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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae

ATP binding cassette (ABC) transporters are the primary means by which bacteria acquire trace elements from the environment. They rely on solute binding proteins (SBPs) to bind the relevant substrate and deliver it to the integral membrane permease for ATP-powered import into the cytoplasm. SBPs of cluster A-I are known to facilitate the transport of essential metals zinc, manganese, and iron, and many have been characterized to date. A group of ABC transporter operons dubbed zinc-regulated genes (zrg) have recently been shown to transport zinc with putative SBPs (zrgA) bearing no homology to the classical cluster A-I family, and a recent crystal structure of a representative protein from Pseudomonas aeruginosa shows no structural similarity to classical SBPs. Thus, the ZrgA proteins appear to represent a newly discovered family of zinc SBPs widespread among Gram-negative bacteria, including human pathogens. Here, we have determined the crystal structure of ZrgA from Vibrio cholerae and characterized its zinc binding in vitro and function in vivo. We also assessed the role of a histidine-rich sequence that appears to be a hallmark of ZrgA proteins that is particularly long in V. cholerae ZrgA. The results show that the zrgA gene is critical to the function of the operon, consistent with a function as an SBP in this system. Further, the His-rich region is not essential to the function of ZrgA, but it does provide additional zinc binding sites in vitro. The structure and zinc binding data for ZrgA reveal interesting differences between it and its homologue from P. aeruginosa, illustrating diversity within this little-studied protein family.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Structure and evolution of time-dependent intermediate shocks

A quantitative description of time-dependent intermediate shocks is formulated using the Cohen-Kulsrud-Burgers equations. In noncoplanar Riemann problems, time-dependent two-three transition intermediate shocks evolve in time as a localized self-similar structure whose strength decreases as 1/the square root of t, and whose width expands as the square root of t. Time-dependent intermediate shocks offer a way of solving the noncoplanar MHD Riemann problem.

Wu, C. C.↗

DOE OSTI2021

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Cohesive and adhesive degradation in PET-based photovoltaic backsheets subjected to ultraviolet accelerated weathering

Delamination between layers in photovoltaic (PV) backsheets is often reported in the literature, causing voids that can collect moisture, diminish module backside heat dissipation, and reduce the backsheet’s effectiveness as a physical barrier. While backsheets with weathering-resistant fluoropolymer outer layers have traditionally been used in modules, more recent backsheets using non-fluoropolymer outer layers, such as polyethylene terephthalate (PET), have been developed. These backsheets have shown signs of premature degradation, and their adhesion degradation, in particular, has not been widely studied. In the present work, the single cantilever beam (SCB) adhesion test was used to quantify the adhesion energy in two commercially available PET-based backsheets. To study the effect of minor changes in formulation, the backsheets were obtained from same manufacturer and product line but during different years. To study the effect of environmental variables on adhesion degradation, the backsheets were subjected to artificial weathering at controlled temperature, humidity, and ultraviolet (UV) radiation in an indoor weathering chamber, and the adhesion energy was quantified at several intervals of exposure time. Layering structure, composition, and adhesion failure mode were compared between the backsheets, using Raman and infrared spectroscopy and thermogravimetric analysis. The results show a large difference in initial (unexposed) adhesion energy between the backsheets, despite very similar structures and compositions. Following exposure, adhesion energy dropped significantly, primarily due to thermo-hydrolytic degradation of the polyurethane (PU)-based adhesive layers. Significant UV-induced adhesion degradation of the PET outer layer surface was also observed. The study represents an important step in understanding adhesion degradation in PET-based backsheets, suggesting ways in which adhesion integrity – and, correspondingly, module service life – can be improved.

14 SOLAR ENERGY↗

NASA NTRS1976

The structure of lightning flashes HF-UHF: 12 September 1975, Atlanta, Georgia

Simultaneous measurement of sferics at 3, 30, 139, and 295 MHz were made during thunderstorms. Wideband electronics and an analogue tape recorder continuously recorded the radiation from lightning with about 300 kHz of bandwidth. The data were obtained during the passage of a cold front. Flashing rate, burst rate and the structure of individual flashes were recorded. The record of a typical flash begins with a sudden burst of closely spaced pulses whose temporal structure is typical of the stepped leader, and ends in a large pulse suggestive of a first return stroke. The remainder of the flash consists of a sequence of pulses of varying amplitude separated by quiet periods of the order of milliseconds. The shape of these pulses and the temporal structure suggest that the first few large pulses are return strokes. Other discharges begin with widely spaced discrete pulses and resemble the preceding discharge less the leader and return stroke phase. The radiation exhibits a similar structure, at each of the frequencies monitored.

