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DOE OSTI2022

SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa

Abstract The intrinsic tenase (Xase) complex, formed by factors (f) VIIIa and fIXa, forms on activated platelet surfaces and catalyzes the activation of factor X to Xa, stimulating thrombin production in the blood coagulation cascade. The structural organization of the membrane-bound Xase complex remains largely unknown, hindering our understanding of the structural underpinnings that guide Xase complex assembly. Here, we aimed to characterize the Xase complex bound to a lipid nanodisc with biolayer interferometry (BLI), Michaelis–Menten kinetics, and small-angle X-ray scattering (SAXS). Using immobilized lipid nanodiscs, we measured binding rates and nanomolar affinities for fVIIIa, fIXa, and the Xase complex. Enzyme kinetic measurements demonstrated the assembly of an active enzyme complex in the presence of lipid nanodiscs. An ab initio molecular envelope of the nanodisc-bound Xase complex allowed us to computationally model fVIIIa and fIXa docked onto a flexible lipid membrane and identify protein–protein interactions. Our results highlight multiple points of contact between fVIIIa and fIXa, including a novel interaction with fIXa at the fVIIIa A1–A3 domain interface. Lastly, we identified hemophilia A/B-related mutations with varying severities at the fVIIIa/fIXa interface that may regulate Xase complex assembly. Together, our results support the use of SAXS as an emergent tool to investigate the membrane-bound Xase complex and illustrate how mutations at the fVIIIa/fIXa dimer interface may disrupt or stabilize the activated enzyme complex.

Hematology↗

DOE OSTI2026

Multitask graph neural networks for elastoplastic response prediction in dual-phase polycrystals

Microstructure-sensitive prediction of elastoplastic response remains a recurring bottleneck in multiscale damage and fatigue modeling, where large ensembles of statistically distinct polycrystals are required to quantify variability and extreme-value behavior. In this work, we develop a multitask graph neural network (GNN) surrogate that maps dual-phase ferrite–martensite polycrystal microstructures to Statistical Volume Element (SVE)-level elastoplastic Quantities of Interest (QoIs). Each SVE is represented as a grain-adjacency graph, with node features encoding phase, geometry, and crystallographic orientation, and edge features encoding relative misorientation. A message-passing graph convolution generates node embeddings, which are pooled into a graph representation and passed to a multitask regression head that jointly predicts 10 scalar QoIs and vector-valued stress–strain responses in orthogonal loading directions across multiple martensite volume fractions and SVE sizes. Results show high accuracy for scalar QoIs and strong agreement for full stress–strain trajectories, with population envelopes reproducing both median behavior and finite-SVE variability across compositions and partition scales. A unified model trained on pooled volume-fraction data preserves most within-regime accuracy relative to regime-specific models while also capturing the broader cross-regime variation reflected in the pooled test set. Distributional comparisons further demonstrate that the surrogate preserves heterogeneity under SVE partitioning, enabling statistically consistent block-wise random-field construction for mesoscale analyses. Overall, the proposed grain-graph surrogate provides a practical pathway to accelerate ensemble-based studies of SVE-level constitutive variability in dual-phase polycrystals.

Crystal plasticity↗

DOE OSTI2020

Large-scale inflatable structures for tunnel protection: a review of the Resilient Tunnel Plug project

