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DOE OSTI2021

BioSecure Digital Twin: Manufacturing Innovation and Cybersecurity Resilience

U.S. national security, prosperity, economy, and well-being require secure, flexible, and resilient Biopharmaceutical Manufacturing. The COVID-19 pandemic reaffirmed that the biomedical production value-chain is vulnerable to disruption and has been under attack from sophisticated nation-state adversaries. Current cyber defenses are inadequate, and the integrity of critical production systems and processes are inherently vulnerable to cyber-attacks, human error, and supply chain disruptions. The following chapter explores how a BioSecure Digital Twin will improve U.S. manufacturing resilience and preparedness to respond to these hazards by significantly improving monitoring, integrity, security, and agility of our manufacturing infrastructure and systems. The BioSecure Digital Twin combines a scalable manufacturing framework with a robust platform for monitoring and control to increase U.S. biopharma manufacturing resilience. Then, the chapter discusses some of the inherent vulnerabilities and challenges at the nexus of health and advanced manufacturing. Next, the chapter highlights that as the Pandemic evolves, we need agility and resilience to overcome significant obstacles. This section highlights an innovative application of Cyber Informed Engineering to developing and deploying a BioSecure Digital Twin to improve the resilience and security of the biopharma industrial supply chain and production processes. Finally, the chapter concludes with a process framework to complement the Digital Twin platform, called the Biopharma (Observe, Orient, Decide, Act) OODA Loop Framework (BOLF), a four-step approach to decision-making outputs from the Digital Twin. The BOLF will help end users leverage twin technology by distilling the available information, focusing the data on context, and rapidly making the best decision while remaining cognizant of changes that can be made as more data becomes available.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2019

Estimation of Behind-the-Meter Solar Generation by Integrating Physical with Statistical Models

Accurate estimation of solar photovoltaic (PV) generation is crucial for distribution grid control and optimization. Unfortunately, most of the residential solar PV installations are behind-the-meter. Thus, utilities only have access to the net load readings. This paper presents an unsupervised framework for estimating solar PV generation by disaggregating the net load readings. The proposed framework synergistically combines a physical PV system performance model with a statistical model for load estimation. Specifically, our algorithm iteratively estimates solar PV generation with a physical model and electric load with the Hidden Markov model regression. The proposed algorithm is also capable of estimating the key technical parameters of the solar PV systems. Our proposed method is validated against net load and solar PV generation data gathered from residential customers located in Austin, Texas. The validation results show that our method reduces mean squared error by 44% compared to the state-of-the-art disaggregation algorithm.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Electromagnetic observables of open-shell nuclei from coupled-cluster theory

Here we develop a new method to describe electromagnetic observables of open-shell nuclei with two nucleons outside a closed shell. This approach combines the equation-of-motion coupled-cluster method for such systems and the Lorentz integral transform technique, expanding the applicability of coupled-cluster theory for electromagnetic observables beyond closed-(sub)shell nuclei. To validate this new approach, we compute the non-energy-weighted dipole sum rule and the dipole polarizability of 16,24 ⁢O in both the closed-(sub)shell and the new equation-of-motion coupled-cluster frameworks, finding agreement within error bars. We then analyze the evolution of the dipole polarizability along the oxygen and calcium isotopic chains. Our predictions agree well with available experimental data and other available theoretical calculations for the closed-(sub)shell 16,22 ⁢O and the open-shell 18 O. In the calcium isotopes, we observe that our dipole polarizability predictions for open-shell nuclei are lower than those of closed-(sub)shell nuclei. We expect that our predictions for 24 O and 54,56 ⁢Ca will motivate future experimental studies at the drip line.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Measurement of C P Violation in B 0 → ψ ( → ℓ + ℓ − ) K S 0 ( → π + π − ) Decays

