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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Role of backbone strain in de novo design of complex α/β protein structures

Abstract We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Band Structure and Charge Ordering of Dirac Semimetal EuAl 4 at Low Temperatures

In this article, EuAl 4 is proposed to host a topological Hall state. This material also undergoes four consecutive antiferromagnetic (AFM) transitions upon cooling below T N1 = 15.4 K in the presence of charge density wave (CDW) order that sets in below T CDW = 140 K. We use angle-resolved photoemission spectroscopy and density-functional-theory calculations to study how magnetic ordering affects the electronic properties in EuAl 4 . Here, we found changes in the band structure upon each of the four consecutive AFM transitions including band splitting, renormalizations, and appearance of new bands forming additional Fermi sheets. In addition we also found significant enhancement of the quasiparticles’ lifetime due to suppression of spin flip scattering, similar to what was previously reported for ferromagnetic EuCd 2 As 2 . Surprisingly, we observe that most significant changes in electronic properties occur not at T N1 , but instead at the AFM3 to AFM4 transition, which coincides with the largest drop in resistivity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Optimal dimensionality selection for independent component analysis of transcriptomic data

Independent component analysis is an unsupervised machine learning algorithm that separates a set of mixed signals into a set of statistically independent source signals. Applied to high-quality gene expression datasets, independent component analysis effectively reveals both the source signals of the transcriptome as co-regulated gene sets, and the activity levels of the underlying regulators across diverse experimental conditions. Two major variables that affect the final gene sets are the diversity of the expression profiles contained in the underlying data, and the user-defined number of independent components, or dimensionality, to compute. Availability of high-quality transcriptomic datasets has grown exponentially as high-throughput technologies have advanced; however, optimal dimensionality selection remains an open question. We computed independent components across a range of dimensionalities for four gene expression datasets with varying dimensions (both in terms of number of genes and number of samples). We computed the correlation between independent components across different dimensionalities to understand how the overall structure evolves as the number of user-defined components increases. We then measured how well the resulting gene clusters reflected known regulatory mechanisms, and developed a set of metrics to assess the accuracy of the decomposition at a given dimension. We found that over-decomposition results in many independent components dominated by a single gene, whereas under-decomposition results in independent components that poorly capture the known regulatory structure. From these results, we developed a new method, called OptICA, for finding the optimal dimensionality that controls for both over- and under-decomposition. Specifically, OptICA selects the highest dimension that produces a low number of components that are dominated by a single gene. We show that OptICA outperforms two previously proposed methods for selecting the number of independent components across four transcriptomic databases of varying sizes. OptICA avoids both over-decomposition and under-decomposition of transcriptomic datasets resulting in the best representation of the organism’s underlying transcriptional regulatory network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A Geometric Measure Theory Approach to Identify Complex Structural Features on Soft Matter Surfaces

The structural features that protrude above or below a soft matter interface are well-known to be related to interfacially mediated chemical reactivity and transport processes. It is a challenge to develop a robust algorithm for identifying these organized surface structures, as the morphology can be highly varied and they may exist on top of an interface containing significant interfacial roughness. A new algorithm that employs concepts from geometric measure theory, algebraic topology, and optimization is developed to identify candidate structures at a soft matter surface, and then, using a probabilistic approach, to rank their likelihood of being a complex structural feature. The algorithm is tested for a surfactant laden water/oil interface, where it is robust to identifying protrusions responsible for water transport against a set identified by visual inspection. To our knowledge, this is the first example of applying geometric measure theory to analyze the properties of a chemical/materials science system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗
DOE OSTI2020

Adaptive Machine Learning for Bragg Coherent Diffraction Imaging (BCDI) of 3D Electron Density Maps with Application to La 2-x Ba x CuO 4 (LBCO) High Temperature Superconductor Studies [PowerPoint]

