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DOE OSTI2022

Lagrangian conditional statistics and flow topology in edge plasma turbulence

Lagrangian statistics and particle transport in edge plasma turbulence are investigated using the Hasegawa–Wakatani model and its modified version. The latter shows the emergence of pronounced zonal flows. Different values of the adiabaticity parameter are considered. The main goal is to characterize the role of coherent structures, i.e., vortices and zonal flows, and their impact on the Lagrangian statistics of particles. Computationally intensive long time simulations following ensembles of test particles over hundreds of eddy turnover times are considered in statistically stationary turbulent flows. The flow topology is characterized using the Lagrangian Okubo–Weiss criterion in order to split the flow into topologically different domains. In elliptic and hyperbolic regions, the probability density functions (PDFs) of the residence time have self-similar algebraic decaying tails. However, in the intermediate regions, the PDFs exhibit exponentially decaying tails. Topologically conditioned PDFs of the Lagrangian velocity, and acceleration and density fluctuations are likewise computed. The differences between the classical Hasegawa–Wakatani system and its modified version are assessed, and the role of zonal flows is highlighted. Here, the density flux spectrum, which characterizes the contributions of different length scales, is studied, and its inertial scaling is found to be in agreement with predictions based on dimensional arguments. Analyzing the angular change of particle tracers at different time scales, corresponding to coarse grained curvature, completes the study, and these multiscale geometric statistics quantify the directional properties of the particle motion in different flow regimes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

The Urban Deployment Model: A Toolset for the Simulation and Performance Characterization of Radiation Detector Deployments in Urban Environments

Static and mobile radiation detectors can be deployed in urban environments for a range of nuclear security applications, including radiological source search-and-tracking scenarios. Modeling detector performance for such applications is challenging, as it does not depend solely on the detector capabilities themselves. Many factors must be taken into consideration, including specific source and background signatures, the topology and constraints of the deployment environment, the presence of nuisance sources, and whether detectors are mobile or static. When considering the simultaneous deployment of multiple, heterogeneous detectors, assessment of the system-wide performance requires the simulation of the individual detectors, and a system-level analysis of the detection performance. In radiological source search-and-tracking scenarios, performance is mostly dominated by the probability of encounter, which depends on the specifics of a given deployment, e.g., static vs. mobile detectors or a combination of both modalities, the number of detectors deployed, the dynamic vs. static setting of false alarm rates, and individual vs. networked operation. The Urban Deployment Model (UDM) toolset was specifically developed to cover the gap in the available generic frameworks for the simulation of radiation detector deployments at city scales. UDM provides a unified and modular framework to support the simulation and performance characterization of heterogeneous detector deployments in urban environments. This paper presents the key components along the UDM workflow.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2021

Experimental Assessment of Elastic Modulus vs. Relative Density for Stretch- and Bend-Dominated Lattices

This project was designed to study the possibility of using structural properties of lattices to replicate the material properties of certain hard to manufacture designs and use topology optimization to determine the lattice type and density required to mimic these properties. The integration of additively manufactured lattice structures with topology optimization highlights the need for well characterized mechanical properties and uncertainty analyses to insure these optimized structures respond as predicted. Stereolithographically printed octet and rhombic dodecahedron lattices were manufactured at 10%, 25% and 65% density by volume. As a separate task, yet integrated into this work, finite element analysis (FEA) was used to predict the printed lattice’s mechanical properties, which were then compared to our experimental results. After comparing FEA and experimentallymeasured elastic moduli, it was determined that the FEA provides highly reliable predictions for the modulus of these printed lattice structures. These lattices also exhibited greater tensile stiffness than that of the solid material demonstrating the flexibility that lattices provide to designing parts with designer structural properties. The accurate printing and reliable modeling of these lattices will enable topology optimization of complex parts from well-characterized rhombic dodecahedron and octet lattice structures of varying densities.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Insulating ground state and 2−𝑘 magnetic structure of candidate Weyl hydrogen-atom K2⁢Mn3⁢(AsO4)3

