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DOE OSTI2024

Sierra/SD – Verification Test Manual – 5.22

Verification and validation (V&V) of scientific computing programs are important at Sandia National Labs due to the expanding role of computational simulation in managing the United States nuclear stockpile. The complexities of structural response calculations used to analyze physical problems, the varieties of codes applied to the calculations, and the importance of accurate predictions when assessing field conditions demand confidence in the consistency and accuracy of computer codes. Confidence in the accuracy of the predictions arising from computer simulations must ultimately be gained through verification and validation. The Sierra salinas structural dynamics analysis code, Sierra/SD, is used at the DOE Laboratories, and in several DOD projects. The roles of Sierra/SD in the qualification of weapon systems and components for normal and hostile environments throughout the Stockpile-to-Target Sequence include to, • Redesign weapon components. • Certify weapon components and systems for target environments such as hypersonic vehicles. • Certify that components will survive the thermal mechanical shock loads associated with hostile environments. • Evaluate current stockpile issues, including issues associated with uncertainty quantification. • Address many other problems that are encountered in stockpile management. The Sierra/SD verification plan is described, and an evolving set of key verification tests are described in detail. The verification tests ensure the correctness of the mathematics and numerical algorithms associated with functionality describing engineering phenomena. Development is in accordance with a set of tailored Software Quality Engineering (SQE) practices. SQE practices guide the overall verification and validation effort.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern↗

DOE OSTI2025

ARM Cloud and Precipitation Measurements and Science Group (CPMSG) 2024 Workshop Report

The mission of the U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility is to improve the understanding and representation of cloud and aerosol processes and their interaction with the Earth's surface in Earth system models (ESMs) by providing comprehensive field observations and supporting advanced data analytics. The ARM Cloud and Precipitation Measurements and Science Group (CPMSG) was chartered in March 2019 to help improve the performance and scientific impact of ARM measurements of clouds and precipitation. The group aims to identify and address gaps in measurement capabilities, maximize the scientific impact of ARM data, and effectively serve the scientific community. To achieve these goals, the group includes experts in cloud and precipitation science, as well as representatives from ARM infrastructure, including instrument mentors, engineers, data quality officers, and data product translators. Prior to CPMSG, early discussions on cloud and precipitation measurements primarily focused on improving radar systems, but have since evolved to include a broader scope involving radiometers and other instruments. Since its formation, the CPMSG has gathered feedback using science traceability matrices. CPMSG aims to keep these as living documents to show the measurement needs, scientific drivers, roadblocks, maturity of measurements and retrievals, and pathways to model improvements. The group meets quarterly to discuss and prioritize measurement and operational improvements.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

ARM Cloud and Precipitation Measurements and Science Group (CPMSG) 2024 Workshop Report

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

ANS Winter 2024 Summary: MCCAFE: The Monte Carlo Constructor for ATR Fuel Elements

The Irradiation Experiment Neutronics Analysis Department at Idaho National Laboratory (INL) has implemented a new analysis workflow for experiments in the Advanced Test Reactor (ATR). One key piece of this workflow is the Monte Carlo Constructor for ATR Fuel Elements, or MCCAFE. For each ATR operating cycle, the Reactor and Nuclear Safety Engineering (RNSE) Department first solves the core in eigenvalue mode and depletes the driver fuel materials. In a separate calculation, neutronics analysts model and deplete the materials of one or more irradiation experiments, usually in a series of fixed-source Monte Carlo N-Particle (MCNP) models of the ATR for neutron transport calculations. It was desirable to use the results of the former calculations to inform the models of the latter. MCCAFE is a Python program developed using American Society of Mechanical Engineers Nuclear Quality Assurance-1 procedures at INL. Its purpose is to take the calculated results from the RNSE depletion solutions and the measured or projected operating parameters from the Nuclear Data Management and Analysis System (NDMAS) to generate fixed-source models of the ATR core at given points in time across one or more cycles.