Levine, D. M.↗

NASA NTRS1989

Alternating-Gradient Photodetector For Far Infrared

Proposed detector of photons of wavelengths in range of 30 to 200 micrometer made of alternating layers of lightly and heavily negatively doped germanium. Formed in sequence by conventional chemical-vapor deposition. Alternating-gradient structure enhances collection of photogenerated charge carriers while suppressing dark current, thus achieving high detectivity. Alternating layers of n+ and n- germanium provides high detectivity in far-infrared spectral region. Also possible to make similar structures with positive doping and with other semiconductors as silicon or gallium arsenide to obtain various spectral response.

Overhauser, Albert W.↗

NASA NTRSDate not supplied

3D Phase-Field Simulations of Pattern Formation During Freeze Casting

We present the results of a combined experimental and phase-field modeling study of pattern formation during freeze casting. Those studies use unidirectional freezing of simple binary liquid mixtures of water and sugars (sucrose and trehalose) in a temperature gradient, which suffice to produce hierarchical templated structures similar to those observed in more complex multi-component freeze-cast systems including lamellae, undulated ridges, and more exotic “jellyfish-like” substructures. Multiscale 3D phase-field simulations reproduce remarkably well those structures quantitatively and identify key properties of the ice-water interface that control their formation. They further reveal that lamellae form as a result of a novel symmetry-breaking secondary instability of partially faceted cellular structures and pinpoint additional secondary instability mechanisms giving rise to smaller-scale substructures.

Kaihua Ji↗

NASA NTRSDate not supplied

3D Phase-Field Simulations of Pattern Formation During Freeze Casting

Kaihua Ji↗

DOE OSTI2021

Centrosymmetric or Noncentrosymmetric? Transition Metals Talking in K 2 TGe 3 S 8 (T = Co, Fe)

Two new quaternary sulfides K 2 TGe 3 S 8 (T=Co, Fe) have been synthesized by a high-temperature solid-state routine and flux growth method. The crystal growth process of K 2 TGe 3 S 8 (T=Co, Fe) was elucidated by in-situ powder X-ray diffraction and DSC thermal analysis. The mm-sized crystals of K 2 TGe 3 S 8 (T=Co, Fe) were grown. K 2 CoGe 3 S 8 crystallizes in a new structure type in centrosymmetric space group P1¯ (No. 2) with unit cell parameters of a = 7.016(1) Å, b = 7.770(1)Å, c = 14.342(1) Å, α = 93.80(1)°, β = 92.65(1)°, γ = 114.04(1)°. K 2 FeGe 3 S 8 crystallizes in K 2 FeGe 3 Se 8 structure type and the noncentrosymmetric space group P2 1 (No. 4) with unit cell parameters of a = 7.1089(5)Å, b = 11.8823(8)Å, c = 16.7588(11)Å, β = 96.604(2)°. There is a high structural similarity between K 2 CoGe 3 S 8 and K 2 FeGe 3 S 8 . The larger volume coupled with higher degrees of distortion of [FeS 4 ] tetrahedra compared to [CoS 4 ] tetrahedra accounts for the structure’s shift from centrosymmetric to noncentrosymmetric. The theory simulation confirms that [TS 4 ]T= Co or Fe tetrahedra play a crucial role in controlling the structure and properties of K 2 TGe 3 S 8 (T = Co, Fe). The measured optical bandgaps of K 2 CoGe 3 S 8 and K 2 FeGe 3 S 8 are 2.1(1) eV and 2.6(1) eV respectively. K 2 FeGe 3 S 8 shows antiferromagnetic ordering at 24K while no magnetic ordering was detected in K 2 CoGe 3 S 8 . In conclusion, the magnetic measurements also demonstrate the divalent nature of transition metals in K 2 TGe 3 S 8 (T = Co, Fe).

