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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix

Abstract Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo‐electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model‐building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix‐AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.

Poon, Billy K.↗
DOE OSTI2022

\(J/\psi \) and \(\psi (2S)\) Production in Small Systems with PHENIX

The suppression of the ψ(2S) nuclear modification factor has been seen as a trademark signature of final-state effects in large collision systems for decades. In small systems, deviations of the nuclear modification from unity had been attributed to cold nuclear matter effects until the observation of strong differential suppression of the ψ(2S) state in p/d+A collisions, which suggests the presence of final-state effects. Here in this paper, we present results of J/ψ and ψ(2S) measurements in the dimuon decay channel for p + p, p+Al, and p+Au collision systems at $\sqrt{s_{NN}}$ = 200 GeV. Key results include the nuclear modification factors R pA as a function of centrality and rapidity. The measurements are compared with shadowing and transport model predictions, as well as complementary measurements at LHC energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Data and Analysis Preservation in the PHENIX Experiment at RHIC

The PHENIX experiment (the Pioneering High Energy Nuclear Interaction eXperiment) is the largest of the four experiments that have operated at the Relativistic Heavy Ion Collider (RHIC), taking data in 2000-2016. PHENIX has made fundamental contributions to the discovery and study of the Quark-Gluon Plasma, advancement of spin physics and other areas. Currently, the PHENIX Collaboration is analyzing large data samples previously collected, while facing challenges in the area of Data and Analysis Preservation. We describe the strategy and practices employed by the PHENIX Collaboration to meet these challenges by leveraging state-of-the-art platforms and tools created and maintained by the High Energy and Nuclear Physics communities, including Zenodo, HEPData, OpenData, REANA and others.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

phenix v. 7.0

SAND2021-6741 O phenix is Sandia's orchestration tool that allows users to quickly deploy, un-deploy, and interact with SCEPTRE ICS environments. phenix is an orchestration tool used for managing the creation, configuration, and deployment of modeling and simulation environments. As an abstraction layer on top of an underlying virtual machine manager called minimega, phenix organizes the network, application, and scenario information for a given deployment. It allows users to create, configure, and deploy experiments in a repeatable and rapid fashion. An application framework provides the flexibility to manipulate an experiment to suit various needs and requirements. phenix also includes a web-based graphical user interface (GUI) where experiments can be created, configured, and interacted with.

Sahakian, Meghan↗
DOE OSTI2025

Spin Physics at PHENIX

Situated at the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory, the PHENIX experiment has for almost two decades been at the forefront of investigations into spin structure and dynamics in high-energy nuclear physics. Although decommissioned in 2016, the PHENIX collaboration has released a number of new results over the past several years that continue to inform the field. Recent longitudinal spin measurements uncover the role of gluon and sea quark polarization in the proton. Transverse spin measurements probe the transverse momentum-dependent (TMD) distributions and higher-twist multiparton correlators that are needed to fully explain partonic dynamics in the initial and final state. Additionally, the effects of heavy ions on spin have been studied by comparing transverse spin measurements between p+p and p+A collisions. These recent results and their wider implications are presented.

PHENIX↗
DOE OSTI2026

pyDiSCaMB : enabling the use of multipolar scattering factors in Phenix

Multipolar scattering models, such as the transferable aspherical atom model, account for atomic chemical interactions and provide a more accurate representation of experimental data. However, the simpler independent atom model (IAM), which assumes non-interacting atoms, is the only model available in the most widely used macromolecular refinement programs. This is primarily because IAM offers a hard-to-beat combination of computational efficiency and modelling power at typical macromolecular resolutions. By contrast, more accurate multipolar modelling has historically been limited due to its computational cost and the absence of an interface between software capable of calculating structure factors and gradients based on multipolar models and software designed for macromolecular refinement. This work introduces pyDiSCaMB , a Python software package designed to integrate between the computational crystallography toolbox ( cctbx ) and the quantum crystallography library DiSCaMB ( Densities in Structural Chemistry and Molecular Biology ), thus enabling multipolar scattering models in Phenix 's toolkit. The implementation, features and capabilities of pyDiSCaMB are presented, the runtimes for the calculation of structure factor and target gradients with respect to atomic parameters are explored, and Fourier images of electrostatic potential, electron density and deformation maps are computed as illustrative examples. The pyDiSCaMB library will make multipolar modelling widely available to the structural biology community, potentially transforming refinement and model-building for both crystallography and cryogenic electron microscopy (cryoEM).

