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DOE OSTI2022

Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation

In neurodegenerative diseases including Alzheimer’s and amyotrophic lateral sclerosis, proteins that bind RNA are found in aggregated forms in autopsied brains. Evidence suggests that RNA aids nucleation of these pathological aggregates; however, the mechanism has not been investigated at the level of atomic structure. Here, we present the 3.4-Å resolution structure of fibrils of full-length recombinant tau protein in the presence of RNA, determined by electron cryomicroscopy (cryo-EM). The structure reveals the familiar in-register cross-β amyloid scaffold but with a small fibril core spanning residues Glu391 to Ala426, a region disordered in the fuzzy coat in all previously studied tau polymorphs. RNA is bound on the fibril surface to the positively charged residues Arg406 and His407 and runs parallel to the fibril axis. The fibrils dissolve when RNase is added, showing that RNA is necessary for fibril integrity. While this structure cannot exist simultaneously with the tau fibril structures extracted from patients’ brains, it could conceivably account for the nucleating effects of RNA cofactors followed by remodeling as fibrils mature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Cusp-artifacts in high order superresolution optical fluctuation imaging

Superresolution optical fluctuation imaging (SOFI) is a simple and affordable super-resolution imaging technique, and attracted a growing community over the past decade. However, the theoretical resolution enhancement of high order SOFI is still not fulfilled. In this study, we identify “cusp artifacts” in high order SOFI images, and show that the high-order cumulants, odd-order moments and balanced-cumulants (bSOFI) are highly vulnerable to cusp artifacts. Our study provides guidelines for developing and screening for fluorescence probes, and improving data acquisition for SOFI. The new insight is important to inspire positive utilization of the cusp artifacts.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Neutron Cross Section Measurement In The Protodune-SP Experiment

Understanding the detector response to neutrons will be critical for performing neutrino oscillation analyses in the next-generation Deep Underground Neutrino Experiment (DUNE). The DUNE physics program is centered around measuring the neutrino flavor composition as a function of their energy both at the near and the far detector. Neutrinos in the DUNE beam will have energies ranging between 100~MeV and 10~GeV, which is significant, because individual neutrino energies will not be known beforehand and will have to be reconstructed. Neutrino interactions in DUNE will produce leptons and hadrons -- including protons, pions, and neutrons. Neutrons can transport energy away from their origin and sometimes go undetected. In addition to the primary neutrons produced by the neutrino, subsequent interactions of the charged hadrons can result in secondary neutrons. Neutrons are a source of missing energy and will bias the neutrino energy measurement. Currently, there is also a 20\% energy scale uncertainty and a 40\% uncertainty on the energy resolution for neutrons in DUNE, which must be addressed. ProtoDUNE Single-Phase (ProtoDUNE-SP) is a 770-ton prototype for the DUNE far detector and was designed to both validate the technology that will be employed in DUNE and to measure cross sections for the charged hadrons (pions, protons, and kaons) at the relevant energies for DUNE. The ProtoDUNE-SP experiment, therefore, is in a unique position to characterize the secondary neutron component for DUNE. This is achieved by searching for candidate neutron interactions in ProtoDUNE-SP events and using these to facilitate a measurement of the neutron inelastic cross section as well as an estimate of the neutron energy and number. The cross section measurement presented here is based on neutrons produced in 1~GeV, $\pi^+$ events captured in 2018 by ProtoDUNE-SP in accordance with the production and cross section models in the GEANT4 simulation toolkit, version 4.1 0.6p1. T he best-fit neutron inelastic cross section, in the kinetic energy range of 114 to 314~MeV, is $1.24_{-0.08}^{+0.10}$~(stat.~$\oplus$~syst.)~barns.