99 - GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

A Generalized approach to the operationalization of Software Quality Models

Comprehensive measures of quality are a research imperative, yet the development of software quality models is a wicked problem. Definitive solutions do not exist and quality is subjective at its most abstract. Definitional measures of quality are contingent on a domain, and even within a domain, the choice of representative characteristics to decompose quality is subjective. Thus, the operationalization of quality models brings even more challenges. A promising approach to quality modeling is the use of hierarchies to represent characteristics, where lower levels of the hierarchy represent concepts closer to real-world observations. Building upon prior hierarchical modeling approaches, we developed the Platform for Investigative software Quality Understanding and Evaluation (PIQUE). PIQUE surmounts several quality modeling challenges because it allows modelers to instantiate abstract hierarchical models in any domain by leveraging organizational tools tailored to their specific contexts. Here, we introduce PIQUE; exemplify its utility with two practical use cases; address challenges associated with parameterizing a PIQUE model; and describe algorithmic techniques that tackle normalization, aggregation, and interpolation of measurements.

Data aggregation↗

DOE OSTI2026

Cyclodextrin-Derived Porous Liquids Enabled by In Situ Solvation Shell Formation

Porous liquids (PLs) represent a unique platform for molecular separations by combining permanent porosity with liquid-phase mobility. However, it remains a formidable challenge to construct and stabilize PLs with sub-5 Å pores using readily available porous host and liquid media. Here, we report the construction of cyclodextrin (CD)-derived PLs enabled by in situ solvation shell formation. The acid–base neutralization reaction between CD and an organic base was leveraged to generate a thin ionic solvation shell around the CD host, effectively liquefying CD and preventing its segregation in the liquid base medium while preserving accessible molecular-scale cavities. Spectroscopic analysis, neutron scattering, density functional theory calculations, and molecular dynamics simulations collectively confirm the structural evolution and existence of abundant internal porosity in PLs. The unique architectures of CD-derived PLs enable highly selective encapsulation of fluorinated alkanes and significantly enhanced uptake of inert gases. This facile and generalizable strategy enables construction of high-quality PLs with engineered ultramicroporosity to facilitate molecular separations.

Cavities↗

DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

How to Build a Quantum Supercomputer: Scaling from Hundreds to Millions of Qubits

In the span of four decades, quantum computation has evolved from an intellectual curiosity to a potentially realizable technology. Today, small-scale demonstrations have become possible for quantum algorithmic primitives on hundreds of physical qubits and proof-of-principle error-correction on a single logical qubit. Nevertheless, despite significant progress and excitement, the path toward a full-stack scalable technology is largely unknown. There are significant outstanding quantum hardware, fabrication, software architecture, and algorithmic challenges that are either unresolved or overlooked. These issues could seriously undermine the arrival of utility-scale quantum computers for the foreseeable future. Here, we provide a comprehensive review of these scaling challenges. We show how the road to scaling could be paved by adopting existing semiconductor technology to build much higher-quality qubits, employing system engineering approaches, and performing distributed quantum computation within heterogeneous high-performance computing infrastructures. These opportunities for research and development could unlock certain promising applications, in particular, efficient quantum simulation/learning of quantum data generated by natural or engineered quantum systems. To estimate the true cost of such promises, we provide a detailed resource and sensitivity analysis for classically hard quantum chemistry calculations on surface-code error-corrected quantum computers given current, target, and desired hardware specifications based on superconducting qubits, accounting for a realistic distribution of errors. Furthermore, we argue that, to tackle industry-scale classical optimization and machine learning problems in a cost-effective manner, heterogeneous quantum-probabilistic computing with custom-designed accelerators should be considered as a complementary path toward scalability.