A measurement of time-dependent C P violation in the decays of B 0 and B ¯ 0 mesons to the final states J / ψ ( → μ + μ − ) K S 0 , ψ ( 2 S ) ( → μ + μ − ) K S 0 and J / ψ ( → e + e − ) K S 0 with K S 0 → π + π − is presented. The data correspond to an integrated luminosity of 6 fb − 1 collected at a center-of-mass energy of s = 13 TeV with the LHCb detector. The C P -violation parameters are measured to be S ψ K S 0 = 0.717 ± 0.013 ( stat ) ± 0.008 ( syst ) and C ψ K S 0 = 0.008 ± 0.012 ( stat ) ± 0.003 ( syst ) . This measurement of S ψ K S 0 represents the most precise single measurement of the CKM angle β to date and is more precise than the current world average. In addition, measurements of the C P -violation parameters of the individual channels are reported and a combination with the LHCb Run 1 measurements is performed. © 2024 CERN, for the LHCb Collaboration 2024 CERN

Aaij, R. (ORCID:0000000305331952)↗

DOE OSTI2025

Field Emission Analysis in SRF Cavities for PIP-II Using GEANT4

Field emission (FE) remains a significant hurdle for achieving optimal performance and reliability in superconducting radiofrequency (SRF) cavities used in accelerator cryomodules. A thorough understanding of the generation and propagation of FE-induced radiation is therefore essential to mitigate this problem. The absence of standardized measurement protocols further complicates the comparison of radiation data across different testing phases and facilities. This highlights the need for a precise quantitative method to diagnose and analyze FE-induced radiation. Such efforts could prove beneficial for improving cavity preparation and cleanroom assembly techniques during the prototype and production stages of Fermilab's Proton Improvement Plan-II (PIP-II) project. This study presents the initial steps of detailed Geant4 simulations aimed at analyzing FE-induced radiation in the low-beta 650 MHz 5-cell elliptical (LB650) cavity. Our goal is to combine these results with radiation diagnostics to enhance diagnostic accuracy and optimize detector positioning. This integrated approach ultimately aims to improve the preparation, assembly, and testing procedures for PIP-II SRF cavities, ensuring the delivery of FE-free cryomodules.

Wijethunga, Sajini A.K. [Fermilab] (ORCID:00000002↗

DOE OSTI2023

Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images

Patient-derived xenografts (PDXs) are an appealing platform for preclinical drug studies. A primary challenge in modeling drug response prediction (DRP) with PDXs and neural networks (NNs) is the limited number of drug response samples. We investigate multimodal neural network (MM-Net) and data augmentation for DRP in PDXs. The MM-Net learns to predict response using drug descriptors, gene expressions (GE), and histology whole-slide images (WSIs). We explore whether combining WSIs with GE improves predictions as compared with models that use GE alone. We propose two data augmentation methods which allow us training multimodal and unimodal NNs without changing architectures with a single larger dataset: 1) combine single-drug and drug-pair treatments by homogenizing drug representations, and 2) augment drug-pairs which doubles the sample size of all drug-pair samples. Unimodal NNs which use GE are compared to assess the contribution of data augmentation. The NN that uses the original and the augmented drug-pair treatments as well as single-drug treatments outperforms NNs that ignore either the augmented drug-pairs or the single-drug treatments. In assessing the multimodal learning based on the MCC metric, MM-Net outperforms all the baselines. Our results show that data augmentation and integration of histology images with GE can improve prediction performance of drug response in PDXs.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Field Emission Analysis in SRF Cavities for PIP-II Using GEANT4

