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DOE OSTI2016

Analysis and Implications of Structural Complexity in Low Lattice Thermal Conductivity High Thermoelectric Performance PbTe–PbSnS 2 Composites

The high-performance PbTe-SnTe-PbS-thermoelectric system forms a completely new composite PbTe PbSnS2 with high n-type figure of merit. Electron diffraction and high-resolution electron microscopy characterization of the thermoelectric composite PbTe + 25% PbSnS2 reveals that the system is nanostructured, with PbSnS(2)nanocrystals in the range Of 80 to 500 nm in size. In most of the cases, they are endotaxially grown within the PbTe matrix. Three independent crystal superstructures were observed for the PbSnS2 inclusions, originating from the same parent SnS-type structure. The presence of the parent structure is not excluded. Modified structural models for two of the superstructures observed in the PbSnS2 precipitates are proposed: Often, more than one of the structural phases am observed In the same nanocrystal, providing one extra phonon scattering factor in the system. Evidence was also found for the growth process of the nanocrystals, starting from PbS and followed by gradual dissolving of SnS. Our findings suggest that this nanostructured thermoelectric composite exhibits unique structural complexity, which Contributes to the low lattice thermal :conductivity reported for these nanocomposite materials.

Ioannidou, Chrysoula↗

DOE OSTI2021

Structural basis for virulence regulation in Vibrio cholerae by unsaturated fatty acid components of bile

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99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

A Two-Stage Approach for Routing Multiple Unmanned Aerial Vehicles with Stochastic Fuel Consumption

The past decade has seen a substantial increase in the use of small unmanned aerial vehicles (UAVs) in both civil and military applications. This article addresses an important aspect of refueling in the context of routing multiple small UAVs to complete a surveillance or data collection mission. Specifically, this article formulates a multiple-UAV routing problem with the refueling constraint of minimizing the overall fuel consumption for all the vehicles as a two-stage stochastic optimization problem with uncertainty associated with the fuel consumption of each vehicle. The two-stage model allows for the application of sample average approximation (SAA). Although the SAA solution asymptotically converges to the optimal solution for the two-stage model, the SAA run time can be prohibitive for medium- and large-scale test instances. Hence, we develop a tabu search-based heuristic that exploits the model structure while considering the uncertainty in fuel consumption. Extensive computational experiments corroborate the benefits of the two-stage model compared to a deterministic model and the effectiveness of the heuristic for obtaining high-quality solutions.

42 ENGINEERING↗

DOE OSTI2017

Advanced Mechanistic 3D Spatial Modeling and Analysis Methods to Accurately Represent Nuclear Facility External Event Scenarios

Probabilistic risk assessment of nuclear power plants initially focused on events initiated by internal faults at the plant, rather than external hazards including earthquakes and flooding. Although the importance of external hazards risk analysis is now well recognized, the methods for analyzing low probability external hazards rely heavily on subjective judgment of specialists, often resulting in substantial conservatism. This research developed a framework to integrate the risk of seismic and flooding events using realistic structural models and simulation of response of nuclear structures. The results of four application case studies are presented.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

Refining perovskite structures to pair distribution function data using collective Glazer modes as a basis

Structural modelling of octahedral tilts in perovskites is typically carried out using the symmetry constraints of the resulting space group. In most cases, this introduces more degrees of freedom than those strictly necessary to describe only the octahedral tilts. It can therefore be a challenge to disentangle the octahedral tilts from other structural distortions such as cation displacements and octahedral distortions. This paper reports the development of constraints for modelling pure octahedral tilts and implementation of the constraints in diffpy-CMI, a powerful package to analyse pair distribution function (PDF) data. The model in the program allows features in the PDF that come from rigid tilts to be separated from non-rigid relaxations, providing an intuitive picture of the tilting. The model has many fewer refinable variables than the unconstrained space group fits and provides robust and stable refinements of the tilt components. It further demonstrates the use of the model on the canonical tilted perovskite CaTiO 3 which has the known Glazer tilt system α + β – β – . The Glazer model fits comparably to the corresponding space-group model Pnma below r = 14 Å and becomes progressively worse than the space-group model at higher r due to non-rigid distortions in the real material.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Modeling inter‐reader variability in clinical target volume delineation for soft tissue sarcomas using diffusion model

