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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Comparing CRT and Pandora Tagged Tracks in ICARUS

The ICARUS Liquid Argon Time Projection Chamber (LArTPC) is used to investigate short-baseline neutrino oscillations and the possible existence of sterile neutrinos. To aid in identifying and rejecting cosmic ray backgrounds, the system is outfitted with external Cosmic Ray Taggers (CRTs). The CRT is able to measure more tracks and at a wider range of angles, useful in further detailing future calibrations. This project compared the most probable values (MPVs) of charge deposition between CRT tagged and TPC tagged tracks. The Y-Z maps of charge scale for both datasets show a strong correlation, not just in their overall structure, but also in how they reflect known detector effects. Both reconstruction paths showed similar structures in their charge distribution, such as less effective wire section or mechanical support, confirming that CRT-tagged tracks, despite being external, respond to the same calibration landscape as Pandora tracks, validating previous Pandora reconstructions and values. Overall, the analysis supports the idea that the CRT tags are a useful addition to ICARUS calibration efforts. Their broad angular range and independence from Pandora reconstruction make them a helpful secondary tool and a potential asset in extending calibration across the detector volume.

Thayer, Abbie [Fermilab; Colorado State U.]↗
DOE OSTI2026

Patch Hierarchical Attention Transformer for Efficient Particle Jet Tagging

Real-time jet tagging is critical for identifying short-lived particle decays in the high-throughput detectors of the Large Hadron Collider, where real-time trigger systems responsible for deciding which collision events to store impose strict latency and accuracy constraints. While transformer architectures achieve the highest jet tagging accuracy when compute is unconstrained, their quadratic self-attention cost makes inference restrictive on trigger budget. Existing efficient variants reduce the computational cost, but hinder the classification performance. To address this limitation, we introduce the Patch Hierarchical Attention Transformer (PHAT-JeT), which combines two mechanisms: a physics-inspired geometric message-passing module that encodes local detector-plane structure, and a hierarchical patch-based attention scheme that computes exact attention within small particle groups while preserving global context through lightweight patch-token communication. Within a restricted budget, PHAT-JeT achieves state-of-the-art accuracy and background rejection among all resource-constrained jet tagging models on four benchmarks (\textsc{hls4ml}, JetClass, Top Tagging, and Quark--Gluon). Our code is available at https://github.com/aaronw5/PHAT-JeT.

Wang, Aaron [Illinois U., Chicago] (ORCID:00000003↗
DOE OSTI2020

TAG… You’re It, Synechocystis sp. PCC 6803!

Triacylglycerol (TAG), a ubiquitous energy storage molecule found mainly in eukaryotes, comprises glycerol esterified with three fatty acids of variable lengths and saturation states. TAG is also considered as a high-value biochemical because it can be converted into fatty acid methyl esters, key components of biodiesel, through transesterification with methanol. Thus, considerable efforts have been made to produce TAGs from CO2 as a renewable energy source.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗
DOE OSTI2026

Search for nonresonant new physics signals in high-mass dilepton events produced in association with b-tagged jets in proton-proton collisions at $\sqrt{s}=13$ TeV

A search for nonresonant new physics phenomena in high-mass dilepton events produced in association with b-tagged jets is performed using proton-proton collision data collected in 2016–2018 by the CMS experiment at the CERN LHC, at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 138 fb −1 . The analysis considers two effective field theory models with dimension-six operators; involving four-fermion contact interactions between two leptons (ℓℓ, electrons or muons) and b or s quarks (bbℓℓ and bsℓℓ). Two lepton flavor combinations (ee and μμ) are required and events are classified as having 0, 1, or ≥2 b-tagged jets in the final state. No significant excess is observed over the standard model backgrounds. Upper limits are set on the production cross section of the new physics signals. These translate into lower limits on the energy scale Λ of 6.9 to 9.0 TeV in the bbℓℓ model, depending on model parameters, and on the ratio of energy scale and effective coupling, Λ/g*, of 2.0 to 2.6 TeV in the bsℓℓ model. Lepton flavor universality is also tested by comparing the dielectron (ee) and dimuon (μμ) mass spectra for different b-tagged jet multiplicities. No significant deviation from the standard model expectation of unity is observed.

