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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Development and Implementation of a Nuclear and Criticality Safety Engineering Pipeline Course at North Carolina State University

Savannah River Nuclear Solutions, owner of both the criticality safety program and accident analysis qualification at Savannah River Site, experienced increasing difficulty in recruiting, training, and retaining key talent areas. In an effort to curb attrition, provide a talent base to recruit from, and introduce potential new hires to niche subject areas, a pipeline college course was developed for a regional university. The course introduces a variety of topic areas particular to criticality safety and nuclear safety at Department of Energy nonreactor nuclear facilities. Several administrative and developmental hurdles were encountered before the course was successfully initiated at North Carolina State University in fall 2024.

criticality↗
DOE OSTI2021

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ~75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Recent Advances in Assessing Environmental Effects of Marine Renewable Energy Around the World

Marine renewable energy (MRE) is increasingly of interest to coastal nations as a source of renewable energy that can support climate change mitigation goals as well as provide secure locally-produced energy for coastal and island communities. MRE extracts power from tidal streams, waves, ocean currents, run of rivers, and gradients in the ocean, with specialized devices developed and tested for each energy resource. Alongside development of MRE technologies and systems, first in Europe and then in North America, Australia, Asia, and other regions, it has been universally recognized that there is also a need to examine potential effects on marine animals, habitats, ecosystem processes, local communities and other sea users, to ensure that the MRE industry can be developed in a responsible and sustainable manner. This paper looks at the status of assessment and monitoring for potential environmental effects associated with MRE projects around the world. Over 80 projects were identified worldwide as having been tested, demonstrated, or commercially deployed with associated environmental monitoring. Five of the projects that represent tidal stream, wave, and run of river projects are examined in more detail to determine the types of data and information collected for those projects, the outputs of the monitoring campaigns, and the actions taken as a result of the data collection and analysis. Recommendations are provided for standardization of the monitoring approaches, instruments, and analysis methods at MRE project sites worldwide.

marine renewable energy, environmental effects, ri↗
DOE OSTI2022

EGS Stimulation Design with Uncertainty Quantification at the EGS Collab Site

Engineering a robust hydraulic connection between wells is one of the most difficult aspects of enhanced geothermal systems (EGS). Designing and constructing such hydraulic connections requires and understanding of the in situ state of stress and the heterogeneities and discontinuities that naturally exist and may control the stimulation. Even with comprehensive stress and formation characterization programs substantial uncertainty remains in these key parameters. This is especially the case in high-temperature EGS environments where drilling conditions are often difficult and a far fewer logging and testing options are available. This paper presents a new approach for explicitly quantifying the uncertainties in the state of stress using a Bayesian Markov Chain Monte Carlo method. This approach produces a probability distribution for the stress tensor, including a general 3D orientation, that reflects the uncertainties in all the observations or indicators used to constrain the stress state. This method is demonstrated on the characterization data for the EGS Collab Experiment 2 site. The output of the analysis is used to guide the design of the planned stimulations. In the case of research projects like EGS Collab, explicitly quantifying the uncertainties in the stress state allow for more rigorous hypothesis testing by allowing conclusions drawn from the experiments to be interpreted in the context of the uncertain knowledge about conditions in the test bed.

Burghardt, Jeffrey A.↗
DOE OSTI2020

Real-time Intrusion Detection for High-bandwidth Research Networks using Unsupervised Deep Learning

Nowadays, data generated by large-scale scientific experiments are on the scale of petabytes per month. These data are transferred through dedicated high-bandwidth networks across distributed collaboration sites for processing, storage, and analysis. Like general purpose networks, research networks experience attacks. However, monitoring traffic in such high-bandwidth network environments is challenging with conventional deep packet inspection (DPI)- based network intrusion detection systems (NIDS). Recently, machine learning (ML) algorithms have shown potential in detecting anomalous patterns with better generalizability and faster speed. Compared to the general purpose networks, traffic movement in research network is less volatile and more likely to benefit from the ML-based anomaly analysis. We present ThunderSecure, an efficient AI-powered system for detecting anomalies in 100G research networks. ThunderSecure implements a high-throughput packet processing infrastructure using multi-cores and GPUs. It takes time-series statistics from a variety of network measurements and uses 2D Convolutional Neural Network (CNN) to explore both spatial and temporal dependencies in network data stream. Patterns of science data traffic are learned with a one-class neural network, which blends an Adversarial Autoencoder (AAE) with Gaussian mixture density estimation. Testing traffic flows exhibiting significant deviations from the learned baseline of normality are marked as anomalies. We trained ThunderSecure on hundreds of billions of science data packets recorded from a 100G research network at Fermi National Accelerator Laboratory. The detection performance was evaluated on traffic captured from the same research network days and weeks after the training with different types of attack flows injected. To the best of our knowledge, this is the first ML work in the area of network anomaly detection that has been validated on such extreme scale datasets. Results show that ThunderSecure can recognize science data traffic that are captured long after the training and make nearly certain detection on those with anomalous flows injected, even in the case when the anomaly-to-normal mixing ratio is 0.1%.