The protection of underground civil infrastructure continues to be a high priority for transportation and transit security agencies. In particular, rail transit tunnels running under bodies of water are susceptible to disruptions due to flooding caused by extraordinary climatic events such as hurricanes or other events resulting from human activities. Several events have taken place in the past decades that have demonstrated the need to mitigate vulnerabilities or, at least, minimize the consequences of catastrophic events. Although it is impossible to prevent all situations that can lead to flooding, damage can be substantially decreased by reducing the area affected by the event. To minimize the effects of an event, a possible approach is to compartmentalize the tunnel system by creating temporary barriers that can contain the propagation of flooding until a more permanent solution can be implemented. One way to create a temporary barrier is by the deployment of a large-scale inflatable structure, also known as an inflatable plug. In such an application, the inflatable structure is prepared for placement, either permanently or temporally, and maintained ready for deployment, inflation, and pressurization when needed. The internal plug pressure imparts a normal force against the tunnel wall surface with the friction between the plug and tunnel surfaces opposing axial movement of the plug. The sealing effectiveness depends on the ability of the inflatable structure to self-deploy and fit, without human intervention, to the intricacies of the perimeter of the conduit being sealed. Primary design constraints include having the plug stowed away from the dynamic envelope of the trains and being able to withhold the pressure of the flooding water. This work presents a compilation of the main aspects of the activities completed for the development of large-scale inflatable structures as part of the Resilient Tunnel Plug (RTP) Project. The main test results and lessons learned are presented to demonstrate the viability of implementing large-scale inflatable plugs for the containment of flooding in rail tunnels systems. Over 400 coupon and specimen tests, 200 reduced scale tests, and 100 full-scale tests were conducted to demonstrate the efficacy of the design of different prototypes over a 10-year research and development project. The culmination of the work was 12 large-scale flooding demonstrations where the inflatable tunnel plug was shown able to be deployed remotely and withstand a simulated flooding event.

42 ENGINEERING↗

DOE OSTI2025

Dataset for manuscript "Equipartition and the temperature of maximum density of TIP4P/2005 water"

We simulate TIP4P/2005 water in the temperature range of 257 K to 318 K with time-steps 0.25, 0.50, 1.00, 2.00, and 4.00 fs. The density-temperature behavior obtained using 0.25 or 0.50 fs are in excellent agreement with each other but differ from those obtained using time-steps that have been shown earlier to lead to a breakdown of equipartition. The temperature of maximum density (TMD) is 277.15 K with time-step 0.25 or 0.50 fs, but is shifted to progressively lower values for longer time-steps, a trend that holds for different thermostat/barostat combinations. Enhancing the water-water dispersion interaction, as has been recommended for simulating disordered proteins in TIP4P/2005, degrades the description of the liquid-vapor phase envelope. We present a simple physically transparent reasoning to highlight the separation of the time-scales between translational and rotational motion. We also develop a metric, Chi, that we term the equipartition anomaly, to detect equipartition violations in simulations that include molecules that are treated as rigid objects. Calculating Chi is shown to be straightforward and sensitive to equipartition violations. A key takeaway from this study is that using sufficiently short time-steps (less than or equal to 0.5 fs) to preserve equipartition is essential for obtaining meaningful liquid water properties and for producing reliable simulation data, as correct-ensemble sampling is fundamental to ensure reproducibility across codes and simulation alogrithms. The included dataset provides the raw data used in the preparation of the graphs noted in the manuscript.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Quantification of neural networks uncertainties with applications to SAFARI-1 axial neutron flux profiles

Deep Neural Networks (DNNs) have been widely used as a data-driven modelling tool in nuclear engineering. However, as a Machine Learning model, Artificial Neural Network (ANN) predictions are subjected to uncertainties originating from the noise in training data, incomplete coverage of the domain, and imperfect neural network architectures. In this work, we target at quantifying the prediction/approximation uncertainties of ANNs using Monte Carlo Dropout (MCD), as well as Bayesian Neural Networks (BNNs) which are solved by variational inference. With a demonstration problem in which neural networks are used to predict the assembly axial neutron flux profiles, the results have shown that the three different neural network models (regular DNNs, DNNs solved with MCD and BNNs) can produce results that agree very well among each other and with the measurement data, on cycles that are not used in the training process. Besides the excellent generalization capability, the uncertainty bands produced by MCD and BNN agree very well, and in general, they can fully envelop the noisy measurement data points. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