MATTS data bank↗
DOE OSTI2022

PHENIX Probing QCD Matter Through Heavy Flavor and Quarkonium at RHIC

Recent results from the PHENIX experiment on heavy flavors and quarkonia production in p + Al, p + Au, d + Au, and Au + Au collision systems at psNN = 200 GeV are summarized. The results are carried out by the measurements of the nuclear modification factors and elliptic flow. The nuclear modification factors measurements give insight into the energy loss of heavy quarks in the quark-gluon plasma medium along their path lengths. The elliptic flow measurements are a good tool to investigate the coupling of heavy quarks with the medium. The measurements are presented as a function of centrality, rapidity, and transverse momentum. The interpretations of the results in light of our current theoretical models, and comparison to LHCb and ALICE measurements are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Passive high explosive neutron inspection (PHENIX): a new method to confirm the presence or absence of high explosives for nuclear treaty verification

Advanced instruments and methods need to be developed now to create a technical basis to support the negotiation of future nuclear arms control treaties. One new capability that is anticipated is the ability to confirm either the declared presence or declared absence of high explosive (HE) material in the presence of special nuclear material (SNM). Towards this goal, Passive HE Neutron Inspection (PHENIX) has been developed and demonstrated as a method for confirming the presence or absence of HE in the presence of plutonium. The method exploits the inherent presence of neutrons associated with the decay of plutonium as an internal probe source for performing prompt gamma-ray neutron activation analysis (PGNAA), searching for the presence of HE as revealed by the emission of characteristic gamma rays following neutron absorption in hydrogen and nitrogen which are building blocks of present-day, military-grade HE. Tests using stoichiometrically-correct hemishells of mock HE with plutonium show that a system can be expected to positively confirm the presence or absence of these signatures, supporting determination of HE presence or absence with Pu, in a few hours. To protect other potentially sensitive gamma-ray signatures from a treaty accountable item, an analog information barrier has been conceptualized and tested which physically prevents the collection of gamma-ray spectral data outside of user selected energy windows strategically chosen to view only narrow spectral regions corresponding to the hydrogen (2223.2 keV) and nitrogen (9807.2 keV, 10,318.2 keV, and 10,829.2 keV) PGNAA signatures.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Scaling Properties of φ -Meson and Light Charged Hadron Production in Small and Large Systems at PHENIX

Recent results on the identified charged-hadron (π ± , K ± , p, p¯) production vat midrapidity region (|η| < 0.35) have been measured by the PHENIX experiment in p + Al, 3 He + Au, Cu + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV and U + U collisions at $\sqrt{s_{NN}}$ = 193 GeV. These measurements are presented through the invariant transverse-momentum (p T ) and transverse-mass (m T ) spectra for different collision centralities. The averaged freeze-out temperature value for different systems was found to be 166.1 ± 2.2 MeV, and do not exhibit any dependence on the collision centrality and $\langle$N parti $\rangle$ values. The particle ratios of K/π and p/π have been measured in different centrality ranges of large and small collision systems. The values of K/π ratios measured in all considered collision systems were found to be consistent with those measured in p+p collisions. Furthermore, the identified charged-hadron nuclear-modification factors (R AB ) are also presented. Enhancement of proton R AB values over meson R AB values was observed in central 3 He+Au, Cu+Au, and U+U collisions. The proton R AB values measured in p+Al collision system were found to be consistent with R AB values of Φ, π ± , K ± , and π 0 mesons, suggesting that the size of the system produced in p+Al collisions is too small for recombination to cause a noticeable increase in proton production.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Checking nonflow assumptions and results via PHENIX published correlations in p+p, p+Au, d+Au, and 3 He+Au at √ s NN=200 GeV