The ideal Weyl "hydrogen-atom" semimetal exhibits only a single pair of Weyl nodes and no other trivial states at the Fermi energy. Such a material would be a panacea in the study of Weyl quasi-particles, allowing direct unambiguous observation of their topological properties. The alluaudite-like K2⁢Mn3⁢(AsO4)3 compound was recently proposed as such a material. Here, we use comprehensive experimental work and first-principle calculations to assess this prediction. We find K2⁢Mn3⁢(AsO4)3 crystallizes in the 𝐶⁢2/𝑐 symmetry with a quasi-one-dimensional Mn sublattice, growing as small needle-like crystals. Bulk property measurements reveal magnetic transitions at ≈8 and ≈4 K, which neutron scattering experiments show correspond to two distinct magnetic orders, first a partially ordered ferrimagnetic 𝐤𝟏=(0,0,0) structure at 8 K and a second transition of 𝐤𝟐=(1,0,0) at 4 K to a fully ordered state. Below the second transition, both ordering vectors are necessary to describe the complex magnetic structure with modulated spin magnitudes. Both of the best-fit magnetic structures in this work are found to break the symmetry necessary for the generation of Weyl nodes, though one of the magnetic structures allowed by 𝐤𝟏 does preserve this symmetry. However, the crystals are optically transparent and ellipsometry measurements reveal a large band gap, undermining expectations of semimetallic behavior. Density functional theory calculations predict an insulating antiferromagnetic ground state, in contrast to previous reports, and suggest potential frustration on the magnetic sublattice. Given the wide tunability of the alluaudite structure, we consider ways to push the system closer to a semimetallic state.

Taddei, Keith M [Argonne National Laboratory]↗

DOE OSTI2020

NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

Comparative network analysis provides effective computational means for gaining novel insights into the structural and functional compositions of biological networks. In recent years, various methods have been developed for biological network alignment, whose main goal is to identify important similarities and critical differences between networks in terms of their topology and composition. A major impediment to advancing network alignment techniques has been the lack of gold-standard benchmarks that can be used for accurate and comprehensive performance assessment of such algorithms. The original NAPAbench (network alignment performance assessment benchmark) was developed to address this problem, and it has been widely utilized by many researchers for the development, evaluation, and comparison of novel network alignment techniques. In this work, we introduce NAPAbench 2—a major update of the original NAPAbench that was introduced in 2012. NAPAbench 2 includes a completely redesigned network synthesis algorithm that can generate protein-protein interaction (PPI) network families whose characteristics closely match those of the latest real PPI networks. Furthermore, the network synthesis algorithm comes with an intuitive GUI that allows users to easily generate PPI network families with an arbitrary number of networks of any size, according to a flexible user-defined phylogeny. In addition, NAPAbench 2 provides updated benchmark datasets—created using the redesigned network synthesis algorithm—which can be used for comprehensive performance assessment of network alignment algorithms and their scalability.

42 ENGINEERING↗

DOE OSTI2023

Enhanced dynamic contingency analysis for power systems

The present disclosure describes systems and techniques that enhance effectiveness and efficiency of a contingency analysis tool that is used for studying the magnitude and likelihood of extreme contingencies and potential cascading events across a power system. The described systems and techniques include deploying the contingency analysis tool in a high-performance computing (HPC) environment and incorporating visual situational awareness approaches to allow power system engineers to quickly and efficiently evaluate multiple power system simulation models. Furthermore, the described systems and techniques include the power system contingency-analysis tool calculating and coordinating protection element settings, as well as assessing controls of the power system using small-signal nomograms, allowing power system engineers to more effectively comprehend, evaluate, and analyze causes and effects of cascading events against a topology of a power system.