Field emission (FE) remains a significant hurdle for achieving optimal performance and reliability in super-conducting radiofrequency (SRF) cavities used in accelerator cryomodules. A thorough understanding of the generation and propagation of FE-induced radiation is therefore essential to mitigate this problem. The absence of standardized measurement protocols further complicates the comparison of radiation data across different testing phases and facilities. This highlights the need for a precise quantitative method to diagnose and analyze FE-induced radiation. Such efforts could prove beneficial for improving cavity preparation and cleanroom assembly techniques during the prototype and production stages of Fermilab's Proton Improvement Plan-II (PIP-II) project. This study presents the initial steps of detailed Geant4 simulations aimed at analyzing FE-induced radiation in the low-beta 650 MHz 5-cell elliptical (LB650) cavity. Our goal is to combine these results with radiation diagnostics to enhance diagnostic accuracy and optimize detector positioning. This integrated approach ultimately aims to improve the preparation, assembly, and testing procedures for PIP-II SRF cavities, ensuring the delivery of FE-free cryomodules.

Wijethunga, S. A.K. [Fermilab] (ORCID:000000028765↗

DOE OSTI2026

Vector boson scattering and anomalous quartic couplings in final states with ℓνqq or ℓℓqq plus jets using proton-proton collisions at $\sqrt{s}=13$ TeV

A measurement is presented of the electroweak vector boson scattering production of ZV (V = W, Z) boson pairs associated with two jets in proton-proton collisions at a center-of-mass energy of 13 TeV. The data, corresponding to an integrated luminosity of 138 fb −1 , were collected at the CERN LHC with the CMS detector during the 2016–2018 data-taking period. The analysis targets final states with a pair of isolated electrons or muons from Z boson decays and three or four jets, depending on the momentum of the vector boson that decays into quarks. Signal strength is measured for events characterized by a large invariant mass of two forward jets with a wide pseudorapidity gap between them. The electroweak production of ZV in association with two jets is measured with an observed (expected) significance of 1.3 (1.8) standard deviations. A combination of the analyses of ZV channel and the previously published WV channel in the lepton plus jets final state places constraints on effective field theory parameters that describe anomalous electroweak production of WW, WZ, and ZZ boson pairs in association with two jets. Several world best limits are set on anomalous quartic gauge couplings in terms of dimension-8 standard model effective field theory operators.

Hadron-Hadron Scattering↗

DOE OSTI2023

Modeling of a spatially resolved ion temperature diagnostic for inertial confinement fusion

Here, the performance of modern laser-driven inertial confinement fusion (ICF) experiments is degraded by contamination of the deuterium–tritium (DT) fuel with high-Z material during compression. Simulations suggest that this mix can be described by the ion temperature distribution of the implosion, given that such contaminants deviate in temperature from the surrounding DT plasma. However, existing neutron time-of-flight (nTOF) diagnostics only measure the spatially integrated ion temperature. This paper describes the techniques and forward modeling used to develop a novel diagnostic imaging system to measure the spatially resolved ion temperature of an ICF implosion for the first time. The technique combines methods in neutron imaging and nTOF diagnostics to measure the ion temperature along one spatial dimension at yields currently achievable on the OMEGA laser. A detailed forward model of the source and imaging system was developed to guide instrument design. The model leverages neutron imaging reconstruction algorithms, radiation hydrodynamics and Monte Carlo simulations, optical ray tracing, and more. The results of the forward model agree with the data collected on OMEGA using the completed diagnostic. The analysis of the experimental data is still ongoing and will be discussed in a separate publication.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Time-Resolved Line Shapes of Single Quantum Emitters via Machine Learned Photon Correlations