Rivera, David Orlando↗

DOE OSTI2020

Improvements to a class of hybrid methods for radiation transport: Nyström reconstruction and defect correction methods

In this study, two modifications are introduced for improving the accuracy, versatility, and robustness of a class of hybrid methods for radiation transport. In general, such methods are constructed by splitting the radiative flux into collided and uncollided components to which low- and high-resolution angular approximations are applied, respectively. In this work we focus on discrete ordinates discretizations of high and low order. The first modification we introduce changes the way in which the collided component is mapped into the uncollided component at the end of each time step in a simulation. The new mapping is a Nyström-type reconstruction that is applicable to arbitrary discrete ordinates quadratures, is guaranteed to preserve positivity of the solution provided that all ordinate weights are positive, is significantly more accurate than previous methods, and can be readily extended to other discretizations such as moment methods, finite element methods, and diffusion approximations. The second modification leverages integral deferred correction (IDC) to iteratively correct for the splitting error introduced by the inconsistency in angular discretization between the collided and uncollided components, in addition to improving the accuracy of the low-order temporal error that is treated by traditional IDC methods. Numerical tests in one- and two-dimensional geometries are used to demonstrate the increased accuracy and efficiency of the proposed modifications. It is found that the two techniques combined yield methods with solution accuracy and memory requirements comparable to that of monolithic discrete ordinates methods while reducing runtime by as much as a factor of between two and ten, depending on the problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Hyperspectral Detection of the Fluorescence Shift between Chirality-Sorted Empty and Water-Filled Single-Wall Carbon Nanotube Enantiomers

Single-wall carbon nanotubes (SWCNTs) have extraordinary electronic and optical properties that depend strongly on their exact chiral structure and their interaction with their inner and outer environment. The fluorescence (PL) of semiconducting SWCNTs, for instance, will shift depending on the molecules with which the SWCNT’s hollow core is filled. These interaction-induced shifts are challenging to resolve on the ensemble level in samples containing a mixture of different filling contents due to the relatively large inhomogeneous line width of the ensemble SWCNT PL compared to the size of these shifts. To circumvent this inhomogeneous broadening, single-tube spectroscopy and hyperspectral imaging are often applied, which until now required time-consuming statistical studies. Here, we present hyperspectral PL microscopy combined with automated SWCNT segmenting based on either principal component analysis or a convolutional neural network, capable of both spatially and spectrally resolving the PL along the length of many individual SWCNTs at the same time and automatically fitting peak positions and line widths of individual SWCNTs. The methodology is demonstrated by accurately determining the emission shifts and line widths of thousands of left- and right-handed empty and water-filled SWCNTs coated with a chiral surfactant, resulting in four statistical distributions which cannot be resolved in ensemble spectroscopy of unsorted samples. The results demonstrate a robust method to quickly probe ensemble properties with single-enantiomer spectral resolution. Moreover, it promises to be an absolute quantitative method to characterize the relative abundances of SWCNTs with different handedness or filling content in macroscopic samples, simply by counting individual species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

The halo light-cone catalogues of ABACUSSUMMIT

We describe a method for generating halo catalogues on the light-cone using the AbacusSummit suite of N-body simulations. The main application of these catalogues is the construction of realistic mock galaxy catalogues and weak lensing maps on the sky. Our algorithm associates the haloes from a set of coarsely spaced snapshots with their positions at the time of light-cone crossing by matching halo particles to on-the-fly light-cone particles. It then records the halo and particle information into an easily accessible product, which we call the AbacusSummit halo light-cone catalogues. Our recommended use of this product is in the halo mass regime of M halo > 2.1 x 10 11 M ⊙ h -1 for the base resolution simulations, i.e. haloes containing at least 100 particles, where the interpolated halo properties are most reliable. To test the validity of the obtained catalogues, we perform various visual inspections and consistency checks. In particular, we construct galaxy mock catalogues of emission-line galaxies (ELGs) at z ~ 1 by adopting a modified version of the AbacusHOD script, which builds on the standard halo occupation distribution (HOD) method by including various extensions. We find that the multipoles of the autocorrelation function are consistent with the predictions from the full-box snapshot, implicitly validating our algorithm. In addition, we compute and output CMB convergence maps and find that the auto- and cross-power spectrum agrees with the theoretical prediction at the sub-per-cent level.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Thermal images collected during large-scale 3D printing with Ingersoll MasterPrint