Beyond Standard Model↗
DOE OSTI2023

Comparison of inclusive and photon-tagged jet suppression in 5.02 TeV Pb+Pb collisions with ATLAS

Parton energy loss in the quark–gluon plasma (QGP) is studied with a measurement of photon-tagged jet production in 1.7 nb –1 of Pb+Pb data and 260 pb –1 of pp data, both at $\sqrt{^S{\text{NN}}}$ = 5.02 TeV, with the ATLAS detector. The process $pp$ → γ +jet+X and its analogue in Pb+Pb collisions is measured in events containing an isolated photon with transverse momentum ($p_{\text{T}}$) above 50 GeV and reported as a function of jet $p_{\text{T}}$. This selection results in a sample of jets with a steeply falling $p_{\text{T}}$ distribution that are mostly initiated by the showering of quarks. The $pp$ and Pb+Pb measurements are used to report the nuclear modification factor, $R_{\text{AA}}$, and the fractional energy loss, $S_{\text{loss}}$, for photon-tagged jets. In addition, the results are compared with the analogous ones for inclusive jets, which have a significantly smaller quark-initiated fraction. The $R_{\text{AA}}$ and $S_{\text{loss}}$ values are found to be significantly different between those for photon-tagged jets and inclusive jets, demonstrating that energy loss in the QGP is sensitive to the colour-charge of the initiating parton. Finally, the results are also compared with a variety of theoretical models of colour-charge-dependent energy loss.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Demonstration of Capture, Cooling, Tagging, and Spectroscopic Characterization of UV Photoproduct Ions in a Cryogenic Ion Trap: Application to 266 nm Photofragment Ions from Rhodamine 6G

We demonstrate a method to determine the structures of the primary photodissociation products from a cryogenically cooled parent ion. In this approach, a target ion is cooled by a pulse of buffer gas and tagged in a 20 K Paul trap. The cold ion is then photodissociated by pulsed (~5 ns) UV laser excitation, and the ionic products are trapped, cooled, and tagged by introduction of a second buffer gas pulse in the same trap. The tagged fragments are then ejected into a triple focusing, UV/vis/IR time-of-flight photofragmentation mass spectrometer which yields vibrational and electronic spectra of the mass-selected photofragments. Furthermore, these methods are demonstrated by application to the 266 nm photodissociation of the Rhodamine 6G cation to yield the R575 fragment ion based on loss of ethene as well as to a weaker secondary fragment arising from loss of m/z 43.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cryogenic “Iodide-Tagging” Photoelectron Spectroscopy: A Sensitive Probe for Specific Binding Sites of Amino Acids

This work showcases cryogenic and temperature-dependent “iodide-tagging” photoelectron spectroscopy to probe specific binding sites of amino acids using the glycine-iodide complex (Gly?I-) as a case study. Multiple Gly?I- isomers were generated from ambient electrospray ionization and kinetically isolated in a cryogenic ion trap. These structures were characterized with temperature-dependent “iodide-tagging” negative ion photoelectron spectroscopy (NIPES) where iodide was used as the “messenger” to interpret electronic energetics and structural information of various Gly?I- isomers. Accompanied by theoretical computations and Franck-Condon simulations, a total of five cluster structures have been identified along with their various binding motifs. This work demonstrates that “iodide-tagging” NIPES is a powerful general means for probing specific binding interactions in biological molecules of interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Radiative lifetime-encoded unicolour security tags using perovskite nanocrystals

Traditional fluorescence-based tags, used for anticounterfeiting, rely on primitive pattern matching and visual identification; additional covert security features such as fluorescent lifetime or pattern masking are advantageous if fraud is to be deterred. Herein, we present an electrohydrodynamically printed unicolour multi-fluorescent-lifetime security tag system composed of lifetime-tunable lead-halide perovskite nanocrystals that can be deciphered with both existing time-correlated single-photon counting fluorescence-lifetime imaging microscopy and a novel time-of-flight prototype. We find that unicolour or matching emission wavelength materials can be prepared through cation-engineering with the partial substitution of formamidinium for ethylenediammonium to generate “hollow” formamidinium lead bromide perovskite nanocrystals; these materials can be successfully printed into fluorescence-lifetime-encoded-quick-read tags that are protected from conventional readers. Furthermore, we also demonstrate that a portable, cost-effective time-of-flight fluorescence-lifetime imaging prototype can also decipher these codes. A single comprehensive approach combining these innovations may be eventually deployed to protect both producers and consumers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Unlocking the potential of DNA-based tagging: current market solutions and expanding horizons