Understanding mesoscale heterogeneity is important for evaluating fatigue and failure of structural materials and for manufacturing processes. Data-driven tools can facilitate in guiding effort investment (measurements and computations) at various stages of the materials development. Our 3D reconstruction approach is to find a set of coefficients which define a bounding surface of the electron density. Data for training the 3D CNN was generated by sampling coefficients from uniform distributions. Test vs. prediction values are shown for the 28 even-valued coefficients for 1000 test structures, with the best and worst performers highlighted. The adaptive part of this work utilized a model independent extremum seeking (ES). The predictions of the CNN were used as the starting point for the ES algorithm. The convergence of the ES algorithm for 3 different structures is illustrated, and the robustness of the adaptive ML approach was demonstrated on experimentally measured 3D crystal from high energy diffraction microscopy. Reconstruction of a non-uniform density volume with different levels of Poisson noise is also shown. Preliminary attempts at reconstructing measured La 2-x Ba x CuO 4 diffraction patterns have so far failed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Improved Accuracy in Semi-Experimental Structure Determination by Resolving Problems Associated with Rotation of Principal Inertial Axes of Isotopologues: Structures of 1,3-Oxazole ( c -C 3 H 3 NO)

The rotational spectrum of the normal isotopologue of 1,3-oxazole (c-C 3 H 3 NO) was observed from 43 to 750 GHz. Over 3900 transitions for the ground vibrational state are measured, assigned, and least-squares fit to sextic centrifugally distorted-rotor Hamiltonians. The measured frequencies and resulting spectroscopic constants from this extended spectral range, combined with previous measurements of the nuclear quadrupole coupling constants, will facilitate astronomical searches for oxazole across the majority of the range of modern radiotelescopes. Spectra for a set of 30 oxazole isotopologues, which include multiple isotopic substitutions of each atom, are used to determine the first semi-experimental equilibrium ($r$$^{SE}_{e}$) structure and semi-experimental substitution structure ($r$$^{SE}_{e}$), each using CCSD(T) computed values for the vibration–rotation interaction and electron-mass corrections. The large number of isotopologues, including 21 isotopologues observed for the first time, and the redundant substitutions of each atom provide sufficient spectroscopic information to determine the $r$$^{SE}_{e}$ structure with the expected high level of accuracy and precision (0.0001 or 0.0002 Å in bond distances and 0.013 to 0.025° in bond angles). In the course of this study, we analyzed a known issue for some $r$$^{SE}_{e}$ structure determinations of near-oblate asymmetric tops in which inclusion of individual isotopologues degrades the structure determination. We demonstrate that this problem primarily arises from the difference in the values of the computed vibration–rotation interaction corrections as evaluated at the computed re geometry vs the $r$$^{SE}_{e}$ geometry of the “real” molecule. Our solution to this problem substantially improves the $r$$^{SE}_{e}$ structure of oxazole and likely can be generalized to many other molecules.

Chemical structure↗
DOE OSTI2022

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Alamo multiphysics solver for phase field simulations with strong-form mechanics and block structured adaptive mesh refinement

Alamo is a high-performance scientific code that uses block-structured adaptive mesh refinement to solve such problems as: the ignition and burn of solid rocket propellant, plasticity, damage and fracture in materials undergoing loading, and the interaction of compressible flow with eroding solid materials. Alamo is powered by AMReX, and provides a set of unique methods, models, and algorithms that enable it to solve solid-mechanics problems (coupled to other physical behavior such as fluid flow or thermal diffusion) using the power of block-structured adaptive mesh refinement.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Golden ratio in venation patterns of dragonfly wings

Abstract The vein pattern in insect wings allows this lightweight structure to carry multiple biological functions. Here, an investigation of the angular distribution of the vein struts in dragonfly wings revealed that the golden angle or golden ratio dominates the venation patterns. We find that the golden angle dominates the intervein angles in regions where thin veins and membranes demand strength reinforcement. A golden ratio partition method has thus been developed that explains a set of preferred intervein angles in distorted polygon-shaped venation cells throughout the venation pattern in dragonfly wings. These observations provide new evidence that the wing structure is spatially optimized, by the golden rule in nature, for supporting biomechanical functions of dragonfly wings.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Analysis of X-ray images and spectra (aXis2000): A toolkit for the analysis of X-ray spectromicroscopy data