This data set contains images produced to test the performance of anomaly and fault detection methods in the context of additive manufacturing. Two print jobs were executed using the Ingersoll MasterPrint with the Model 30 Strangpresse extruder. The material used was Techmer compounded polylactic acid (PLA) with wood flour as a filler (80/20 PLA/WF by weight). The first print job consists of the 3D printing of a hexagonal cylinder with a two-bead wall. This print was sliced at a gantry velocity of 3000 millimeter per minute, and an extruder screw speed of 68.14 rotations per minute. This are considered the normal operating conditions. A second hexagonal cylinder was printed using a reduced extruder screw speed, 15% lower than under normal operating conditions. The images were collected with a Teledyne FLIR Lepton 3.5 infra-red camera, a small form factor radiometric long-wave infrared camera with a spectral range of 8 µm to 14 µm. Sensor resolution was 160x120 pixels, with a pixel size of 12 µm, a temperature range of -10 - 450°C, and an accuracy of +/- 10°C in its low gain configuration. Images in this data set were collected with cameras oriented at the printer nozzle. The nozzle camera setup consisted of two cameras located 12.5cm from the nozzle center. These were mounted directly to the print head, so that the camera positions relative to the print direction would remain constant as it rotated around its C-axis to follow the print path. One camera was placed ahead of the nozzle to capture the previous layer immediately before being covered by the new layer of material, while the second camera was placed behind the nozzle and captured the freshly extruded bead. Images are collecting during each phase of the print: (a) idle (i.e., no material deposited), (b) extrusion (i.e., to prime the extruder), and (c) printing (deposition of material to manufacture the hexagonal cylinder).

36 MATERIALS SCIENCE↗

DOE OSTI2022

Object-Based Evaluation of Tropical Precipitation Systems in DYAMOND Simulations over the Maritime Continent

The present study uses an object-based evaluation metric to examine the precipitation bias over the Maritime Continent in the global cloud-resolving models. We specifically focus on the difference between the models that directly resolve convection and those using convection parameterization. The 40-day hindcast experiments of the DYnamics of the Atmospheric general circulation Modeled On Non-hydrostatic Domain (DYAMOND) intercomparison project are evaluated against the high-resolution satellite rainfall products. The hindcast of the Central Weather Bureau Global Forecast System (CWBGFS) under the DYAMOND protocol is also included. The results indicate that most models simulate insufficient numbers of large precipitation system [object-based precipitation system (OPS), > 370 km in scale], indicating weaker convection organization. The observation indicates that the maximum precipitation within the OPS intensifies with increasing object size. All of the models capture this positive relationship, but most of them overestimate the sensitivity. Most of the models overestimate both the frequency and intensity of small OPS (< 160 km), except for the models with convection parameterization [i.e., CWBGFS, European Centre for Medium-Range Weather Forecasts Integrated Forecasting System (IFS)-9 km]. Although most of the models can reproduce the observed peak time of diurnal precipitation over the land area in the Maritime Continent, the simulated fractional contribution of different sizes of OPS to the total precipitation varies from model to model, and their peak times do not follow the observed ones with delayed peak times as the size of OPS increases from small, mid-size, to large categories. Most of the models reasonably capture the mean diurnal cycle peak time, but only the models with convection parameterization and Model for Prediction Across Scales (MPAS) can represent the diurnal evolution of fractional contribution from different OPSs. The implications of the current results to the upscale processes of the tropical convection systems in the global models are also discussed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Toward SBND's First Cross Section Measurements

The Short-Baseline Near Detector (SBND) is one of the Liquid Argon Time Projection Chamber (LArTPC) neutrino detectors positioned along the axis of the Booster Neutrino Beam (BNB) at Fermilab, and is the near detector in the Short-Baseline Neutrino (SBN) Program. The detector completed commissioning and began taking neutrino data in the summer of 2024. SBND is characterized by superb imaging capabilities and recorded over two million neutrino interactions during its first physics run, which concluded in July 2025. Thanks to its unique combination of measurement resolution and statistics, SBND is carrying out a rich program of neutrino interaction measurements and novel searches for physics beyond the Standard Model (BSM). As the near detector, it will enable the full potential of the SBN sterile neutrino program by performing a precise characterization of the unoscillated event rate and constraining BNB flux and neutrino-argon cross-section systematic uncertainties. In addition, SBND will provide valuable model constraints for DUNE by leveraging the significant overlap in phase space between neutrino interactions in the two experiments. In this talk, I will present the current efforts within the SBND cross section program, discuss their status, and outline the plans for the first physics publications.