Mohseni, Masoud↗

DOE OSTI2025

Fast and High-Fidelity SNAP Gate Enabled by Optimal Control on Floquet-Engineered Systems

Superconducting cavities with high quality factors, coupled to nonlinear ancilla, provide a promising platform for quantum information storage and manipulation. However, the commonly used selective number-dependent arbitrary phase (SNAP) gate faces significant challenges in ultra-high-coherence cavities, where weak dispersive shifts result in prolonged gate times. Here, we propose a protocol to achieve high-fidelity SNAP gates that are orders of magnitude faster than the standard implementation, breaking the speed limit set by the bare dispersive shift. This enhancement is achieved by dynamically amplifying dispersive coupling via sideband interactions, followed by quantum optimal control on Floquet-engineered systems. Additionally, we present a unified perturbation theory that explains both the gate acceleration and associated benign drive-induced decoherence, corroborated by Floquet\textendash Markov simulations. These results pave the way for the experimental realization of high-fidelity control of weakly coupled, high-coherence cavities, and expanding the scope of optimal control techniques in Floquet quantum systems.

You, Xinyuan [Fermilab]↗

DOE OSTI2026

Sample Preparation Laboratory (SPL) Best Practices: CGD as the Primary Acceptance Method

The traditional paradigm applied to the construction of nuclear safety related systems, structures, and components (SSCs), like SPL, involves an owner/licensee hiring an EPC firm with an NQA 1 program to manage the engineering, procurement, and construction of the desired SSC. This traditional approach would have posed significant barriers to the successful completion of the SPL. As a smaller capital project, in the $\$$100–$\$$200 million range, there was concern that employing one of the larger EPC companies would escalate costs and extend the projected schedule beyond what would be feasible for the Department of Energy (DOE). The traditional acceptance method employed for nuclear facilities with credited safety functions requires the use of an EPC firm applying American Society of Mechanical Engineers (ASME) NQA 1 nuclear quality assurance (NQA) to accept safety SSCs. In lieu of this approach, INL elected to apply its own NQA 1 program to hire an EPC firm operating a commercial quality program. This method used commercial grade dedication (CGD) as outlined in NQA 1 which had not been applied at this scale. Use of the commercial supply chain was identified as a key factor to the successful completion of SPL. Favorable conditions enabling the use of CGD included: • INL serving as both the designer and the design authority • Design created by an NQA 1 qualified source • A mature CGD program • Availability of a CGD subject matter expert (SME) • A strong construction management program. This white paper elaborates on the methodology employed in the construction of the SPL, the successes achieved, and best practices implemented.

42 - ENGINEERING↗

DOE OSTI2026

Constitutive and inducible oleoresin defenses share genetic architectures and mechanisms in Pinus taeda

The oleoresin defense system of loblolly pine (Pinus taeda) protects trees from insects and pathogens and is an important source of renewable biofuels and chemicals, but the genetic basis of oleoresin production is poorly understood. We characterized the genetic architecture of oleoresin flow, resin canal number, stem wood terpene content, and monoterpene composition in two clonal populations of P. taeda. We used quantitative genetic analyses, genome-wide association studies (GWASs), multiplex network learning, and gene expression profiling to elucidate shared gene networks underlying defense traits and to identify high-quality candidates for breeding and engineering loblolly pine. Genetic analyses revealed polygenic inheritance and trait-to-trait correlations provide strong evidence for shared genes regulating constitutive and induced oleoresin flow. We identified 236 single nucleotide polymorphisms associated with oleoresin flow, resin canal number, and terpene composition and highlight candidate genes likely involved in terpene biosynthesis, cambial meristem reprogramming, and pathogen perception and immune signaling. Fourteen GWAS candidates were methyl jasmonate-responsive in tissues where resin canals initiate and terpene production occurs. Integrating quantitative genetics, GWAS, gene expression, and multiplex network analyses enabled the prioritization of high-quality candidate genes. This work advances the development of more resilient loblolly pine optimized for ecological performance, renewable chemical, and biofuel production.