Abstract Background Accurate delineation of the clinical target volume (CTV) is essential in the radiotherapy treatment of soft tissue sarcomas. However, this process is subject to inter‐reader variability due to the need for clinical assessment of risk and extent of potential microscopic spread. This can lead to inconsistencies in treatment planning, potentially impacting treatment outcomes. Most existing automatic CTV delineation methods do not account for this variability and can only generate a single CTV for each case. Purpose This study aims to develop a deep learning‐based technique to generate multiple CTV contours for each case, simulating the inter‐reader variability in the clinical practice. Methods We employed a publicly available dataset consisting of fluorodeoxyglucose positron emission tomography (FDG‐PET), x‐ray computed tomography (CT), and pre‐contrast T1‐weighted magnetic resonance imaging (MRI) scans from 51 patients with soft tissue sarcoma, along with an independent validation set containing five additional patients. An experienced reader drew a contour of the gross tumor volume (GTV) for each patient based on multi‐modality images. Subsequently, two additional readers, together with the first one, were responsible for contouring three CTVs in total based on the GTV. We developed a diffusion model‐based deep learning method that is capable of generating arbitrary number of different and plausible CTVs to mimic the inter‐reader variability in CTV delineation. The proposed model incorporates a separate encoder to extract features from the GTV masks, leveraging the critical role of GTV information in accurate CTV delineation. Results The proposed diffusion model demonstrated superior performance with the highest Dice Index (0.902 compared to values below 0.881 for state‐of‐the‐art models) and the best generalized energy distance (GED) (0.209 compared to values exceeding 0.221 for state‐of‐the‐art models). It also achieved the second‐highest recall and precision metrics among the compared ambiguous image segmentation models. Results from both datasets exhibited consistent trends, reinforcing the reliability of our findings. Additionally, ablation studies exploring different model structures and input configurations highlighted the significance of incorporating prior GTV information for accurate CTV delineation. Conclusions The proposed diffusion model successfully generates multiple plausible CTV contours for soft tissue sarcomas, effectively capturing inter‐reader variability in CTV delineation.

Dong, Yafei [Yale Biomedical Imaging Institute Yal↗

DOE OSTI2023

Synthesis, crystal and electronic structure of the Zintl phase Ba 16 Sb 11 . A case study uncovering greater structural complexity via monoclinic distortion of the tetragonal Ca 16 Sb 11 structure type

The binary Zintl phase Ba 16 Sb 11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba 16 Sb 11 appears to crystallize in the tetragonal Ca 16 Sb 11 structure type (space group $P\bar{4}2_1$m with a=13.5647(9) Å, c=12.4124(12)Å, Z=2, R 1 = 3.14%; wR 2 = 4.77%), there exists an extensive structural disorder. Some Ba 16 Sb 11 crystals were found to be monoclinic and the structure was solved and refined in space group P2 1 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R 1 =5.84 %; wR 2 =9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba 32 Sb 22 (=2×Ba 16 Sb 11 ) can be rationalized as (Ba 2+ ) 32 (Sb 3– ) 20 [Sb 2 ] 4– . Notably, the partitioning of the valence electrons is done taking into an account the homoatomic Sb–Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba 16 Sb 11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Equity implications of net-zero emissions: A multi-model analysis of energy expenditures across income classes under economy-wide deep decarbonization policies

