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DOE OSTI2025

Computational design of potent and selective binders of BAK and BAX

Potent and selective binders of the key proapoptotic proteins BAK and BAX have not been described. We use computational protein design to generate high affinity binders of BAK and BAX with greater than 100-fold specificity for their target. Both binders activate their targets when at low concentration, driving pore formation, but inhibit membrane permeabilization when in excess. Crystallography shows that the BAK binder induces BAK unfolding, exposing the α6 helix and BH3 domain. Together, these data suggest that upon binding, BAK or BAX unfold; at high binder concentrations, self-association of the partially folded BAK or BAX proteins is blocked and the membrane remains intact, whereas at low concentrations, dimers form, and the membrane ruptures. Our designed binders modulate apoptosis via direct, specific interactions with BAK and BAX and reveal that for therapeutic strategies targeting BAK and BAX, inhibition requires saturating binder concentrations at the site of action.

Berger, Stephanie↗

DOE OSTI2025

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions

ABSTRACT During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA inStreptococcus pneumoniaeandStreptococcus mutansmaintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones fromS. pneumoniaeandStreptococcus pyogeneswith other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion ofprsAandslrAgenes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin inS. pneumoniae. Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that theS. pneumoniaePrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time,S. pyogenes PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. IMPORTANCE Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that theStreptococcus pyogenesSlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show thatStreptococcus pneumoniaePrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.

Microbiology↗

DOE OSTI2025

Seasonal variations of the atmospheric muon neutrino spectrum measured with IceCube

This study presents an analysis of seasonal variations in the atmospheric muon neutrino flux, using 11.3 years of data from the IceCube Neutrino Observatory. By leveraging a novel spectral unfolding method, we explore the energy range from 125 GeV to 10 TeV for zenith angles from 90° to 110°, corresponding to the Antarctic atmosphere. Our findings reveal that the differential measurement of the amplitudes of the seasonal variation is consistent with an energy-dependent decrease reaching (-4.5 ± 1.2)% during Austral winter and increase to (+ 3.9 ± 1.3)% during Austral summer relative to the annual average at 10 TeV. While the unfolded flux exceeds the model predictions by up to 30%, the differential measurement of the seasonal to annual average flux remains unaffected. The measured seasonal variations of the muon neutrino spectrum are consistent with theoretical predictions using the MCEq code and the NRLMSISE-00 atmospheric model.

Astroparticle Physics and High-Energy Cosmic Pheno↗

DOE OSTI2024

Inhibition of the eukaryotic initiation factor-2α kinase PERK decreases risk of autoimmune diabetes in mice

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress–responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eukaryotic translation initiation factor-2α (eIF2α). In T1D, maladaptive unfolded protein response (UPR) in insulin-producing β cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2α kinase PKR-like ER kinase (PERK), a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved β cell mass in T1D-susceptible mice. Single-cell RNA-Seq of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen-processing and presentation pathways in β cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein programmed death-ligand 1 (PD-L1) in β cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-βH1 human β cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances β cell immunogenicity and that inhibition of PERK may offer a strategy for preventing or delaying the development of T1D.

Research & Experimental Medicine↗

DOE OSTI2024

Returning CP-observables to the frames they belong

Optimal kinematic observables are often defined in specific frames and then approximated at the reconstruction level. We show how multi-dimensional unfolding methods allow us to reconstruct these observables in their proper rest frame and in a probabilistically faithful way. We illustrate our approach with a measurement of a CP-phase in the top Yukawa coupling. Our method makes use of key advantages of generative unfolding, but as a constructed observable it fits into standard LHC analysis frameworks.

Physics↗

DOE OSTI2021

Universal Monte Carlo Event Generator

With the Jefferson Lab 12 GeV physics program underway and plans for the future Electron-Ion Collider (EIC), the nuclear physics community is entering a new era of exploration of QCD phenomena involving extensive data taking and event-level processing. This brings with it the potential for unprecedented access to multidimensional particle momentum distributions (PMDs) that can be connected to various theoretical frameworks by unfolding the emergent quantum mechanical properties of QCD using the PMDs. In practice, the PMDs are rendered as discretized histograms (typically one- or two-dimensional projections), and detector effects must be taken into account to unfold the pure detector effect-free PMDs that can be connected with theory. One of the challenges in this new era is obtaining faithful reconstructions of the multidimensional PMDs that preserve all of the inherent particle correlations. In this LDRD project we developed a novel approach using machine learning (ML) that solves this challenge, by avoiding entirely the need to use histograms as the main numerical technique to obtain the detector effect-free PMDs. The new approach is, moreover, scalable to higher dimensional PMDs. The central idea involves training neural networks (NNs) to generate synthetic event-level data (momenta 4-vectors of final state particles) to preserve all correlations among the particles. This is achieved by converting the trial synthetic vertex-level events to detector-level events using detector simulators. The NNs are then tuned using a specialized distance metric between the synthetic detector events and the real detector events.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Measuring Saturn's Electron Beam Energy Spectrum using Webb's Wedges