Spectromicroscopy refers to analytical methods that combine imaging and spectroscopy to provide detailed, spatially resolved analytical information about a sample, such as the type and quantitative spatial distributions of chemical components, geometric or magnetic alignment information, crystal structure, etc. The analysis of X-ray images and spectra (aXis2000) software described in this work provides a set of routines within a single, integrated, graphical-oriented package to read, display, manipulate and analyze spectromicroscopy data, with particular focus on soft X-ray spectromicroscopy methods such as scanning transmission X-ray microscopy (STXM), X-ray photoemission electron microscopy (XPEEM), scanning photoelectron X-ray microscopy (SPEM) and transmission X-ray microscopy (TXM). Here, this free software is described and compared to other software that can provide similar or complementary capabilities. Examples of spectromicroscopic analyses using advanced features of aXis2000 are provided.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Commutative Algebra Modeling in Materials Science – A Case Study on Metal–Organic Frameworks (MOFs)

Metal-organic frameworks (MOFs) are a class of important crystalline and highly porous materials whose hierarchical geometry and chemistry hinder interpretable predictions in materials properties. Commutative algebra is a branch of abstract algebra that has been rarely applied in data and material sciences. We introduce the first ever commutative algebra modeling and prediction in materials science. Specifically, category-specific commutative algebra (CSCA) is proposed as a new framework for MOF representation and learning. It integrates element-based categorization with multiscale algebraic invariants to encode both local coordination motifs and global network organization of MOFs. These algebraically consistent, chemically aware representations enable compact, interpretable, and data efficient modeling of MOF properties such as Henry’s constants and uptake capacities for common gases. Compared to traditional geometric and graph-based approaches, CSCA achieves comparable or superior predictive accuracy while substantially improving interpretability and stability across data sets. By aligning commutative algebra with the chemical hierarchy, the CSCA establishes a rigorous and generalizable paradigm for understanding structure and property relationships in porous materials and provides a nonlinear algebra-based framework for data-driven material discovery.

Khaemba, Caleb S.↗
DOE OSTI2021

Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion

Persistent anion binding in a wide range of solution environments is a key challenge that continues to motivate and demand new strategies in synthetic receptor design. Though strong binding in low-polarity solvents has become routine, our ability to maintain high affinities in high-polarity solvents has not yet reached the standard set by nature. Anions are bound and transported regularly in aqueous environments by proteins that use secondary and tertiary structure to isolate anion binding sites from water. Inspired by this principle of solvent exclusion, we created a sequence-defined foldameric capsule whose global minimum conformation displays a helical folded state and is preorganized for 1:1 anion complexation. The high stability of the folded geometry and its ability to exclude solvent were supported by solid-state and solution phase studies. This capsule then withstood a 4-fold increase in solvent dielectric constant (εr) from dichloromethane (9) to acetonitrile (36) while maintaining a high and solvent-independent affinity of 10 5 M –1 ; ΔG ~ 28 kJ mol –1 . This behavior is unusual. More typical of solvent-dependent behavior, Cl – affinities were seen to plummet in control compounds, such as aryl-triazole macrocycles and pentads, with their solvent-exposed binding cavities susceptible to dielectric screening. Finally, dimethyl sulfoxide denatures the foldamer by putative solvent binding, which then lowers the foldamer’s Cl – affinity to normal levels. Furthermore, the design of this capsule demonstrates a new prototype for the development of potent receptors that can operate in polar solvents and has the potential to help manage hydrophilic anions present in the hydrosphere and biosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Rapid sensing of hidden objects and defects using a single-pixel diffractive terahertz sensor

Abstract Terahertz waves offer advantages for nondestructive detection of hidden objects/defects in materials, as they can penetrate most optically-opaque materials. However, existing terahertz inspection systems face throughput and accuracy restrictions due to their limited imaging speed and resolution. Furthermore, machine-vision-based systems using large-pixel-count imaging encounter bottlenecks due to their data storage, transmission and processing requirements. Here, we report a diffractive sensor that rapidly detects hidden defects/objects within a 3D sample using a single-pixel terahertz detector, eliminating sample scanning or image formation/processing. Leveraging deep-learning-optimized diffractive layers, this diffractive sensor can all-optically probe the 3D structural information of samples by outputting a spectrum, directly indicating the presence/absence of hidden structures or defects. We experimentally validated this framework using a single-pixel terahertz time-domain spectroscopy set-up and 3D-printed diffractive layers, successfully detecting unknown hidden defects inside silicon samples. This technique is valuable for applications including security screening, biomedical sensing and industrial quality control.