Solid-state single-photon emitters (SPEs) are quantum light sources that combine atomlike optical properties with solid-state integration and fabrication capabilities. SPEs are hindered by spectral diffusion, where the emitter’s surrounding environment induces random energy fluctuations. Timescales of spectral diffusion span nanoseconds to minutes and require probing single emitters to remove ensemble averaging. Photon correlation Fourier spectroscopy (PCFS) can be used to measure time-resolved single emitter line shapes, but is hindered by poor signal-to-noise ratio in the measured correlation functions at early times due to low photon counts. Here, we develop a framework to simulate PCFS correlation functions directly from diffusing spectra that match well with experimental data for single colloidal quantum dots. We use these simulated datasets to train a deep ensemble autoencoder machine learning model that outputs accurate, noiseless, and probabilistic reconstructions of the noisy correlations. Using this model, we obtain reconstructed time-resolved single dot emission line shapes at timescales as low as 10 ns, which are otherwise completely obscured by noise. This enables PCFS to extract optical coherence times on the same timescales as Hong-Ou-Mandel two-photon interference, but with the advantage of providing spectral information in addition to estimates of photon indistinguishability. Further, our machine learning approach is broadly applicable to different photon correlation spectroscopy techniques and SPE systems, offering an enhanced tool for probing single emitter line shapes on previously inaccessible timescales.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

A total of 19 months of daily weather logging on the US east coast: the WFIP3 event log

The Third Wind Forecast Improvement Project (WFIP3) is a multi-institutional field campaign designed to advance the understanding and prediction of the offshore atmospheric boundary layer along the US east coast. Extending from February 2024 through August 2025, WFIP3 combines long-term coastal and offshore measurements with targeted modeling and forecasting efforts. This data paper presents the WFIP3 event log, a curated record of 578 d of meteorological phenomena and field observations that complements the campaign's extensive high-frequency datasets. The event log provides both manually documented daily weather discussions and automatically derived indicators of atmospheric processes – including low-level jets, wind ramps, extreme wind veer, and weak wind conditions – based on observations from scanning lidars deployed at three coastal and offshore sites. The dataset offers structured metadata, standardized time and site identifiers, and consistent terminology to facilitate its integration with WFIP3's observational and modeling data products. The log supports diverse applications, from model evaluation and forecast verification to the selection of case studies on offshore boundary-layer dynamics. The WFIP3 event log is publicly available through the US Department of Energy's Wind Data Hub, providing the research community with a transparent and enduring contextual reference for the interpretation and use of WFIP3 measurements.

17 WIND ENERGY↗

DOE OSTI2024

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high-resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Development of Lightweight Structural Materials with Improved Properties for Fission Batteries

The notion of a “fission battery” conveys a vision focused on realizing very simple “plug-and-play” nuclear systems that can be integrated into a variety of applications requiring affordable, reliable energy in the form of electricity and/or heat and function without operations and maintenance staff. Fission batteries require lightweight structural materials to increase their mobility, and the lightweight materials must demonstrate structural resilience under various conditions. The objective of this work is to develop lattice structured lightweight structural material featuring a good combination of mechanical properties using advanced modeling and simulation together with an advanced additive manufacturing technique such as laser powder bed fusion. The preliminary results show that different lattice structures and types can be successfully meshed using nTopology software, and the lattice structure data can be successfully transformed to Multiphysics Object-Oriented Simulation (MOOSE) Environment input. Finite Element Analysis (FEA) displays that, at macro/engineering scale simulation, the weight saving design has an obvious effect on tensile behavior such as effective elastic modulus and yield stress. The novel approaches of this work are (1) development of lattice structures for improved mechanical properties using advanced simulation and modeling techniques; and (2) model predictions of the mechanical properties (e.g., strength and stress distribution) of macroscopic materials in order to preliminarily select a lattice structure for additive manufacturing.

36 MATERIALS SCIENCE↗

DOE OSTI2024

COMPUTER-AIDED LATTICE DESIGN AND ADVANCED MODELING FOR THE DEVELOPMENT OF LIGHTWEIGHT STRUCTURAL MATERIALS

36 MATERIALS SCIENCE↗

DOE OSTI2021

Search for the doubly charmed baryon $ {\varXi}_{cc}^{+} $ in the $ {\varXi}_c^{+}{\pi}^{-}{\pi}^{+} $ final state

