry and stopping of nucleons in the collision producing initial triangular shapes, and a potential within the equation of state of the medium produced in the collisions. The strength of $v_3\{\Psi_1\}$ was found to decrease with increasing energy, becoming consistent with zero in the region of 3.9 -- 4.5 GeV. A comparison to simulation currently suggests that the initial triangular shape does not vanish and cannot solely explain the disappearance of $v_3\{\Psi_1\}$. This work provides a multitude of new measurements to improve both heavy-ion simulations and our understanding of the equation of state for dense nuclear matter.

Nuclear modification factors quantify suppression in particle production due to nuclear effects. They are defined as a ratio of invariant yields, with a numerator derived from a given species of nuclear collision and a denominator derived from a hypothetically equivalent ensemble of independent proton-proton collisions. At large momentum transfer Q^2 and low momentum fraction x, the neutral pion nuclear modification factor R_d+Au for d+Au collisions is useful for investigating initial state gluon saturation. The large initial state gluon multiplicity of the Au nucleus causes saturation effects to occur at lower energies in d+Au collisions, as compared to p+p collisions, resulting in a relative suppression. Measuring the relative suppression R_d+Au can therefore test the validity of competing models describing saturation, including the framework of a color glass condensate (CGC).

Measurements at low x are of particular interest because in this region linear pQCD evolution equations begin to break down. The Froissart theorem places a robust theoretical upper limit on the behavior of hadronic cross sections: a cross section can increase at most like ln^2(E). Equivalently, an hadronic structure function can increase at most like ln^2(1/x). Adherence to this theorem is necessary to preserve S-matrix unitarity; no physical system should exhibit behavior to the contrary. However linear evolution equations, which dictate structure function behavior, predict an unchecked growth of low-x gluons, in violation of the theorem. For this reason, it is expected that gluon saturation, via non-linear evolution, will take place at low x to steer the gluon distribution function back within the limitations of the Froissart bound.

Greater suppression is expected at lower Q^2; however, at low x, regions of high Q^2 are more difficult to access experimentally. Pushing out to higher Q^2 is important for discriminating between competing theoretical models.

In practice, regions of low x and high Q^2 translate to measurements at, respectively, high rapidity η and high transverse momentum p⊥. The high rapidity 3.1 < η < 3.9 Muon Piston Calorimeter (MPC) detector at PHENIX is ideally suited for measurements of neutral pion R_d+Au probing regions of low x. At √s = 200 GeV, a combinatoric analysis of neutral pion decay products in the MPC can obtain measurements of R_d+Au up to a transverse momentum of p⊥ = 2 GeV/c. However, at p⊥ greater than 2 GeV/c, photons from neutral pion decay have insufficient spatial separation to be independently resolved in the detector. In this analysis the transverse momentum range of the detector, measuring R_d+Au at √s = 200 GeV, is extended to p⊥ = 3.5 GeV/c by studying photon pairs from neutral pions that resolve in the MPC as a single cluster. Increased suppression is reproduced at low p⊥, in agreement with previous data. For p⊥ > 2 GeV/c Cronin enhancement is not observed, as anticipated by the CGC framework. However, the data can not rule out the possibility that the observed suppression is the result of extreme nuclear shadowing. Also presented are invariant neutral pion yields for p+p and d+Au collisions and the invariant neutral pion cross section for p+p collisions at √s = 200 GeV.