The commercialization of DNA tagging is a growing trend that demonstrates the increasing practicality of this novel approach. This interdisciplinary technology is based on the distinctive characteristics of DNA as a molecule that can remain stable in varying environmental conditions and store data following appropriate preparation. Moreover, newly developed technologies could simplify DNA synthesis and the encoding of data within DNA. The implementation of DNA tagging presents distinctive benefits in comparison to conventional labelling techniques, including universal product code (UPC) barcoding, radio-frequency identification (RFID), quick response (QR) codes, and Bluetooth technologies, by surmounting the limitations encountered by these systems. The discourse pertains to extant DNA-tagging mechanisms along with prospective implementations in a wide range of domains, including but not limited to art, the metaverse, forensics, wildlife monitoring, and the military. The potential of DNA labelling in various contexts underscores the importance of continued research and development in this rapidly evolving field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Transforming jet flavour tagging at ATLAS

Jet flavour tagging enables the identification of jets originating from heavy-flavour quarks in proton–proton collisions at the Large Hadron Collider, playing a critical role in its physics programmes. This paper presents GN2, a transformer-based flavour tagging algorithm deployed by the ATLAS Collaboration that represents a different methodology compared to previous approaches. Designed to classify jets based on the flavour of their constituent particles, GN2 processes low-level tracking information in an end-to-end architecture and incorporates physics-informed auxiliary training objectives to enhance both interpretability and performance. Its performance is validated in both simulation and collision data. The measured c-jet (light-jet) rejection in data is improved by a factor of 3.5 (1.8) for a 70% b-jet tagging efficiency, compared to the previous algorithm. GN2 provides substantial benefits for physics analyses involving heavy-flavour jets, such as measurements of Higgs boson pair production and the couplings of bottom and charm quarks to the Higgs boson, and demonstrates the impact of advanced machine learning methods in experimental particle physics.

Characterization and analytical techniques↗
DOE OSTI2024

Accuracy versus precision in boosted top tagging with the ATLAS detector

The identification of top quark decays where the top quark has a large momentum transverse to the beam axis, known as top tagging , is a crucial component in many measurements of Standard Model processes and searches for beyond the Standard Model physics at the Large Hadron Collider. Machine learning techniques have improved the performance of top tagging algorithms, but the size of the systematic uncertainties for all proposed algorithms has not been systematically studied. This paper presents the performance of several machine learning based top tagging algorithms on a dataset constructed from simulated proton-proton collision events measured with the ATLAS detector at $\sqrt{s}$ = 13 TeV. The systematic uncertainties associated with these algorithms are estimated through an approximate procedure that is not meant to be used in a physics analysis, but is appropriate for the level of precision required for this study. The most performant algorithms are found to have the largest uncertainties, motivating the development of methods to reduce these uncertainties without compromising performance. To enable such efforts in the wider scientific community, the datasets used in this paper are made publicly available.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering

Abstract Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Measurement of cross sections for production of a $Z$ boson in association with a flavor-inclusive or doubly $b$-tagged large-radius jet in proton-proton collisions at $\sqrt{s}$ = $13$ $\mathrm{TeV}$ with the ATLAS experiment

We present measurements of cross sections for production of a leptonically decaying $Z$ boson in association with a large-radius jet in 13 TeV proton-proton collisions at the LHC, using 36 fb –1 of data from the ATLAS detector. Integrated and differential cross sections are measured at particle level in both a flavor inclusive and a doubly $b$-tagged fiducial phase space. The large-radius jet mass and transverse momentum, its kinematic relationship to the Z boson, and the angular separation of $b$-tagged small-radius track jets within the large-radius jet are measured. This measurement constitutes an important test of perturbative quantum chromodynamics in kinematic and flavor configurations relevant to several Higgs boson and beyond-Standard-Model physics analyses. The results highlight issues with modeling of additional hadronic activity in the flavor-inclusive selection, and a distinction between flavor-number schemes in the $b$-tagged phase space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1

Onchocerca volvulus causes blindness, onchocerciasis, skin infections and devastating neurological diseases such as nodding syndrome. New treatments are needed because the currently used drug, ivermectin, is contraindicated in pregnant women and those co-infected with Loa loa . The Seattle Structural Genomics Center for Infectious Disease (SSGCID) produced, crystallized and determined the apo structure of N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 (His- Ov MIF-1). Ov MIF-1 is a possible drug target. His- Ov MIF-1 has a unique jellyfish-like structure with a prototypical macrophage migration inhibitory factor (MIF) trimer as the `head' and a unique C-terminal `tail'. Deleting the N-terminal tag reveals an Ov MIF-1 structure with a larger cavity than that observed in human MIF that can be targeted for drug repurposing and discovery. Removal of the tag will be necessary to determine the actual biological oligomer of Ov MIF-1 because size-exclusion chomatographic analysis of His- Ov MIF-1 suggests a monomer, while PISA analysis suggests a hexamer stabilized by the unique C-terminal tails.