36 MATERIALS SCIENCE↗

NASA NTRS1981

VLA observations of solar active regions at 6 cm wavelength

Synthesized maps of two solar active regions obtained from observations with the Very Large Array (VLA) with 9-arcsec resolution are presented. The most intense sources in these regions are found to be associated with filamentary structures and magnetic neutral lines as shown in H-alpha and photospheric magnetograms. These sources are not located directly over sunspots in disagreement with earlier observations. EUV and X-ray observations have suggested that similar structures should be visible at cm wavelengths around but, outside of, sunspots if the magnetic field is sufficiently strong. These results are consistent with the locations of hot (greater than 1,000,000 K) plasmas in active regions expected from generalization based on optical photographs. Given the sizes of the radio sources, the volume emission measures of soft X-rays observed from OSO-8 rule out the possibility of thermal bremsstrahlung being of any significance, as far as the 6 cm emission is concerned. Therefore, gyroresonance absorption process is the most likely cause of 6 cm emission from these sources, and its likelihood is enhanced by the magnetic field geometry that is known to exist over filaments and neutral lines.

Kundu, M. R.↗

NASA NTRS1984

Intermediate phases in some rare earth-ruthenium systems

The phase equilibria and crystal structures of intermediate phases were investigated in eight representative RE-Ru systems using powder X-ray diffraction and metallographic techniques. The Fe3C, Mn5C2 and Er5Ru3 structures occur in all but the Ce-Ru systems. Phases analogous to Er5Ru3 possess an unknown crystal structure similar to Er5Rh3(I). MgCu2 and MgZn2 type Laves phases are encountered in the light rare earth and heavy rare earth systems, respectively, and RERu2 phases, where RE = Nd and Sm, possess both the Laves phase structures. An intermediate phase, NdRu, with an unknown structure, occurs only in the Nd-Ru system. A bcc structure with 40 atoms per unit cell is encountered in the phases Er3Ru2 and Y3Ru2. The behavior of cerium in Ce-Ru alloys is unique in that four unidentified structures, not encountered in other RE-Ru systems, have been encountered. Also a phase designated as Ce3Ru is found with the Th7Fe3 type structure.

Sharifrazi, P.↗

DOE OSTI2025

Harnessing Nanobodies for Precision Targeting of Proteoforms: Opportunities and Challenges in Therapeutics and Diagnostics

Proteoforms are biologically distinct yet structurally similar proteins that play key roles in driving disease progression but are rarely accounted for in the development of therapeutics and diagnostics. Nanobodies (Nbs) have emerged as a therapeutic and diagnostic “silver bullet” as they possess unique structural and functional attributes that offer advantages over traditional antibodies. One of the most profound advantages of Nbs is the heightened sensitivity and ability to distinguish subtle changes in the conformation of a given protein. Thus, Nbs have significant potential as therapeutic and diagnostic agents that can identify and distinguish specific pathological proteoforms that underlie a given disease. However, there remain significant challenges in obtaining sufficient quantities and purities of specific proteoform antigens that are required for engineering proteoform-specific Nbs. Recent advancements in chemical biology tools for precision proteoform synthesis have made this task feasible for the first time. In this perspective, we discuss the advantages and challenges associated with developing proteoform-specific Nbs and how success in this endeavor will significantly advance the fields of therapeutics and diagnostics.

Antigens↗

NASA NTRS1992

Quasi-linear regime of gravitational instability as a clue to understanding the large-scale structure in the Universe

In the late seventies, an image of the large-scale structure in the Universe began to emerge as a result of the accumulation of the galaxy redshifts. Most of the galaxies are found to concentrate in large filaments and perhaps sheets leaving most of the volume empty. Similar structures were predicted theoretically in the frame of the adiabatic theory of galaxy formation (Zeldovich) and later in the hot dark matter cosmology. However, both scenarios have been ruled out by the observations. With these scenarios the dynamical part of the scenario was also erroneously rejected by many as well. In this talk, I derive the Zeldovich approximation from the exact dynamic equations and show that it is always better than the standard linear approximation. The advantage of the Zeldovich approximation is the greatest in the quasi-linear regime when delta(sub rms) is less than 1 (delta identical to delta(rho)/rho), but the displacement of the matter is essential. The range of scales in the quasi-linear regime depends upon the slope of the initial spectrum and increases with decreasing n, where n is the exponent, if the initial spectrum is approximated by a simple power law P(k) varies as k(exp n).