It is very difficult to measure the voltage of the load on the Saturn accelerator. Time-resolved measurements such as vacuum voltmeters and V-dot monitors are impractical at best and completely change the pulsed power behavior at the load at worst. We would like to know the load voltage of the machine so that we could correctly model the radiation transport and tune our x-ray unfold methodology and circuit simulations of the accelerator. Step wedges have been used for decades as a tool to measure the end - point energies of high energy particle beams. Typically, the technique is used for multi-megavolt accelerators, but we have adapted it to Saturn's modest <2 MV end-point energy and modified the standard bremsstrahlung x-ray source to extract the electron beam without changing the physics of the load region. We found clear evidence of high energy electrons >2 MV. We also attempted to unfold an electron energy spectrum using a machine learning algorithm and while these results come with large uncertainties, they qualitatively agree with PIC simulation results.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Progress Towards A Measurement of Neutrino Induced Charged Current Neutral Pion Production in the MicroBooNE Experiment

An analysis of MicroBooNE data with a signal of one muon, one neutral pion, and no charged pions is presented. Studying neutral pion production in the MicroBooNE detector provides an opportunity to better understand neutrino-argon interactions, and is crucial for future accelerator-based neutrino oscillation experiments. This analysis presents the progress towards the first measurement of the differential cross section for charged current (CC) $π^0$ production in neutrino-argon interactions. Using a dataset corresponding to about 7 × 10 20 protons on target (POT), we present an analysis which aims to measure the single differential cross sections as a function of the $π^0$ kinematic variables such as momentum and scattering angle. The Wiener-SVD technique for unfolding the measurement is presented and demonstrated using multiple generator predictions. A future iteration of this analysis will compare an unfolded data measurement to these models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Measurement of Triple-Differential Inclusive Muon Neutrino Charged-Current Cross Sections on Argon with the MicroBooNE Detector

We report the first measurement of the differential cross section $d^2σ(E_ν)/dcos(θ_µ)dP_µ$for inclusive muon neutrino charged-current scattering on argon. This measurement utilizes data from6.5×10 20 protons on target of exposure collected using the MicroBooNE liquid argon time projection chamber located on-axis in the Fermilab Booster Neutrino Beam with a mean neutrino energy of approximately 0.8 GeV. In this note, the mapping from reconstructed kinematics to truth quantities, particularly from reconstructed to true neutrino energy, is validated by comparing the distribution of reconstructed hadronic energy in data to that of the model prediction in different muon scattering angle bins after conditional constraint from the muon momentum distribution in data. The success of this validation gives confidence that the missing energy in the MicroBooNE detector is well-modeled within its uncertainties in simulation, enabling the unfolding to an energy-dependent triple-differential measurement over muon momentum, muon scattering angle, and neutrino energy. The unfolded measurement covers an extensive phase space, providing a wealth of information useful for future LArTPC experiments measuring neutrino oscillations. Comparisons with model predictions show the best agreement with Neut 5.4.0.1 at low energy, and with NuWro 19.02.01 at higher energies, particularly at forward muon scattering angles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Passive Confirmation of the Presence Of High-Explosive Material Via Neutron Transmission Spectroscopy

The goal of this project was to explore a novel approach for identifying presence and potential types of high explosives (HE) in treaty-controlled items with passive neutron sources by using passive neutron transmission spectroscopy. We predominantly look to measure relative elemental abundance of Carbon, Hydrogen, Oxygen, and Nitrogen (CHON) since most relevant materials are certain mix of these elements, as shown in Table 1. Previously, most studies exploring potential identification of CHON elemental content of targets in the vicinity of passive neutron source were focused solely on gamma spectroscopy using high resolution gamma detectors. Using neutron transmission spectroscopy with pulse-shape discrimination (PSD) capable organic scintillators is not only a novel idea in of itself, but arguably necessary for accurate identification of the CHON elemental content of an interrogated target. While high resolution gamma spectroscopy in principle can determine a presence of hydrogen and nitrogen, it is effectively blind to a quantitatively measuring areal densities of C, O. The initially proposed approach, described in detail in the project proposal, was to leverage previous Monte Carlo study on neutron transmission spectroscopy using slab shaped target interrogated with well-collimated (“pencil”) neutron beam. In this study, a simulated test CO 2 target was interrogated by a pencil neutron beam and transmitted neutron spectra were measured using PSD capable organic scintillator using MLEM based unfolding technique. To establish relative elemental content of carbon and oxygen, the unfolded neutron spectrum was fit with a parametrized combination of their respective elemental spectral templates. The individual spectral template was calculated by convoluting ENDF neutron crosssection with the known resolution of the PSD detector used in the study. This approach in the studied configuration successfully quantitatively established relative elemental composition of carbon and oxygen.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2026