Constellation's best estimate alternate source term methodology overview

Safety analyses for a nuclear power plants need to consider postulated accidents that results in at risk of accidental release of radiation. The regulations require plant specific safety analysis reports to include an evaluation of the requirements of 10CFR50.67. Such a safety analysis report mandates limits such that calculated radiological consequences relative to certain dose locations do not exceed a total effective dose equivalent (TEDE) limits following a postulated release of radioactivity. Calculations are performed to estimate the radiological consequences, in terms of dose, to people and equipment to ensure the estimated doses are within the prescribed limits. Analysis should demonstrate, with reasonable assurance, that these prescribed limits are complied with. Conventional methodologies utilize conservative approaches to address lack of uncertainty quantification in the utilized approaches, methods, and/or inputs. These built-in excess conservatisms often result in compounding effects and hence overly conservative results in the estimated radiological consequences, which leads to inaccurate margin evaluation for operation and accident mitigation. Therefore, evaluating accurate dose consequences is needed for both operational and safety reasons. The research documented in this paper provides an overview of Constellation's Best Estimate Alternate Source Term (BEAST) Methodology. BEAST methodology relies upon the use of realistic yet bounding input distributions for key analysis parameters, which replaces use of conservative deterministic singular inputs that bound overall analysis domain. This approach enables evaluating a more accurate accident analysis response, while enabling a bounding licensing basis envelope via more accurate quantification of uncertainty in the application. Therefore, built-in margin for a given scenario is more accurately evaluated.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

An Instrumented Capsule Design to Measure Thermal Conductivity in Miniature UO2 Specimens

Numerous separate effects irradiations of miniature nuclear fuel specimens have been conducted in the High Flux Isotope Reactor (HFIR) under the experimental platform designated as MiniFuel. MiniFuel is a static irradiation capability in which microstructural evolution and fuel performance phenomena are observed during postirradiation examination thereby offering a snapshot of the terminal fuel characteristics. This approach inherently requires fielding an irradiation where the experimental conditions are determined using predictive models and the pertinent outcomes are measured at the end of the test. Static irradiations can provide useful insights to the relationships between fuel performance and the pivotal irradiation conditions, namely temperature and burnup, but the ability to monitor fuel performance in situ would further support fuel development and qualification. To this end, an instrumented experiment design is being developed at Oak Ridge National Laboratory to capture thermal conductivity degradation and fission gas release during HFIR irradiation. These phenomena will be monitored using unique capsule designs that each target a different phenomenon. This paper details the thermal conductivity capsule (TCC) design and its expected performance envelope as determined using computer models. Each TCC will contain a miniature UO2 disc specimen (~0.5 mm thick × 5 mm diameter) sandwiched between metallic slugs with embedded thermocouples. The coupling of in situ temperature measurements, known thermal conductivity of the metallic components, and heat generation rates computed using high-fidelity neutronics models make the thermal conductivity measurement possible. This paper describes the reactor physics and heat transfer models used to predict the capsule’s performance and the methodology for calculating the fuel specimen’s thermal conductivity from the thermocouple measurements.

Gorton, Jacob [ORNL] (ORCID:0000000269806083)↗

DOE OSTI2025

Micromechanical Properties of the SiC and Pyrolytic Carbon Layers in Tristructural-Isotropic Coated Particles

Tristructural isotropic (TRISO) coated particle fuel was initially developed for high temperature gas cooled reactors (HTGR) and has been proposed for several other advanced reactor concepts. The design of TRISO particles focuses on preventing the release of fission products in normal and off-normal reactor conditions. The particle design features an actinide bearing fuel kernel that is surrounded by three pyrolytic carbon (PyC) layers and a silicon carbide layer (SiC). The mechanical stability of the particle and fission product retention for both metallic and gaseous fission products depend on the SiC layer. Post irradiation examination (PIE) of TRISO fuel from the first two US DOE Advanced Gas Reactor Fuel Development and Qualification Program irradiation campaigns, AGR-1 and AGR-2, had identified a low rate of particles exhibiting cracking in the SiC layer that did not propagate across the SiC layer. While cracking in the SiC is rare for test conditions and particles associated with the AGR program, understanding the stress state and mechanical properties of the SiC and PyC layers related to particle architecture can aid predicting thermomechanical response of TRISO fuel under the prescribed operation envelope and beyond as well as aiding in the development of similar fuel concepts for other advanced reactors. The presented investigation shows the relationship of the mechanical properties and mechanical response (e.g., understanding crack propagation) of the SiC and PyC layers relative to position within the particle. Testing was conducted on the inner and outer PyC layers of TRISO particles to quantify differences in mechanical behavior.