Li, Jingxi (ORCID:0000000165958680)↗
DOE OSTI2023

Scalable generalized screening for high-order terms in the many-body expansion: Algorithm, open-source implementation, and demonstration

The many-body expansion lies at the heart of numerous fragment-based methods that are intended to sidestep the nonlinear scaling of ab initio quantum chemistry, making electronic structure calculations feasible in large systems. In principle, inclusion of higher-order n-body terms ought to improve the accuracy in a controllable way, but unfavorable combinatorics often defeats this in practice and applications with n ≥ 4 are rare. Here, we outline an algorithm to overcome this combinatorial bottleneck, based on a bottom-up approach to energy-based screening. This is implemented within a new open-source software application (“Fragme∩t”), which is integrated with a lightweight semi-empirical method that is used to cull subsystems, attenuating the combinatorial growth of higher-order terms in the graph that is used to manage the calculations. This facilitates applications of unprecedented size, and we report four-body calculations in (H2O)64 clusters that afford relative energies within 0.1 kcal/mol/monomer of the supersystem result using less than 10% of the unique subsystems. We also report n-body calculations in (H2O)20 clusters up to n = 8, at which point the expansion terminates naturally due to screening. These are the largest n-body calculations reported to date using ab initio electronic structure theory, and they confirm that high-order n-body terms are mostly artifacts of basis-set superposition error.

Chemistry↗
DOE OSTI2021

Scalar fields in 3D asymptotically flat higher-spin gravity

Abstract In this work we construct a novel associative algebra and use it to define a theory of higher-spin gravity in (2 + 1)-dimensional asymptotically flat spacetimes. Our construction is based on a quotient of the universal enveloping algebra of i s l ( 2 , R ) with respect to the ideal generated by its Casimir elements, the mass squared M 2 and the three-dimensional analogue of the square of the Pauli–Lubanski vector S and propose to call the resulting associative algebra i h s ( M 2 , S ) . We provide a definition of its generators and even though we are not yet able to provide the complete set of multiplication rules of this algebra our analysis allows us to study many interesting and relevant sub-structures of i h s ( M 2 , S ) . We then show how to consistently couple a scalar field to an i h s ( M 2 , S ) higher-spin gauge theory.

Physics↗
DOE OSTI2022

Actinide opacities for modelling the spectra and light curves of kilonovae

ABSTRACT We extend previous ab initio calculations of lanthanide opacities to include a complete set of actinide opacities for use in the modelling of kilonova (KN) light curves and spectra. Detailed, fine-structure line features are generated using the configuration-interaction approach. These actinide opacities display similar trends to those observed for lanthanide opacities, such as the lighter actinides producing higher opacity than the heavier ones for relevant conditions in the dynamical ejecta. A line-binned treatment is employed to pre-compute opacity tables for 14 actinide elements (89 ≤ Z ≤ 102) over a grid of relevant temperatures and densities. These tabular opacities will be made publicly available for general usage in KN modelling. We demonstrate the usefulness of these opacities in KN simulations by exploring the sensitivity of light curves and spectra to different actinide abundance distributions that are predicted by different nuclear theories, as well as to different choices of ejecta mass and velocity. We find very little sensitivity to the two considered distributions, indicating that opacities for actinides with Z ≥ 99 do not contribute strongly. On the other hand, a single actinide element, protactinium, is found to produce faint spectral features in the far-infrared at late times (5–7 d post merger). More generally, we find that the choice of ejecta mass and velocity have the most significant effect on KN emission for this study.

79 ASTRONOMY AND ASTROPHYSICS↗