Samaan, Nader A.↗

DOE OSTI2026

SOLPS-ITER modeling of a dedicated divertor for negative triangularity operation on DIII-D

The design of a new dedicated divertor for negative triangularity (NT) operation on DIII-D with neutral baffles and pumping is informed by SOLPS-ITER transport modeling. This dedicated NT divertor is the latest step in a progression of NT shapes with various divertor characteristics explored on DIII-D, including NT shapes at reduced triangularity and a campaign with stronger shaping that included new armored components on the outboard side. SOLPS simulations played a key role in these divertor designs. Interpretive simulations, using cross-field diffusivities constrained by experimental data in the NT Shelf shape were used to inform the design of the 2023 armor campaign components. A similar procedure used armor campaign data to predict conditions for the dedicated NT divertor. The predictive simulations were used to assess the divertor fluxes, detachment threshold, pumped flux, and neutral leakage. For the dedicated NT divertor, SOLPS simulations and two-point-modeling were used to show the relative impact of magnetic topology (mainly longer connection length) and divertor closure on the divertor conditions relative to the armor campaign. It is predicted that the dedicated NT divertor reaches detachment (measured by target ion flux rollover) at a lower upstream density (≈(1.75−−2.4)×1⁢019m−3) as compared to the armor campaign shape. For the preliminary design geometry, divertor closure reduces the neutral leakage by ≈10%. Parametric optimization indicating further ≈20%–60% improvement in the leakage flux and recycled flux crossing the pump entrance is possible for relatively minor changes to the divertor and baffle layout.

Lore, Jeremy [ORNL] (ORCID:000000029192465X)↗

DOE OSTI2026

A System Level Comparative Study of SecondarySide Rectifiers for UAV Wireless Power Transfer in High-Altitude Airborne Energy Platforms

Wireless power transfer (WPT) systems for unmanned aerial vehicles (UAVs) must satisfy stringent design requirements to ensure reliable operation under constraints related to efficiency, thermal performance, altitude, weight, and reliability, particularly in airborne and high-altitude environments. Thermal management becomes increasingly challenging at higher altitudes due to reduced air density, while reliability is strongly affected by the number and complexity of active components. The weight and compactness of secondary-side rectifiers directly impact UAV flight endurance and system integration, influencing energy consumption and payload allocation. These factors collectively define the practical feasibility of UAV WPT systems and guide rectifier topology selection. This paper presents a comparative and experimentally validated evaluation framework for secondary-side rectifiers under UAV-specific constraints. Three representative rectifier architectures are analyzed using component-based assessment of weight, thermal behavior, and reliability, together with experimental efficiency measurements obtained from a 1 kW WPT prototype. The results show that the single-switch active rectifier achieves the highest peak efficiency of approximately 93.2% and an overall efficiency of 91%, while also offering advantages in weight and reliability. The findings demonstrate how constraint-oriented analysis, combined with experimental validation, enables informed selection of secondary-side rectifiers for UAV wireless power transfer applications, including emerging airborne and high-altitude platforms.

Asa, Erdem [ORNL] (ORCID:0000000190884812)↗

DOE OSTI2020

Quantum chemical topology and natural bond orbital analysis of M–O covalency in M(OC 6 H 5 ) 4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np)

Covalency is complex yet central to our understanding of chemical bonding, particularly in the actinide series. In this work, we assess covalency in a series of isostructural d and f transition element compounds M(OC 6 H 5 ) 4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np) using scalar relativistic hybrid density functional theory in conjunction with the Natural Bond Orbital (NBO), quantum theory of atoms in molecules (QTAIM) and interacting quantum atoms (IQA) approaches. The IQA exchange–correlation covalency metric is evaluated for the first time for actinides other than uranium, in order to assess its applicability in the 5f series. It is found to have excellent correlation with NBO and QTAIM covalency metrics, making it a promising addition to the computational toolkit for analysing metal–ligand bonding. Our range of metrics agree that the actinide-oxygen bonds are the most covalent of the elements studied, with those of the heavier group 4 elements the least. Within the early actinide series, Th stands apart from the other three elements considered, being consistently the least covalent.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Bismuth as a Reactive Solvent in the Synthesis of Multicomponent Transition-Metal-Bearing Bismuthides