Kimble, Amber D. (ORCID:0000000167851596)↗
DOE OSTI2022

Understanding the EMC effect with tagged DIS measurements

Understanding the modification of quarks in nucleons within nuclei (EMC effect) is a longstanding open question in nuclear physics. Recent experimental results from electron scattering at Jefferson Lab strengthen the correlation between the EMC effect and short- range correlated pairs (SRC) of nucleons in nuclei. That means that the EMC effect is probably driven by the high-momentum highly-virtual nucleons of the SRC pairs. This connection can be tested experimentally by measuring electron deep inelastic scattering from a nucleon and detecting its correlated SRC partner nucleon (tagging). This allows us to measure the quark modification of high-momentum nucleons. Two tagged experiments on deuterium are underway at Jefferson Lab of which one already took data and the other will take data in the upcoming years. In my talk, I will present the current knowledge of the EMC effect and its correlation to SRC pair and the status of the tagged measurements at Jefferson Lab.

Hauenstein, Florian↗
DOE OSTI2024

Interpreting and Accelerating Transformers for Jet Tagging

Attention-based transformers are ubiquitous in machine learning applications from natural language processing to computer vision. In high energy physics, one central application is to classify collimated particle showers in colliders based on the particle of origin, known as jet tagging. In this work, we study the interpretatbility and prospects for acceleration of Particle Transformer (ParT), a state-of-the-art model, leverages particle-level attention to improve jet-tagging performance. We analyzing ParT's attention maps and particle-pair correlations in the eta-phi plane, revealing intriguing features, such as a binary attention pattern that identifies critical substructure in jets. These insights enhance our understanding of the model's internal workings and learning process and hint at ways to improve its efficiency. Along these lines, we also explore low-rank attention, attention alternatives, and dynamic quantization to accelerate transformers for jet tagging. With quantization, we achieve a 50% reduction in model size and a 10% increase in inference speed without compromising accuracy. These combined efforts enhance both the performance and the interpretability of transformers in high-energy physics, opening avenues for more efficient and physics-driven model designs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2003

Tagging Water Sources in Atmospheric Models

Tagging of water sources in atmospheric models allows for quantitative diagnostics of how water is transported from its source region to its sink region. In this presentation, we review how this methodology is applied to global atmospheric models. We will present several applications of the methodology. In one example, the regional sources of water for the North American Monsoon system are evaluated by tagging the surface evaporation. In another example, the tagged water is used to quantify the global water cycling rate and residence time. We will also discuss the need for more research and the importance of these diagnostics in water cycle studies.

Bosilovich, M.↗
NASA NTRS2010

Multiple Velocity Profile Measurements in Hypersonic Flows using Sequentially-Imaged Fluorescence Tagging

Nitric-oxide planar laser-induced fluorescence (NO PLIF) was used to perform velocity measurements in hypersonic flows by generating multiple tagged lines which fluoresce as they convect downstream. For each laser pulse, a single interline, progressive scan intensified CCD camera was used to obtain separate images of the initial undelayed and delayed NO molecules that had been tagged by the laser. The CCD configuration allowed for sub-microsecond acquisition of both images, resulting in sub-microsecond temporal resolution as well as sub-mm spatial resolution (0.5-mm x 0.7-mm). Determination of axial velocity was made by application of a cross-correlation analysis of the horizontal shift of individual tagged lines. Quantification of systematic errors, the contribution of gating/exposure duration errors, and influence of collision rate on fluorescence to temporal uncertainty were made. Quantification of the spatial uncertainty depended upon the analysis technique and signal-to-noise of the acquired profiles. This investigation focused on two hypersonic flow experiments: (1) a reaction control system (RCS) jet on an Orion Crew Exploration Vehicle (CEV) wind tunnel model and (2) a 10-degree half-angle wedge containing a 2-mm tall, 4-mm wide cylindrical boundary layer trip. The experiments were performed at the NASA Langley Research Center's 31-inch Mach 10 wind tunnel.

Bathel, Brett F.↗