Gong, Qian↗
DOE OSTI2021

Low-latency NuMI Trigger for the CHIPS-5 Neutrino Detector

The CHIPS R&D project aims to develop affordable water Cherenkov detectors for large-scale underwater installations. In 2019, a 5kt prototype detector CHIPS-5 was deployed in northern Minnesota to study neutrinos generated by the nearby NuMI beam. This contribution presents a dedicated low-latency time distribution system for CHIPS-5 that delivers timing signals from the Fermilab accelerator to the detector with sub-nanosecond precision. Exploiting existing NOvA infrastructure, the time distribution system achieves this only with open-source software and conventional network elements. In a time-of-flight study, the presented system has reliably offered a time budget of $610 \pm 330\text{ ms}$ for on-site triggering. This permits advanced analysis in real-time as well as a novel hardware-assisted active triggering mode, which reduces DAQ computing load and network bandwidth outside triggered time windows.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

A comparison of the power potential for surface- and seabed-deployed tidal turbines in the San Juan Archipelago, Salish Sea, WA

The San Juan archipelago lies along the axis of tidal movement between Straits of Juan de Fuca and Strait of Georgia in the Salish Sea. The amplitude of the tidal exchange produces significant tidal currents between the islands, as well as in Rosario and Haro Straits. These are of interest as a future source of electrical power generation, given the islands’ dependence on electricity supply by a subsea cable from the mainland. Here, we evaluate the tidal current energy potential in this region through a re-analysis of measurements collected by the National Ocean Service (NOS) and a high-resolution numerical model. Given the considerable variations in water depth and vertical velocity profiles across candidate tidal energy sites, we consider the trade-offs between tidal turbines deployed from a floating platform and those anchored to the seabed. Measurement re-analysis indicates several locations that could support tidal current power generation by MW-scale turbines with an acceptable balance between turbine size, rated power, and capacity factor. Even for relatively large (30 m) turbine diameters, surface-deployed turbines would be expected to produce up to 30 % more electricity than the same turbine deployed near the seabed due to vertical shear, with this difference increasing for smaller diameter turbines. A benchmark comparison at the measurement locations with the highest power generation potential shows relatively good model fidelity, though, even with relatively high resolution, time-average power density disagreements of ± 50 % persist throughout the water column. Nonetheless, the simulation identifies several locations with power generation potential more than twice as high as locations in the measurement re-analysis. These sites were either not surveyed by NOS or excluded due to data quality issues. Altogether, these results demonstrate the complimentary of models and measurements for tidal energy site assessment and suggest that tidal currents could be an important source of electricity generation in the San Juan archipelago.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis -elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Seismic isolation: A pathway to standardized advanced nuclear reactors

Standardizing advanced nuclear reactors is a pathway to substantially reducing their overnight capital cost and achieving parity with other power sources, including renewables and fossil fuels. The seismic load case has thwarted standardization of nuclear power plants because site-specific seismic hazard and local near-surface geology has triggered soil-structure-interaction analysis, design, equipment qualification, regulatory review, and licensing, ensuring that each build is different. To achieve standardized or site-independent certified advanced reactor designs, the impact of the seismic load case on the engineering and construction cost and time must be substantially mitigated. Seismic isolation is a mature technology that has been used for more than 30 years in non-nuclear sectors to substantially reduce earthquake demands in buildings and other infrastructure. In this paper, seismic isolation is used to enable standardization of advanced reactor designs, aimed at the complete re-use of a site-independent, certified design and repeated procurement of safety-class equipment. A pathway to standardized designs using seismic isolation is demonstrated for two fundamentally different advanced reactors: a molten salt reactor and a high temperature gas reactor. Each reactor building is equipped with three specialized pieces of safety-class equipment, namely, a reactor vessel, a steam generator, and a control rod drive mechanism housing that is attached to the reactor head. Analysis is performed per ASCE and ASME standards to design the buildings and the equipment for two base conditions: conventional (fixed base) and base isolated. The impact of the seismic load case is characterized for the reinforced concrete walls in the buildings and for the equipment, measured using vessel wall thickness and horizontal accelerations. Here the analysis results show that the fixed-base buildings, designed for a site of low seismic hazard (peak ground acceleration, PGA = 0.15 g) could be constructed at a site of much greater seismic hazard (PGA = 0.7 g) if seismic base isolation is employed. Importantly, the scope of the site-specific analysis, design, and qualification would be limited to the seismic isolators and the isolated substructure, drastically reducing plant-specific engineering, review, and licensing, and time to construction start. Regulatory challenges and opportunities with standardized reactor designs are identified.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Engineering evaluation of the EQSIM simulated ground-motion database: The San Francisco Bay Area region