genome-wide association study↗

DOE OSTI2025

A split ribozyme system for in vivo plant RNA imaging and genetic engineering

RNA plays a central role in plants, governing various cellular and physiological processes. Monitoring its dynamic abundance provides a discerning understanding of molecular mechanisms underlying plant responses to internal (developmental) and external (environmental) stimuli, paving the way for advances in plant biotechnology to engineer crops with improved resilience, quality and productivity. In general, traditional methods for analysis of RNA abundance in plants require destructive, labour-intensive and time-consuming assays. To overcome these limitations, we developed a transformative innovation for in vivo RNA imaging in plants. Specifically, we established a synthetic split ribozyme system that converts various RNA signals to orthogonal protein outputs, enabling in vivo visualisation of various RNA signals in plants. We demonstrated the utility of this system in transient expression experiments (i.e., leaf infiltration in Nicotiana benthamiana ) to detect RNAs derived from transgenes and tobacco rattle virus, respectively. Also, we successfully engineered a split ribozyme-based biosensor in Arabidopsis thaliana for in vivo visualisation of endogenous gene expression at the cellular level, demonstrating the feasibility of multi-scale (e.g., cellular and tissue level) RNA imaging in plants. Furthermore, we developed a platform for easy incorporation of different protein outputs, allowing for flexible choice of reporters to optimise the detection of target RNAs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Understanding the Role of Extrinsic Impurities in Bulk Nb SRF Cavities

High gradient and high quality factor superconducting radiofrequency (SRF) cavities are essential for efficient particle acceleration in next-generation accelerators. This work demonstrates that the superconducting performance of bulk niobium can be enhanced through a controlled introduction of interstitial oxygen and nitrogen. Thermal and chemical surface treatments modify the concentration and distribution of these impurities, enabling systematic tuning of SRF cavity performance. By combining cavity RF measurements with quantitative materials characterizations, we isolate the impact of impurity concentration on BCS surface resistance and identify the mechanisms by which interstitial impurities alter the superconducting properties of niobium. We find that nitrogen is an order of magnitude more effective than oxygen in reducing BCS resistance at 16 MV/m and that the reduction arises from a combination of mean free path optimization and superconducting gap enhancement. Using these insights, we develop a predictive model that estimates cavity performance directly from room temperature sample material studies, reducing the reliance on full-scale cryogenic tests for surface treatment development. We then apply this model to explore co-doping strategies, demonstrating that combining interstitial oxygen and nitrogen achieves a synergistic reduction in BCS resistance. These results establish co-doping as a viable path for the development of surface-engineered niobium for future high quality factor SRF applications.

Hu, Hannah [Chicago U.]↗

DOE OSTI2024

Biofuels as Heavy Fuel Oil Substitutes in the Maritime Sector: Findings and Potential Pathways

The United States Department of Energy has commissioned four national laboratories to evaluate the feasibility of biofuels in the maritime sector. This effort is briefly described including the overall project goals, structure and aims. The large two-stroke crosshead engines used to power large merchant vessels were of particular interest since they can burn lower combustion quality fuels relative to four-stroke engines. This characteristic allows for consideration of pyrolysis oils and hydrothermal liquefaction (HTL) oils which are feedstock agnostic and, in the raw state, are more economical compared to distillate drop-in fuels. Pyrolysis and HTL oils are collectively known as bio-intermediates since they require additional processing for use in distillate fuel systems. The key limiting feature is that these bio-intermediate fuels will cause asphaltene precipitation when blended with heavy fuel oils (HFOs) such as very low sulfur fuel oil (VLSFO) unless they are upgraded to remove water and oxygenates. Economics are the key driver at this point in time, and preliminary techno-economic analyses (TEAs) indicate that bio-intermediates have potentially lower cost relative to other biofuels such as biodiesel and renewable diesel. Additionally, life cycle analyses (LCAs) of feedstocks and pathways show the life cycle carbon reduction benefit relative to heavy fuel oils. In addition to TEA and LCA results, we also present on the technical feasibility of these fuels. These studies have focused on the properties of biofuel blends with VLSFO that are critical to the fuel systems of maritime vessels fueled with HFOs. These properties include the compatibility with fuel system metals, viscosity, and blend stability. Aging studies with blends of VLSFO with biodiesel, HTL, and pyrolysis oils are also presented. Future efforts being planned to conduct additional biofuel testing, including the use of biofuels as pilot fuels in zero carbon shipping options fueled with ammonia and methanol, ship-based demonstrations, and bioresource competition studies.