With companies, states, and countries targeting net-zero emissions around midcentury, there are questions about how these targets alter household welfare and finances, including distributional effects across income groups. This paper examines the distributional dimensions of technology transitions and net-zero policies with a focus on welfare impacts across household incomes. The analysis uses a model intercomparison with a range of energy-economy models using harmonized policy scenarios reaching economy-wide, net-zero CO 2 emissions across the United States in 2050. Here we employ a novel linking approach that connects output from detailed energy system models with survey microdata on energy expenditures across income classes to provide distributional analysis of net-zero policies. Although there are differences in model structure and input assumptions, we find broad agreement in qualitative trends in policy incidence and energy burdens across income groups. Models generally agree that direct energy expenditures for many households will likely decline over time with reference and net-zero policies. However, there is variation in the extent of changes relative to current levels, energy burdens relative to reference levels, and electricity expenditures. Policy design, primarily how climate policy revenues are used, has first-order impacts on distributional outcomes. Net-zero policy costs, in both absolute and relative terms, are unevenly distributed across households, and relative increases in energy expenditures are higher for lowest-income households. However, we also find that recycled revenues from climate policies have countervailing effects when rebated on a per-capita basis, offsetting higher energy burdens and potentially even leading to net progressive outcomes. Model results also show carbon Laffer curves, where revenues from net-zero policies increase but then decline with higher stringencies, which can diminish the progressive effects of climate policies. We also illustrate how using annual income deciles for distributional analysis instead of expenditure deciles can overstate the progressivity of emissions policies by overweighting revenue impacts on the lowest-income deciles.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Folded network and structural transition in molten tin

The fundamental relationships between the structure and properties of liquids are far from being well understood. For instance, the structural origins of many liquid anomalies still remain unclear, but liquid-liquid transitions (LLT) are believed to hold a key. However, experimental demonstrations of LLTs have been rather challenging. Here, we report experimental and theoretical evidence of a second-order-like LLT in molten tin, one which favors a percolating covalent bond network at high temperatures. The observed structural transition originates from the fluctuating metallic/covalent behavior of atomic bonding, and consequently a new paradigm of liquid structure emerges. The liquid structure, described in the form of a folded network, bridges two well-established structural models for disordered systems, i.e., the random packing of hard-spheres and a continuous random network, offering a large structural midground for liquids and glasses. Our findings provide an unparalleled physical picture of the atomic arrangement for a plethora of liquids, shedding light on the thermodynamic and dynamic anomalies of liquids but also entailing far-reaching implications for studying liquid polyamorphism and dynamical transitions in liquids.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing

Antibody therapeutics are one of the most important classes of drugs. Antibody structures have become an integral part of predicting the behavior of potential therapeutics, either directly or as the basis of modeling. Structures of Fab:antigen complexes have even greater value. While the crystallization and structure determination of Fabs is easy relative to many other protein classes, especially membrane proteins, broad screening and optimization of crystalline hits is still necessary. Through a comprehensive review of rabbit Fab crystal contacts and their incompatibility with human Fabs, we identified a small secondary structural element from the rabbit light chain constant domain potentially responsible for hindering the crystallization of human Fabs. Upon replacing the human kappa constant domain FG loop (HQGLSSP) with the two residue shorter rabbit loop (QGTTS), we dramatically improved the crystallization of human Fabs and Fab:antigen complexes. Our design, which we call “Crystal Kappa”, enables rapid crystallization of human fabs and fab complexes in a broad range of conditions, with less material in smaller screens or from dilute solutions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Sierra/SD – User’s Guide for NasGen – 5.20

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Sierra/SD – User’s Guide for NasGen – 5.18

NasGen provides a path for migration of structural models from NASTRAN bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Presto). Many tools at Sandia National Labs (SNL) use the Exodus format. NasGen was written specifically for Salinas and Presto but should be usable with a number of these packages.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Sierra/SD – User’s Guide for NasGen (V.5.16)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Sierra/SD – User’s Guide for NasGen – 5.22

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Sierra/SD – User’s Guide for NasGen (V.5.24)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Sierra/SD – User’s Guide for NasGen – 5.28

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Sierra/SD– User’s Guide for NasGen - 5.30

NasGen provides a path for migration of structural models from NASTRAN bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Presto). Many tools at Sandia National Labs use the Exodus format. NasGen was written specifically for Salinas and Presto but should be usable with a number of these packages.

97 MATHEMATICS AND COMPUTING↗