Ground-motion simulations for infrequent earthquake scenarios are gaining increasing interest in the engineering community for their potential to inform performance-based structural design and assessment, particularly in regions where major earthquakes are expected, but recordings from consistent historical events are not available. However, the absence of empirical data makes the evaluation of such scenarios and the interpretation of the simulation results very challenging. In this context, this paper presents the evaluation of the first EQSIM (v.1.1.0) ground-motion simulations generated for the San Francisco Bay Area (SFBA) region. The current database, which is at the first stages of development, includes eight realizations of a Hayward Fault M w 7 event. The evaluation of the simulated motions is first conducted on the average ground-motion amplitudes through comparison against the NGA-W2 GMPEs and a selected population of real records. A methodology for selecting a population of real records consistent with the simulated event is proposed. The objective of the proposed evaluation is twofold: (1) build confidence in the realistic character of the simulated motions for their use in engineering applications and (2) offer a critical physics-based interpretation of the simulation results that can help improve key features of the simulation models. To further investigate the implications of using the simulated ground motions for site-specific structural assessments, the ASCE7-16 approach is employed for the analysis of two hazard-consistent near-field sites in the SFBA. Results are discussed. Furthermore, this study offers a critical review of the EQSIM (v.1.1.0) SFBA ground-motion simulations and suggestions for improving the earthquake rupture models.

58 GEOSCIENCES↗
DOE OSTI2020

Applicability of the Delplot method for the determination of catalytic reaction sequences: Hydrodeoxygenation of $\gamma$-valerolactone on Ni 2 P/MCM-41

Contact-time measurements based on sites are used to investigate the reaction sequence of the hydrodeoxygenation of γ-valerolactone (GVL) on Ni 2 P/MCM-41. Here the study is carried out at 300 °C and 0.5 MPa with site times of 0.29–6.1 s. A reaction network is proposed in which pentanoic acid and 2-methyltetrahydrofuran (2-MTHF) are formed in parallel initially and pentanal, butane and pentane are formed subsequently. A first-rank Delplot analysis (selectivity) gives a good fit, but higher-rank Delplots do not. The lack of applicability is explained by the magnitude of the rate constants, in which the rate constant for one of the later steps (the consumption of pentanal) is substantially larger than those for the preceding steps. For this reason, pentanal demonstrated the characteristics of a primary product and consequently affected the discrimination of higher rank products. A simulation of a model sequence with assumed rate constants confirms the reason why the Delplot method does not work for this reaction. Since the rate constants cannot be determined a priori to be of close magnitude, the Delplot method cannot be generally used to ascertain reaction sequences.

42 ENGINEERING↗
DOE OSTI2022

Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike’s stability. Taken together, the network approach serves as a valuable tool to evaluate communication “hot-spots” in proteins to guide design of stable immunogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV)

We analyzed the spike protein S1/S2 cleavage of selected strains of a prototype coronavirus, mouse hepatitis virus (MHV) by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of selected MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found that in vitro cleavability varied across MHV strains in line with predicted results—but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

Abstract Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N 6 -methyladenosine (m 6 A) modifications near the 3′ end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m 6 As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m 6 A ensembles, and maintaining multiple of these m 6 As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Rhizosphere Microbiome Diversity Potentially Supports Robust Nature of Field Pennycress ( Thlaspi arvense L.) in Dryland Cropping Systems of Eastern Washington

ABSTRACT Field pennycress ( Thlaspi arvense L.) is an annual in the Brassicaceae family and is currently being developed as an oilseed intermediate crop suitable for renewable biodiesel and jet fuel. It displays many desirable characteristics for this role including cold tolerance, a rapid life cycle, and a seed fatty acid profile conducive to bioenergy generation. These traits make field pennycress favorable for winter oilseed cultivation in the inland Pacific Northwest (iPNW). Simultaneously, intermediate crops are an increasingly recognized component of both agronomic sustainability and soil health management. Intermediate crops enhance soil microbial diversity, which benefits both soil and plant health. To understand the impact of field pennycress on soil microbial diversity, two natural accessions and seven experimental accessions were grown at three sites in Eastern Washington. Aboveground biomass and rhizosphere soil were then collected. Soil genomic DNA was extracted from rhizosphere samples and used to generate an amplicon library for bacterial (16S) and fungal (ITS) rRNA sequences. The resulting libraries were analyzed in QIIME2, which revealed that not only did the fad2 deficient line from the Spring32‐10 background have significantly increased aboveground biomass production compared to other pennycress genotypes, but also displayed significantly higher β‐diversity in the rhizosphere community specifically at the site experiencing the driest conditions. ANCOM analysis showed that multiple sequences similar to beneficial plant and soil health enhancing organisms such as Trichoderma spirale , Pseudomonas spp., and Methylobacterium goesingense were found to be enriched in the microbiome of the fad2 Spring32‐10 background also at that site. To add additional context to rhizosphere community data, root exudates from two pennycress genotypes were captured in magenta boxes and analyzed using HPLC. Future work will expand our understanding of the mechanisms by which field pennycress creates diversity in the rhizosphere, thus expanding our ability to cultivate this crop in the iPNW.

54 ENVIRONMENTAL SCIENCES↗