Employment of liquid bismuth (Bi) allows the facile single-crystal growth of compounds containing elements with high melting points, provided that these elements have reasonably high solubility in Bi. Utilization of the Bi flux approach yielded two new ternary bismuthides, SrNi 0.17(1) Bi 2 [a defect variant of the BaCuSn 2 type, space group Cmcm , α = 4.879(2) Å, b = 17.580(6) Å, and c = 4.696(2) Å] and CaTi 3 Bi 4 [NdTi 3 (Sn 0.1 Sb 0.9 ) 4 structure type, space group Fmmm , a = 5.6295(7) Å, b = 9.8389(1) Å, and c = 23.905(3) Å]. In addition, the ternary antimonide CaV3Sb4, isostructural with CaTi 3 Bi 4 , was synthesized from antimony (Sb) flux, and analyzed with the goal of validating structural assessment of the bismuthide analogue, where the X-ray crystallographic work proved to be very challenging. All synthesized compounds exhibit complex crystal structures featuring quasi-two-dimensional building blocks of different topologies. First-principle calculations reveal hypervalent bonding in the homoatomic Bi subunits. Lastly, physical property measurements indicate metallic conductivity and the absence of localized magnetism in the studied compounds.

36 MATERIALS SCIENCE↗

DOE OSTI2023

A Randomization-Based, Zero-Trust Cyberattack Detection Method for Hierarchical Systems

This paper demonstrates a novel randomization-based approach for verifying power system control signals with application to detecting cyberattacks. We consider fully connected hierarchical systems containing multiple local agents and a global "trust" agent. The global agent uses a time-varying randomized assignment scheme to identify corrupt network links based on principles of zero trust and majority rule. To evaluate the performance of this detection approach, we implement our algorithm in MATLAB and run it against nearly 43 million unique attack scenarios spanning a range of system sizes. For each scenario, the algorithm determines whether the identified corruptions satisfy a set of validity constraints reflecting network topology and uses that result to say whether the recovered state value for one or more local agents is malicious. We compare the algorithm's determination to the true state of the system to assess performance and find that classification accuracy converges to 100% as system size increases, suggesting that the validity constraints become more difficult to satisfy for larger systems. We further explore the scenarios that evade detection to understand practical implications for employing this detection approach.

cybersecurity↗

DOE OSTI2023

Aspects of scaling and scalability for flow-based sampling of lattice QCD

Recent applications of machine-learned normalizing flows to sampling in lattice field theory suggest that such methods may be able to mitigate critical slowing down and topological freezing. However, these demonstrations have been at the scale of toy models, and it remains to be determined whether they can be applied to state-of-the-art lattice quantum chromodynamics calculations. Assessing the viability of sampling algorithms for lattice field theory at scale has traditionally been accomplished using simple cost scaling laws, but as we discuss in this work, their utility is limited for flow-based approaches. We conclude that flow-based approaches to sampling are better thought of as a broad family of algorithms with different scaling properties, and that scalability must be assessed experimentally.

Abbott, Ryan↗

DOE OSTI2023

FES 2023 Theory & Simulation Performance Target

The Report for the 2023 Theory & Simulation Performance Target (TSPT) is presented herein. The 1st, 2nd and 3rd Quarter Reports are given in Sec. I, Sec. II and Sec. III. These are unchanged from those previously submitted, except that in this final document the equations, figures and citations have been automatically renumbered. The 4th Quarter Report is given in Sec. IV. The following material presents verification calculations of several widely used three-dimensional (3D) magnetohydrodynamic (MHD) equilibrium codes in strongly shaped configurations; for both fixed and free-boundary equilibria; for the so-called vacuum case and for the case of high plasma pressure; and, for magnetic fields that have nested magnetic surfaces and for fields that have a magnetic island. The configurations studied includes the recently discovered “precise-QA” case [Phys. Rev. Lett., 128, 035001 (2002)] and other highly optimized configurations. Because of the strong (extreme) shaping, the latter of these pose challenges to the 3D MHD codes. A new method is introduced for constructing coordinates in arbitrarily shaped toroidal domains, and this can improve the robustness of 3D equilibrium calculations. Beyond the equilibrium calculation, this report demonstrates the capability of performing non-linear extended-MHD modelling of optimized stellarator equilibria. This capability allows the assessment not only of linear stability thresholds but also of the nonlinear evolution of unstable equilibria to new configurations that might be far from the original configuration, with significantly different transport properties and magnetic topology. They also enable the self-consistent determination of pressure profiles in non-integrable magnetic topology through the use of highly anisotropic thermal-transport equations. The calculations presented here represent the first demonstration of extended-MHD calculations in strongly-shaped, optimized quasi-symmetric configurations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗

DOE OSTI2021

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing [Book Chapter]

Embryonic morphogenesis is strictly dependent on tight spatiotemporal control of developmental gene expression, which is typically achieved through the concerted activity of multiple enhancers driving cell type-specific expression of a target gene. Mammalian genomes are organized in topologically associated domains, providing a preferred environment and framework for interactions between transcriptional enhancers and gene promoters. While epigenomic profiling and three-dimensional chromatin conformation capture have significantly increased the accuracy of identifying enhancers, assessment of subregional enhancer activities via transgenic reporter assays in mice remains the gold standard for assigning enhancer activity in vivo. Once this activity is defined, the ideal method to explore the functional necessity of a transcriptional enhancer and its contribution to target gene dosage and morphological or physiological processes is deletion of the enhancer sequence from the mouse genome. Here we present detailed protocols for efficient introduction of enhancer-reporter transgenes and CRISPR-mediated genomic deletions into the mouse genome, including a step-by-step guide for pronuclear microinjection of fertilized mouse eggs. We provide instructions for the assembly and genomic integration of enhancer-reporter cassettes that have been used for validation of thousands of putative enhancer sequences accessible through the VISTA enhancer browser, including a recently published method for robust site-directed transgenesis at the H11 safe-harbor locus. Together, these methods enable rapid and large-scale assessment of enhancer activities and sequence variants in mice, which is essential to understand mammalian genome function and genetic diseases.

cis-regulatory elements↗

DOE OSTI2026

Computational prediction of ferromagnetic 𝐴⁢𝑇 6 ⁢𝑋 6 kagome compounds

We present a systematic high-throughput density-functional-theory investigation of the structural and magnetic stability of 312 substitutional compounds in the magnetic kagome 𝐴⁢𝑇 6⁢ 𝑋 6 family. Our screening confirms the stability of many previously reported structures and predicts several additional stable candidates. Within collinear spin configurations, we find that Fe-based systems predominantly adopt antiferromagnetic ground states, whereas Mn-based analogs exhibit a more balanced distribution between ferromagnetic and antiferromagnetic order. For compounds exhibiting several nearly degenerate collinear configurations, we analyze the nature of their magnetic ground states, assess the possible emergence of noncollinear order, and discuss the limitations and uncertainties inherent to standard density-functional approaches. Our electronic structure analysis further reveals that predicted ferromagnetic kagome systems display characteristic features of topological metals, with rich magnetic configurations that can be tuned by chemical substitution. Altogether, these ferromagnetic kagome compounds constitute a broad and still largely unexplored materials platform for the emergence of exciting magnetotransport phenomena.

Density functional calculations↗

DOE OSTI2022

Understanding Heterogeneities in Quantum Materials

Quantum materials are usually heterogeneous, with structural defects, impurities, surfaces, edges, interfaces, and disorder. These heterogeneities are sometimes viewed as liabilities within conventional systems; however, their electronic and magnetic structures often define and affect the quantum phenomena such as coherence, interaction, entanglement, and topological effects in the host system. Therefore, a critical need is to understand the roles of heterogeneities in order to endow materials with new quantum functions for energy and quantum information science applications. In this article, several representative examples are reviewed on the recent progress in connecting the heterogeneities to the quantum behaviors of real materials. Specifically, three intertwined topic areas are assessed: i) Reveal the structural, electronic, magnetic, vibrational, and optical degrees of freedom of heterogeneities. ii) Understand the effect of heterogeneities on the behaviors of quantum states in host material systems. iii) Control heterogeneities for new quantum functions. This progress is achieved by establishing the atomistic-level structure-property relationships associated with heterogeneities in quantum materials. Finally, the understanding of the interactions between electronic, magnetic, photonic, and vibrational states of heterogeneities enables the design of new quantum materials, including topological matter and quantum light emitters based on heterogenous 2D materials.

36 MATERIALS SCIENCE↗