Montoya, Katherine [ORNL] (ORCID:0000000326955086)↗

DOE OSTI2022

Intense infrared lasers for strong-field science

The advent of chirped-pulse amplification in the 1980s and femtosecond Ti:sapphire lasers in the 1990s enabled transformative advances in intense laser–matter interaction physics. Whereas most of experiments have been conducted in the limited near-infrared range of 0.8–1 μm, theories predict that many physical phenomena such as high harmonic generation in gases favor long laser wavelengths in terms of extending the high-energy cutoff. Significant progress has been made in developing few-cycle, carrier-envelope phase-stabilized, high-peak-power lasers in the 1.6–2 μm range that has laid the foundation for attosecond X ray sources in the water window. Even longer wavelength lasers are becoming available that are suitable to study light filamentation, high harmonic generation, and laser–plasma interaction in the relativistic regime. Long-wavelength lasers are suitable for sub-bandgap strong-field excitation of a wide range of solid materials, including semiconductors. In the strong-field limit, bulk crystals also produce high-order harmonics. In this review, we first introduce several important wavelength scaling laws in strong-field physics, then describe recent breakthroughs in short- (1.4–3 μm), mid- (3–8 μm), and long-wave (8–15 μm) infrared laser technology, and finally provide examples of strong-field applications of these novel lasers. Furthermore, some of the broadband ultrafast infrared lasers will have profound effects on medicine, environmental protection, and national defense, because their wavelengths cover the water absorption band, the molecular fingerprint region, as well as the atmospheric infrared transparent window.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

High-repetition rate, CEP-stable shortwave infrared source with two-cycle pulses for field-resolved spectroscopy

We report on a passively carrier-envelope phase (CEP)-stable optical parametric amplifier generating two-cycle pulses at 2060 nm with energies of up to 2.25 µJ operating at a repetition rate of 400 kHz, specifically designed for applications in field-resolved spectroscopy. The measured pulse duration is 13.6 fs, resulting in two cycles of the carrier wave. Due to the robust CEP-stable front-end design, we achieve an open-loop CEP stability of 250 mrad (rms) and the capability for fast CEP modulation.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Scattering of an utlrashort laser pulse by a spherical air bubble

The scattering of an ultrashort laser pulse by an air bubble in water is investigated by means of the Lorenz-Mie theory and the Debye expansion. A 70 fs, 800 nm pulse is considered as a plane wave with a Gaussian temporal envelope. The transient response is treated with the theory derived from Gouesbet and Gréhan [ Part. Part. Syst. Charact. 17 , 213 –224 ( 2000 ) ], taking now into account chromatic dispersion and absorption of water. It is observed that contrary to the case of water droplet in air, the Debye modes p ≥ 1 start their transient scattering at the same time and the same angle (≈90 ° ) and for a large size parameter, they differentiate as time elapses. A parametric study on the size parameter and the spatial extension of the pulse is performed to identify regimes where the different Debye mode are distinguishable in time. Dependence on the scattering angle is also treated. Finally, by considering pulse chirp, it is shown that the laser/bubble distance has an influence on the separability of modes p = 0 and p = 1.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Propagation effects in polarization-gated attosecond soft-X-ray pulse generation

Accurate estimation of the duration of soft-x-ray pulses from high-harmonic generation (HHG) remains challenging given their higher photon energies and broad spectral bandwidth. The carrier-envelope-phase (CEP) dependence of generated soft-x-ray spectra is indicative of attosecond pulse generation, but advanced simulations are needed to infer the pulse duration from such data. Here, we employ macroscopic propagation simulations to reproduce experimental polarization-gated CEP-dependent soft-x-ray spectra. The simulations indicate chirped pulses, which we theoretically find to be compressible in hydrogen plasmas, suggesting this as a viable compression scheme for broadband soft-x-rays from HHG.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Multi-millijoule hollow-core fiber compression of short-wave infrared pulses to a single cycle

Approaches for efficient pulse compression can enable dramatic increases in the available peak power, as well as enable the generation of isolated attosecond X-ray pulses. Achieving high compression ratios for longer wavelength drivers has, however, been challenging. We present the compression of few-cycle 2.1 µm central wavelength short-wave infrared laser pulses to 6.9 fs with 2.35 mJ pulse energy at a 10 kHz repetition rate. Electric field resolved measurements reveal a single cycle light field oscillation. With a carrier-envelope-phase stability of 131 mrad and average power fluctuations below 1 %, the system constitutes an excellent light source for strong-field experiments and attosecond physics.