A search for the doubly charmed baryon $ {\varXi}_{cc}^{+} $ is performed in the $ {\varXi}_c^{+}{\pi}^{-}{\pi}^{+} $ invariant-mass spectrum, where the $ {\varXi}_c^{+} $ baryon is reconstructed in the pK - π + final state. The study uses proton-proton collision data collected with the LHCb detector at a centre- of-mass energy of 13 TeV, corresponding to a total integrated luminosity of 5.4 fb -1 . No significant signal is observed in the invariant-mass range of 3.4–3.8 GeV/ c 2 . Upper limits are set on the ratio of branching fractions multiplied by the production cross-section with respect to the $ {\varXi}_{cc}^{++} $ →( $ {\varXi}_c^{+} $ → pK - π + ) π + decay for different $ {\varXi}_{cc}^{+} $ mass and lifetime hypotheses in the rapidity range from 2.0 to 4.5 and the transverse momentum range from 2.5 to 25 GeV/ c . The results from this search are combined with a previously published search for the $ {\varXi}_{cc}^{+} $ → $ {\varLambda}_c^{+} $ K - π + decay mode, yielding a maximum local significance of 4.0 standard deviations around the mass of 3620 MeV/ c 2 , including systematic uncertainties. Taking into account the look-elsewhere effect in the 3.5–3.7 GeV/ c 2 mass window, the combined global significance is 2.9 standard deviations including systematic uncertainties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Search for flavour-changing neutral $tqH$ interactions with $H$ → γγ in $pp$ collisions at $ \sqrt{s} $ = 13 TeV using the ATLAS detector

A search for flavour-changing neutral interactions involving the top quark, the Higgs boson and an up-type quark q (q = c, u) is presented. The proton-proton collision data set used, with an integrated luminosity of 139 fb –1 , was collected at $\sqrt{s}$ = 13 TeV by the ATLAS experiment at the Large Hadron Collider. Both the decay process t → qH in $t\bar{t}$ production and the production process pp → tH, with the Higgs boson decaying into two photons, are investigated. No significant excess is observed and upper limits are set on the t → cH and the t → uH branching ratios of 4.3 × 10 –4 and 3.8 × 10 –4 , respectively, at the 95% confidence level, while the expected limits in the absence of signal are 4.7 × 10 –4 and 3.9 × 10 –4 . Combining this search with ATLAS searches in the H → τ + τ – and H → $b\bar{b}$ final states yields observed (expected) upper limits on the t → cH branching ratio of 5.8 × 10 –4 (3.0 × 10 –4 ) at the 95% confidence level. The corresponding observed (expected) upper limit on the t → uH branching ratio is 4.0 × 10 –4 (2.4 × 10 –4 ).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Uncertainty-Aware and Explainable Human Error Detection in the Operation of Nuclear Power Plants

The timely and accurate identification of incidents, such as human factor error, is important to restore nuclear power plants (NPPs) to a stable state. However, the identification of abnormal operating conditions is difficult because of the existence of multiple scenarios. In addition, to implement mitigation actions rapidly after an incident occurs, operators must accurately identify an incident by monitoring the trends of many variables. The mental burden posed by this can increase human error and cause failure in identifying incidents. Failure to identify incidents directly results in erroneous mitigation measures, which are detrimental to NPPs. In this study, we leverage uncertainty-aware models to identify such errors and thereby increase the chances of mitigating them. We use the data collected from a physical test bed. The goal is to identify both certain and accurate models. For this, the two main aspects of focus in this study are explainable artificial intelligence (XAI) and uncertainty quantification (UQ). While XAI elucidates the decision pathway, UQ evaluates decision reliability. Their integration paints a comprehensive picture, signifying that understanding decisions and their confidence should be interlinked. Thus, in this study we leverage UQ measures (e.g. entropy and mutual information) along with Shapley additive explanations to gain insights into the features contributing to both accuracy and uncertainty in error identification. Furthermore, our results show that uncertainty-aware models combined with XAI tools can explain the artificial intelligence–prescribed decisions, with the potential of better explaining errors for the operators.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