Kass, Michael↗

DOE OSTI2025

Quality Assurance Program Plan for SFR Metallic Fuel Data Qualification

This document contains an evaluation of the applicability of the current Quality Assurance Standards from the American Society of Mechanical Engineers Standard NQA-1 (NQA-1) criteria and identifies and describes the quality assurance process(es) by which attributes of historical, analytical, and other data associated with sodium-cooled fast reactor [SFR] metallic fuel will be evaluated. This process is being instituted to facilitate validation of data to the extent that such data may be used to support future licensing efforts associated with advanced reactor designs. The initial data to be evaluated under this program were generated during the US Integral Fast Reactor program between 1984-1994, where the data include, but are not limited to, research and development data and associated documents, test plans and associated protocols, operations and test data, technical reports, and information associated with past United States Nuclear Regulatory Commission reviews of SFR designs. It is recognized that managing the data generated by large research and development projects presents a significant challenge for retaining data integrity and availability. American Society of Mechanical Engineers Standard NQA-1 (NQA-1) 2008/2009a provides appropriate requirements for this plan.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Remote sensing of planetary boundary layer from ground and space: Structure, thermodynamics, and boundary layer clouds

The planetary boundary layer (PBL) is a critical interface between Earth's surface and atmosphere, influencing atmospheric convection, weather patterns, and air quality. Recognized by the 2017 National Academies of Sciences, Engineering, and Medicine Earth Science Decadal Survey as an Incubation Targeted Observable, high-quality and effective observation of the PBL has become a priority. This paper reviews surface-based and satellite remote sensing techniques for characterizing PBL features, including PBL height (PBLH), boundary layer thermodynamics, turbulence, and boundary layer clouds (BLCs). These elements are treated as interconnected aspects of the PBL system, while recognizing that different instruments retrieve different physical manifestations of the PBL. The review summarizes recent advances and limitations in Micro-Pulse Lidar (MPL), Doppler lidar, Raman lidar, Differential Absorption Lidar (DIAL), ceilometers, wind profilers, GNSS Radio Occultation, radar, and hyperspectral sounders. These observations help trace dynamic processes within the PBL and link PBL structure to broader weather and climate processes. The review also highlights persistent observational gaps over oceans, remote land, and polar regions, where continuous surface-based profiling is sparse. By comparing instrument capabilities, practical limitations, and interpretation issues, this review emphasizes the need for integrated remote sensing approaches and careful definition of the retrieved PBL quantities.

Boundary layer clouds↗

DOE OSTI2025

In situ probing of structure and deagglomeration of SnO 2 colloids via small-angle X-ray scattering

Transforming dry nanopowders into stable colloidal dispersions remains challenging due to the cohesive forces between the nanoparticles (NPs) which promote agglomeration. Effective dispersion and deagglomeration of these agglomerates is a critical process in the formulation and preparation of nanoparticle-based functional materials via the colloidal route. Understanding the deagglomeration dynamics provides information to improve microstructural quality in various applications by enabling engineering of agglomerate size, structure and morphology. However, the deagglomeration process dynamics with respect to the evolution of the fractal agglomerate structures, particularly for very small NPs, is still poorly understood and requires further investigation. This study employs in situ small-angle X-ray scattering (SAXS) to investigate the sonication-induced deagglomeration of SnO 2 NPs. Electrostatically stabilized SnO 2 colloids with varying primary particle size (6–21 nm) are investigated in a specifically designed in situ cell using synchrotron-based SAXS to study the influence of sonication time and intensity on the nanoscaled agglomerates. Complete structural analysis via SAXS reveals a direct correlation between changes in agglomerate size and structure, size-dependent deagglomeration behavior and a dependence on the overall energy introduced during sonication into the dispersion regardless of the actual power as well as ultrasonic process parameters in case of SnO 2 NPs. The results suggest that control of the dispersion process during ultrasonic deagglomeration results in tailoring agglomerates with respect to size and structure.

Deagglomeration↗