Recently the PHENIX Collaboration has made available two-particle correlation Fourier coefficients for multiple detector combinations in minimum bias p+p and 0–5% central p+Au, d+Au, and 3 He+Au collisions at √ s NN = 200 GeV [Phys. Rev. C 105, 024901 (2022)]. Using these coefficients for three sets of two-particle correlations, azimuthal anisotropy coefficients v 2 and v 3 are extracted for midrapidity charged hadrons as a function of transverse momentum. In this paper, we use the available coefficients to explore various nonflow hypotheses as well as to compare the results with theoretical model calculations. The nonflow methods fail basic closure tests with ampt and pythia/angantyr, particularly when including correlations with particles in the low multiplicity light-projectile going direction. In data, the nonflow adjusted v 2 results are modestly lower in p+Au and the adjusted v 3 results are more significantly higher in p+Au and d+Au. However, the resulting higher values for the ratio v 3 /v 2 in p+Au at RHIC compared to p+Pb at the LHC is additional evidence for a significant overcorrection. Incorporating these additional checks, the conclusion that these flow coefficients are dominated by initial geometry coupled with final-state interactions (e.g., hydrodynamic expansion of quark-gluon plasma) remains true, and explanations based solely on initial-state glasma are ruled out. The detailed balance between intrinsic and fluctuation-driven geometry and the exact role of weakly versus strongly coupled prehydrodynamic evolution remains an open question for triangular flow, requiring further theoretical and experimental investigation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Transverse Single-Spin Asymmetries of Midrapidity Direct Photons and Neutral Mesons at PHENIX

Results are presented for the transverse single-spin asymmetries of direct photons, neutral pions, and eta mesons for |\eta|<0.35 | η | < 0.35 from p^\uparrow + p p ↑ + p collisions with \sqrt{s} = 200 s = 200 GeV at PHENIX. As hadrons, \pi^0 π 0 and \eta η mesons are sensitive to both initial- and final-state effects and at midrapidity probe the dynamics of gluons along with a mix of quark flavors. Because direct photon production does not include hadronization, the direct photon TSSA is only sensitive to initial-state effects and at midrapidity provides a clean probe of the gluon dynamics in transversely polarized protons. All three of these results will help constrain the collinear twist-3 trigluon correlation function as well as the gluon Sivers function, improving our knowledge of spin-dependent gluon dynamics in QCD.

Lewis, Nicole↗
DOE OSTI2021

New PHENIX Results on Mid-Rapidity Bottom and Charm Production in Au+Au collisions at $\sqrt{s_{NN}}$= 200 GeV

Energy loss of quarks in the hot and dense medium has been studied for decades. Both the experimental and theoretical efforts have hinted that the energy loss is quark mass dependent. Although experiments at the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC) have found that the electrons from heavy quarks are less or similarly suppressed compared to the light hadrons, the mass ordering of the suppression between charm and bottom quarks is not yet clear due to large experimental uncertainties. We have fully exploited the events recorded at mid-rapidity in Au+Au collisions at center-of-mass energy of 200 GeV by the PHENIX experiment at RHIC to study the invariant yield of electrons from open heavy flavors. Latest results on the nuclear modification factors for charm and bottom separated heavy flavor electrons are reviewed in this proceeding. The implications of these results on the understanding of the quark mass and medium size dependence of the energy loss are also discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Measurements of J/ ψ Production vs. Event Multiplicity in Forward Rapidity in p + p Collisions in the PHENIX Experiment

J / Ψ, a charmonium bound state made of a charm and an anti-charm quark, was discovered in the 1970s and confirmed the quark model. Because the mass of charm quarks is significantly above the quantum chromodynamics (QCD) scale Λ QCD , charmonia are considered excellent probes to test perturbative quantum chromodynamics (pQCD) calculations. In recent decades, they have been studied extensively at different high-energy colliders. However, their production mechanisms, which involve multiple scales, are still not very well understood. Recently, in high-multiplicity p + p collisions at RHIC and at the LHC, a significant enhancement of J / Ψ production yield has been observed, which suggests a strong contribution of multi-parton interaction (MPI). This is different from the traditional pQCD picture, where charm quark pairs are produced from a single hard scattering between partons in p + p collisions. In this work, we will report the J / Ψ normalized production yield as a function of normalized charged particle multiplicity over a board range of rapidity and event multiplicity in the J / Ψ → μ + μ – channel with PHENIX Run 15 p + p data at $\sqrt s$ =200 GeV. The results are compared with PYTHIA 8 simulations with the MPI option turned on and off. Finally, the outlooks of J / Ψ in p + Au and Au + p collisions, along with color glass condensate (CGC) predictions and the multiplicity-dependent Ψ(2S) /J / Ψ ratio in p + p data, will be briefly discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Improved joint X-ray and neutron refinement procedure in Phenix

Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.

36 MATERIALS SCIENCE↗