Oh, Sungbin [Fermilab]↗

DOE OSTI2026

Developing New Beam Constraints to Improve Sterile Neutrino Searches at NOvA

NOvA is a long-baseline neutrino oscillation experiment utilizing two functionally identical liquid scintillator detectors located 14 mrad off-axis from the NuMI beam at Fermilab. The position of the Near Detector (ND), 1 km from the neutrino production target, means it sees a range of off-axis angles (12.6-17.2 mrad), resulting in a noticeable energy gradient across the detector face. In addition, the neutrino production points vary widely along the decay pipe, which leads to a distribution of true neutrino baselines (L), and limits the sensitivity of our current sterile neutrino searches. This work presents a new "baseline reconstruction" technique designed to exploit our off-axis position to triangulate the precise origin of neutrinos within the NuMI beamline. By projecting the total momentum vector of Charged Current (CC) and Neutral Current (NC) interactions back to the central beam axis, we estimate the individual baseline for each event. We describe the technique, evaluate its performance, and demonstrate how this can improve the sensitivity of future searches for sterile neutrinos through reduced flux systematic uncertainties and improved L/E resolution.

Burns, Jessica [Cincinnati U.]↗

DOE OSTI2022

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

The development of multiple chromosome-scale reference genome sequences in many taxonomic groups has yielded a high-resolution view of the patterns and processes of molecular evolution. Nonetheless, leveraging information across multiple genomes remains a significant challenge in nearly all eukaryotic systems. These challenges range from studying the evolution of chromosome structure, to finding candidate genes for quantitative trait loci, to testing hypotheses about speciation and adaptation. Here, we present GENESPACE, which addresses these challenges by integrating conserved gene order and orthology to define the expected physical position of all genes across multiple genomes. We demonstrate this utility by dissecting presence–absence, copy-number, and structural variation at three levels of biological organization: spanning 300 million years of vertebrate sex chromosome evolution, across the diversity of the Poaceae (grass) plant family, and among 26 maize cultivars. The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant addition to existing gene family and synteny programs, especially in polyploid, outbred, and other complex genomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Aerosol Vertical Turbulent Mass Flux Retrievals Through Novel Remote Sensing Algorithm

Abstract Integrated measurements of aerosol, radiation, cloud, and turbulent transport in the planetary boundary layer (PBL) are essential for understanding and modeling climate and air quality. Here, we developed a new technique for the identification of convective turbulent regions and deriving the vertical distribution of aerosol turbulent mass fluxes within PBL. The algorithm uses retrievals from coherent Doppler lidars and a high spectral resolution lidar. The technique was applied to study particle mass fluxes over 2 months (November–December 2020) during the campaign conducted at the DOE Atmospheric Radiation Measurement Southern Great Plains (SGP) site in Lamont, Oklahoma. The algorithm developed here is capable of continuously deriving vertically resolved (curtains) aerosol mass fluxes. Our data analysis shows that at the site, the 30‐min averaged fluxes at 135 m above the surface were mainly positive (upward) at ∼1 μg m −2 s −1 , suggesting that the surface is the primary source of the particle mass supplied to the boundary layer at the SGP site. Analyses of the individual case studies have revealed that not all the derived fluxes can be linked to surface emissions. Both positive and negative values in a range of ±5 μg m −2 s −1 can be caused by convective thermals interacting between the residual layer and the mixed layer and by rotation of the horizontal wind with the height. Large erroneous negative fluxes can also be caused by drizzling/precipitating clouds. We anticipate that the application of the current technique will lead to a more realistic representation of aerosol mass budgets and bidirectional mixing rates.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Abstract In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226–234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Code for paper "Reconstructing an Implosion with Space-Time Smoothing of Velocimetry Traces"

New diagnostics to obtain high-temporal resolution observation of surface velocity provide a rich collection of data from high-explosive (HE) experiments. Using this data to estimate the temporal evolution of an imploding, HE-driven surface is of great interest for validating simulation of the physical system and for design of future experiments. This is the code for a paper in which we propose a method for using a Gaussian process to estimate the surface position over time and provide uncertainty estimates on that reconstruction accounting for measurement error, uncertainty to sparse spatial sampling velocity data, and robustness to outlying observations. In the paper, the code is applied on data from a hemispherical HE implosion experiment. This code is for release with the paper for peer-review, replicating the results and making the figures from the paper.