Using AI to Reproduce Neutrino Cross Section Analysis - Prototyping the Neutrino Discovery Platform

The Neutrino Discovery Platform (NDP) aims to accelerate DUNE-era science by making the neutrino program's existing datasets analyzable through fast, reproducible, and auditable workflows. We report a working version of two of its layers, data curation and agentic orchestration, built and tested end to end on MINERvA open data. The guiding lesson throughout is that a cross section is a measurement, and not just a plotted shape, only if it carries a defensible systematic-uncertainty budget, a trustworthy unfolding, and a reproducible record. Using a single medium-energy playlist pair from the MINERvA open-data release (about $2.05\times10^{17}$ protons on target of data), we first reproduced the shapes of two published charged-current inclusive $\nu_\mu$ measurements through a complete extraction ladder: selection, background subtraction, D'Agostini unfolding, efficiency correction, and flux normalization. These shape-level reproductions ran and tracked the published results, but they lacked the systematic-uncertainty machinery that defines a MINERvA cross section. To supply it, we vendored and built the MINERvA Analysis Toolkit and developed a many-universe systematic-uncertainty tool that produces a portable covariance artifact, a parallel event-loop runner, and a per-run auditability harness. Validated against a published covariance release, the toolchain reproduces the released statistical, flux, and muon-energy-scale terms and shows that they account for roughly 63\% of the total variance, with the remainder unreleased. Using this same infrastructure, we then performed a measurement of our own design, the hadronic recoil-energy distribution of low-energy ($E_\nu<2.5$~GeV) charged-current inclusive events, and found data/simulation shape agreement of $\chi^2/\mathrm{ndf}=1.26$. Together these results show that the platform supports original physics and not only reproductions.

Breaux, Auto [Tulane U. (main)]↗

DOE OSTI2024

EFT Workshop at Notre Dame

The LPC EFT workshop was held April 25-26, 2024 at the University of Notre Dame. The workshop was organized into five thematic sessions: "how far beyond linear" discusses issues of truncation and validity in interpretation of results with an eye towards practicality; "reconstruction-level results" visits the question of how best to design analyses directly targeting inference of EFT parameters; "logistics of combining likelihoods" addresses the challenges of bringing a diverse array of measurements into a cohesive whole; "unfolded results" tackles the question of designing fiducial measurements for later use in EFT interpretations, and the benefits and limitations of unfolding; and "building a sample library" addresses how best to generate simulation samples for use in data analysis. This document serves as a summary of presentations, subsequent discussions, and actionable items identified over the course of the workshop.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Toward the Neutrino Discovery Platform: An Auditable, Uncertainty-Bearing Toolchain for MINERvA Open-Data Cross-Section Analysis

Breaux, Auto [Tulane U. (main)]↗

DOE OSTI2025

Differential cross-section measurements of Higgs boson production in the H → τ + τ - decay channel in pp collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

Differential measurements of Higgs boson production in the τ-lepton-pair decay channel are presented in the gluon fusion, vector-boson fusion (VBF), VH and $t\overline{t}H$ associated production modes, with particular focus on the VBF production mode. The data used to perform the measurements correspond to 140 fb -1 of proton-proton collisions collected by the ATLAS experiment at the LHC. Two methods are used to perform the measurements: the Simplified Template Cross-Section (STXS) approach and an Unfolded Fiducial Differential measurement considering only the VBF phase space. For the STXS measurement, events are categorized by their production mode and kinematic properties such as the Higgs boson’s transverse momentum (${p}_{\textrm{T}}^{\textrm{H}}$ ), the number of jets produced in association with the Higgs boson, or the invariant mass of the two leading jets (mjj). For the VBF production mode, the ratio of the measured cross-section to the Standard Model prediction for m jj > 1.5 TeV and ${p}_{\textrm{T}}^{\textrm{H}}$ > 200 GeV (${p}_{\textrm{T}}^{\textrm{H}}$ < 200 GeV) is ${1.29}_{-0.34}^{+0.39}$ (${0.12}_{-0.33}^{+0.34}$ ). This is the first VBF measurement for the higher-${p}_{\textrm{T}}^{\textrm{H}}$ criteria, and the most precise for the lower-${p}_{\textrm{T}}^{\textrm{H}}$ criteria. The fiducial cross-section measurements, which only consider the kinematic properties of the event, are performed as functions of variables characterizing the VBF topology, such as the signed ΔΦ jj between the two leading jets. The measurements have a precision of 30%–50% and agree well with the Standard Model predictions. These results are interpreted in the SMEFT framework, and place the strongest constraints to date on the CP-odd Wilson coefficient ${c}_{H\overset{\sim }{W}}$ .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