Shandarin, Sergei F.↗

DOE OSTI2023

Intercalation And High-Pressure Effects On Structural Phase Transitions In Layered As x P 1-x Alloys

This project was aimed at understanding the role of composition, intercalation, and high pressure on the structural evolution of black phosphorous (BP) and layered arsenic phosphorous alloys, As y P 1-y . Under normal conditions, BP is the most stable phase of phosphorous, known as the α-phase, characterized by an orthorhombic honeycomb puckered crystal structure with the Cmca space group. On the other hand, the most stable phase of arsenic is its β-phase, known as gray arsenic (g-As), which has a rhombohedral buckled layered crystal structure with the R3m space group. In a wide range of compositions (y < 0.83), the arsenic phosphorous alloys form the α-phase, known as black arsenic phosphorous (b-As y P 1-y ) with a similar structure to BP. The project was aimed at the synthesis of BP and b-As y P 1-y with different compositions and at studying the structural evolution of these materials during intercalation with alkali metal (especially Li), and under high-pressure conditions. The main goals were to gain a better understanding of these processes and structural changes taking place under these conditions. In particular, the project was aimed at addressing whether such conditions could induce a structural transition between the α- and β-phases. For this, a series of systematic in-situ studies were conducted, including electrochemical lithium intercalation in an in-situ electrochemical cell, and high-pressure experiments in a diamond anvil cell (DAC). Overall, both types of experiments have shown that above a certain composition-dependent threshold level of intercalation or high pressure, the system undergoes phase segregation rather than phase transition. Specifically, the segregation of the excess arsenic was observed, and a single-phase system of b-As y P 1-y transformed into a two-phase system consisting of b-As y P 1-y and g-As, through the following process: 1∗(b-As y P 1-y ) → 1∗(b As y-δ P 1-y ) + δ∗(g-As). Also, the study showed that intercalation and high-pressure are two competing rather than synergistic processes causing at least a partial cancelation of these two factors

36 MATERIALS SCIENCE↗

DOE OSTI2024

Understanding Trace Iron and Chromium Incorporation During Gibbsite Crystallization and Effects on Mineral Dissolution

Incorporation of pollutants, e.g., heavy metals, or critical elements, e.g., lithium, as impurities in mineral phases can significantly affect their mobility or sequestration in the environment. Even when present at low concentrations, impurities can alter the solubility and reactivity of the host mineral. Here, in this study, we investigate the incorporation of trace amounts of iron (Fe 3+ ) and chromium (Cr 3+ ) during the crystal growth of the aluminum (Al 3+ ) hydroxide, gibbsite, a major component of bauxite ores, an important soil mineral, and a dominant mineral phase in stored radioactive wastes. Using a comprehensive suite of analytical techniques, we show that both Cr 3+ and Fe 3+ can be incorporated into the gibbsite lattice during coprecipitation by replacing Al 3+ in octahedral sites. These small amounts are consistent with limited to no structural isomorphism shared between Al 3+ and Cr 3+ /Fe 3+ hydroxide precipitates, nor room temperature miscibility of their isostructural M 2 O 3 oxide forms, in contrast with oxyhydroxide forms where Al 3+ and Fe 3+ share similar structural topologies. Despite the limited uptake of Cr 3+ /Fe 3+ , we show that these impurities have significant implications for gibbsite dissolution behavior. The limited uptake of Cr 3+ /Fe 3+ (e.g. 0.43% Cr 3+ and 0.4% Fe 3+ ), we show that these impurities have significant implications for gibbsite dissolution behavior and subsequent reactivity in complex environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Excess Density as a Descriptor for Electrolyte Solvent Design