Grosskopf, Michael↗

DOE OSTI2021

Spatial Resolution of a microCT Scanner

We have measured the spatial resolution of the 450 kV test-bed microCT scanner. We have also modeled the resolution analytically. The model and measurement show correspondence within 5%. Our measurement method was to use a thin tungsten wire to act as an impulse function. Therefore, the image is the impulse response, also called the point spread function (PSF) of the system. The Fourier transform (FT) of the impulse response is the modulation transfer function (MTF) of the system. We report the MTF here. By moving the wire at different positions in the scan field of view (FOV), we can measure MTF at different positions in the FOV. Since our imaging system is radially symmetric, we report MTF in two directions, radial and tangential as shown in Figure 1. The radial direction is along the line from isocenter to the wire, and the tangential is perpendicular to it.

42 ENGINEERING↗

DOE OSTI2026

Status of the Short-Baseline Near Detector at Fermilab

The Short-Baseline Near Detector (SBND) is one of the Liquid Argon Time Projection Chamber (LArTPC) neutrino detectors positioned along the axis of the Booster Neutrino Beam (BNB) at Fermilab, and is the near detector in the Short-Baseline Neutrino (SBN) Program. The detector has completed Run 1, successfully recording approximately 3 million neutrino interactions, and started Run 2 in the autumn of 2025. SBND is characterized by superb imaging capabilities and will record around 3 million neutrino interactions per year. Thanks to its unique combination of measurement resolution and statistics, SBND will soon carry out a rich program of neutrino interaction measurements and novel searches for physics beyond the Standard Model (BSM). As the near detector, it will enable the full potential of the SBN sterile neutrino program by performing a precise characterization of the unoscillated event rate and constraining the BNB flux and neutrino-argon cross-section systematic uncertainties. In this talk, the physics reach, current status, and future prospects of SBND are discussed.

Del Tutto, Marco [Fermilab]↗

DOE OSTI2026

Status of the Short-Baseline Near Detector at Fermilab

The Short-Baseline Near Detector (SBND) is one of the Liquid Argon Time Projection Chamber (LArTPC) neutrino detectors positioned along the axis of the Booster Neutrino Beam (BNB) at Fermilab, and is the near detector in the Short-Baseline Neutrino (SBN) Program. The detector has completed Run 1, successfully recording approximately 3 million neutrino interactions, and started Run 2 in the autumn of 2025. SBND is characterized by superb imaging capabilities and will record around 3 million neutrino interactions per year. Thanks to its unique combination of measurement resolution and statistics, SBND will soon carry out a rich program of neutrino interaction measurements and novel searches for physics beyond the Standard Model (BSM). As the near detector, it will enable the full potential of the SBN sterile neutrino program by performing a precise characterization of the unoscillated event rate and constraining the BNB flux and neutrino-argon cross-section systematic uncertainties. In this talk, the physics reach, current status, and future prospects of SBND are discussed.

Del Tutto, Marco [Fermilab]↗

DOE OSTI2023

Studies of time resolution, light yield, and crosstalk using SiPM-on-tile calorimetry for the future Electron-Ion Collider

We recently proposed a high-granularity calorimeter insert for the Electron-Ion Collider (EIC) that is based on plastic scintillator tiles readout with silicon photomultipliers. In this work, we concretize its design by characterizing its building blocks with measurements of light yield, optical crosstalk, and timing resolutions using cosmic-rays, an LED, and a beta source. We also compared two approaches for the optical isolation of cells: "megatiles" with grooved boundaries between cells, and a 3D-printed plastic frame hosting individual cells. Further, we found that the latter suppresses optical crosstalk to negligible levels while providing an easier assembly method. Overall, these performance studies can help inform calorimeter design and realistic simulations of 5D showers (time, energy, position) for the EIC and other experiments.

47 OTHER INSTRUMENTATION↗