ATHENA: A unique radiation environment platform at the National Ignition Facility

This paper describes the ATHENA platform, an energy tuning assembly, which was developed to spectrally shape the National Ignition Facility (NIF) deuterium–tritium fusion neutron source to a thermonuclear (fusion) plus prompt fission neutron spectrum with a capability to act as a short-pulse neutron source. This unique, otherwise inaccessible radiation environment complements existing experimental facilities and capabilities. Here, the flexible ATHENA irradiation positions were modeled using an ensemble of Monte Carlo simulations with stochastic sampling of the nuclear cross-sections to characterize the radiation environments and uncertainty for the platform. Validation of the internal neutron spectrum produced from fielding ATHENA at NIF occurred through neutron flux unfolding with 20 measured activation products.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2021

A compact neutron spectrometer system

A portable neutron spectrometer, nSpec, has been developed for passive interrogation of fast neutrons ( 1 MeV) from neutron sources. The design of the system includes four EJ-301 liquid scintillation cells, a custom stand, and tungsten caps for gamma-ray shielding. Data acquisition settings were optimized to provide a dynamic range of up to > 15 MeV neutron energy. Additionally, the detector response matrix was characterized using a time-of-flight method based on gamma-ray tagged neutron emission from 252 Cf. The spectrum unfolding was characterized using measured and simulated spectra of AmBe and 252 Cf with the GRAVEL and MLEM methods. Monte Carlo methods were used to examine the uncertainty propagation and determine sufficient counts for a measurement.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Quantification of the light output anistropy in deuterated stilbene

Deuterated stilbene is an organic scintillator that is a desirable material for fast neutron spectroscopy using spectrum unfolding techniques without requiring time-of-flight information. Due to the crystal structure of the material, some anisotropy of the light output exists, which is dependent on the direction of heavy charged particle recoil relative to the crystal structure. The anisotropy of trans-stilbene (hereafter referred to as stilbene) has been well characterized in previous work, but for deuterated stilbene, the anisotropy has only been partially characterized along the a and b crystal axes, while the artificial c' axis, which shows the largest anisotropy in stilbene, has not been characterized until this publication. Here, in this work, two deuterated stilbene crystals were characterized with neutron energies up to 35 MeV at the Los Alamos Neutron Science Center. For one of the crystals, the response is characterized along the a, b, and c' axes. This characterization shows a distinct anisotropy along the axes in deuterated stilbene, which is very similar to that found in regular stilbene, such that the a axis is the brightest, while the b' and c' axes are approximately 3% and 20%–35% lower relative to the a axis.

36 MATERIALS SCIENCE↗

DOE OSTI2023

The Cost and Benefit of Enhancing Cybersecurity for Hybrid AC/DC Grids

As critical interfaces of AC grids and DC grids inside a hybrid AC/DC grid, the voltage-sourced-converter (VSC) has been demonstrated to be vulnerable to false data injection (FDI) cyber-attacks. As a result, the cyber-attack-induced AC grid frequency deviations and DC grid voltage deviations threaten the secure operation. Here, to enhance cybersecurity in a not only feasible but also cost-effective manner, this paper proposes a cost-benefit-based cyber-defense strategy for a hybrid AC/DC grid. First, this paper establishes a spatial-temporal dual cyber-attack evaluation model, in which the cyber-attack-induced frequency and voltage deviations are modelled in both a spatially and temporally dual manner. Then, the proposed cost-benefit-based cyber-defense strategy is modelled as a VSC commitment problem to achieve the trade-off between maximizing the cyber-defense benefits and minimizing the cyber-defense costs. The VSC commitment problem is then mathematically convexified into a mixed-integer second-order cone programming (MISOCP) problem, which could be efficiently solved in an event-triggered manner against unfolding cyber-attack events. Simulation results on a test hybrid AC/DC grid verified the feasibility and the cost-effectiveness of the proposed cyber-defense strategy.

cost-benefit analysis↗