Blöchl, Johannes [Ludwig Maximilian Univ. of Munic↗

DOE OSTI2021

Optimal generation and isolation of attosecond pulses in an overdriven ionized medium

We identify optimal conditions for the generation and isolation of attosecond pulses in an overdriven ionized medium. In a high-pressure and highly ionized gas, the spatiotemporal wavefront rotation of a driving laser can be optimized, leading to complete spatial separation of successive attosecond bursts in the far field. The resulting isolated attosecond pulses (IAPs) are much more divergent such that they are spatially separated from the driving laser in the far field. We show that the time delay of near-field harmonic emission along the radial distance determines the divergence of the attosecond burst in the far field. Here, the generated IAPs are phase matched upon propagation in the second half of the gas medium. Validity of the generation scheme is tested at different carrier–envelope phases for a few-cycle laser pulse and by synthesizing the fundamental and its second harmonic field for a long-duration pulse.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Trends in relativistic laser–matter interaction: the promises of structured light

Time and space envelope, frequency and wavelength distributions, polarization, and phase are quantities that define the properties of laser light. Controlling them opens up strategies for manipulating the properties of atoms in various media. At relativistic intensity, matter is rapidly transformed into a plasma state, which is modifying the laser’s propagation, its absorption enabling the generation of intense magnetic and electric fields. In this context, structured light presents exciting, promising, and challenging opportunities for research. This review article aims to explain the concepts of structured light, their applications to real experiments at relativistic intensities, practical considerations, and some scientific perspectives.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Diverse signatures of convergent evolution in cactus-associated yeasts

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently approximately 17 times. Using a machine learning–based approach, we further found that cactophily can be predicted with 76% accuracy from both functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which we found to be likely associated with altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall–degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved independently through disparate molecular mechanisms. Notably, we found that multiple cactophilic species and their close relatives have been reported as emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle—and perhaps more generally lifestyles favoring thermotolerance—might preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high-throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory

The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC’s ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model’s predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Novel perspective on a conventional technique: Impact of ultra-low temperature on bacterial viability and protein extraction

Ultra-low temperature (ULT) storage of microbial biomass is routinely practiced in biological laboratories. However, there is very little insight regarding the effects of biomass storage at ULT and the structure of the cell envelope, on cell viability. Eventually, these aspects influence bacterial cell lysis which is one of the critical steps for biomolecular extraction, especially protein extraction. Therefore, we studied the effects of ULT-storage (-80°C) on three different bacterial platforms: Escherichia coli , Bacillus subtilis and the cyanobacterium Synechocystis sp. PCC 6803. By using a propidium iodide assay and a modified MTT assay we determined the impact of ULT storage on cellular viability. Subsequently, the protein extraction efficiency was determined by analyzing the amount of protein released following the storage. The results successfully established that longer the ULT-storage time lower is the cell viability and larger is the protein extraction efficiency. Interestingly, E . coli and B . subtilis exhibited significant reduction in cell viability over Synechocystis 6803. This indicates that the cell membrane structure and composition may play a major role on cell viability in ULT storage. Interestingly, E . coli exhibited concomitant increase in cell lysis efficiency resulting in a 4.5-fold increase (from 109 μg/ml of protein on day 0 to 464 μg/ml of protein on day 2) in the extracted protein titer following ULT storage. Furthermore, our investigations confirmed that the protein function, tested through the extraction of fluorescent proteins from cells stored at ULT, remained unaltered. These results established the plausibility of using ULT storage to improve protein extraction efficiency. Towards this, the impact of shorter ULT storage time was investigated to make the strategy more time efficient to be adopted into protocols. Interestingly, E . coli transformants expressing mCherry yielded 2.7-fold increase (93 μg/mL to 254 μg/mL) after 10 mins, while 4-fold increase (380 μg/mL) after 120 mins of ULT storage in the extracted soluble protein. We thereby substantiate that: (1) the storage time of bacterial cells in -80°C affect cell viability and can alter protein extraction efficiency; and (2) exercising a simple ULT-storage prior to bacterial cell lysis can improve the desired protein yield without impacting its function.

59 BASIC BIOLOGICAL SCIENCES↗