Electrolytes mediate interactions between the cathode and anode and determine performance characteristics of batteries. Mixtures of multiple solvents are often used in electrolytes to achieve desired properties, such as viscosity, dielectric constant, boiling point, and melting point. Conventionally, multi-component electrolyte properties are approximated with linear mixing, but in practice, significant deviations are observed. Excess quantities can provide insights into the molecular behavior of the mixture and could form the basis for designing high-performance electrolytes. Here we investigate the excess density of commonly used Li-ion battery solvents such as cyclic carbonates, linear carbonates, ethers, and nitriles with molecular dynamics simulations. We additionally investigate electrolytes consisting of these solvents and a salt. The results smoothly vary with mole percent and are fit to permutation-invariant Redlich-Kister polynomials. Mixtures of similar solvents, such as cyclic-cyclic carbonate mixtures, tend to have excess properties that are lower in magnitude compared to mixtures of dissimilar substances, such as carbonate-nitrile mixtures. We perform experimental testing using our automated test stand, Clio, to provide validation to the observed simulation trends. We quantify the structure similarity using SOAP fingerprints to create a descriptor for excess density, enabling the design of electrolyte properties. To a first approximation, this will allow us to estimate the deviation of a mixture from ideal behavior based solely upon the structural dissimilarity of the components.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Machine Learning for Mapping Multipactor Susceptibility in RF Systems: Capabilities and Generalization Constraints

Multipactor is a surface-driven electron avalanche phenomenon that degrades the performance and reliability of radio-frequency (RF) systems in particle accelerator and vacuum electronics applications. Multipactor behavior in a given device structure is conventionally assessed through susceptibility charts, which provide a parameter-space characterization of the instability. In this work, we assess the capabilities of machine-learning (ML) models to learn and predict such susceptibility charts and analyze the constraints governing their generalization across materials. Using a simulation-derived dataset spanning six distinct secondary-electron-yield material profiles in a canonical two-surface planar geometry, we train supervised regression models and artificial neural networks to predict the time-averaged electron growth rate, δavg, across the relevant parameter space. Model performance is evaluated using metrics that explicitly probe the structure of susceptibility charts, including Intersection over Union, Structural Similarity Index, and correlation analysis. Tree-based ensemble models outperform neural-network models in reconstructing susceptibility regions and in generalizing across material domains. Principal-component analysis reveals disjoint material feature distributions, indicating that the piecewise mode structure of multipactor susceptibility is difficult to represent with a single global model and that generalization is constrained by data coverage rather than by model complexity. An exhaustive reduced-coverage study further shows that sparse material-space coverage can yield mean performance in the same general range but producing large variability in the susceptibility-region overlap. These results clarify the capabilities of ML-based surrogate models for parameter-space characterization of multipactor discharge. They also provide guidance for their appropriate use in RF system design.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration

Abstract Motivation Volumetric 3D object analyses are being applied in research fields such as structural bioinformatics, biophysics, and structural biology, with potential integration of artificial intelligence/machine learning (AI/ML) techniques. One such method, 3D Zernike moments, has proven valuable in analyzing protein structures (e.g., protein fold classification, protein–protein interaction analysis, and molecular dynamics simulations). Their compactness and efficiency make them amenable to large-scale analyses. Established methods for deriving 3D Zernike moments, however, can be inefficient, particularly when higher order terms are required, hindering broader applications. As the volume of experimental and computationally-predicted protein structure information continues to increase, structural biology has become a “big data” science requiring more efficient analysis tools. Results This application note presents a Python-based software package, ZMPY3D, to accelerate computation of 3D Zernike moments by vectorizing the mathematical formulae and using graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow together with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithm development. The ZMPY3D package can be installed via PyPI, and the source code is available from GitHub. Volumetric-based protein 3D structural similarity scores and transform matrix of superposition functionalities have both been implemented, creating a powerful computational tool that will allow the research community to amalgamate 3D Zernike moments with existing AI/ML tools, to advance research and education in protein structure bioinformatics. Availability and implementation ZMPY3D, implemented in Python, is available on GitHub (https://github.com/tawssie/ZMPY3D) and PyPI, released under the GPL License.

Lai, Jhih-Siang (ORCID:0000000156775890)↗