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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2

SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The molecular basis of Human FN3K mediated phosphorylation of glycated substrates

Abstract Glycation, a non-enzymatic post-translational modification occurring on proteins, can be actively reversed via site-specific phosphorylation of the fructose-lysine moiety by FN3K kinase, to impact the cellular function of the target protein. A regulatory axis between FN3K and glycated protein targets has been associated with conditions like diabetes and cancer. However, the molecular basis of this relationship has not been explored so far. Here, we determined a series of crystal structures of HsFN3K in the apo-state, and in complex with different nucleotide analogs together with a sugar substrate mimic to reveal the features important for its kinase activity and substrate recognition. Additionally, the dynamics in sugar substrate binding during the kinase catalytic cycle provide important mechanistic insights into HsFN3K function. Our structural work provides the molecular basis for rational small molecule design targeting FN3K.

Science & Technology - Other Topics↗
DOE OSTI2025

A substrate-multiplexed platform for profiling enzymatic potential of plant family 1 glycosyltransferases

Plants have expanded various biosynthetic enzyme families to produce a wide diversity of natural products; however, most enzymes encoded in plant genomes remain uncharacterized, highlighting the need for new functional genomic approaches. Here, we report a platform enabling the rapid functional characterization of plant family 1 glycosyltransferases, which serve important roles in plant development, defense, and communication. Using substrate-multiplexed reactions, mass spectrometry, and automated analysis, we screen 85 enzymes against a diverse library of 453 natural products, for a total of nearly 40,000 possible reactions. The resulting dataset reveals a widespread promiscuity and a strong preference for planar, hydroxylated aromatic substrates among family 1 glycosyltransferases. We also characterize glycosyltransferases with an unusually wide substrate scope and with a non-canonical Cys-Asp catalytic dyad. This work establishes a widely-applicable enzymatic screening pipeline, reflects the immense glycosylation capability of plants, and has implications in biocatalysis, metabolic engineering, and gene discovery.

Sirirungruang, Sasilada↗
DOE OSTI2021

Thermal stability and diffusion characteristics of ultrathin amorphous carbon films grown on crystalline and nitrogenated silicon substrates by filtered cathodic vacuum arc deposition

Amorphous carbon (a-C) films are widely used as protective overcoats in many technology sectors, principally due to their excellent thermophysical properties and chemical inertness. The growth and thermal stability of sub-5-nm-thick a-C films synthesized by filtered cathodic vacuum arc on pure (crystalline) and nitrogenated (amorphous) silicon substrate surfaces were investigated in this study. Samples of a-C/Si and a-C/SiN x /Si stacks were thermally annealed for various durations and subsequently characterized by high-resolution transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). The TEM images confirmed the continuity and uniformity of the a-C films and the 5-nm-thick SiN x underlayer formed by silicon nitrogenation using radio-frequency sputtering. The EELS analysis of cross-sectional samples revealed the thermal stability of the a-C films and the efficacy of the SiNx underlayer to prevent carbon migration into the silicon substrate, even after prolonged heating. The obtained results provide insight into the important attributes of an underlayer in heated multilayered media for preventing elemental intermixing with the substrate, while preserving the structural stability of the a-C film at the stack surface. An important contribution of this investigation is the establishment of an experimental framework for accurately assessing the thermal stability and elemental diffusion in layered microstructures exposed to elevated temperatures.

42 ENGINEERING↗
DOE OSTI2022

Structure of the glucosyltransferase domain of TcdA in complex with RhoA provides insights into substrate recognition

Clostridioides difficile is one of the most common causes of antibiotic-associated diarrhea in developed countries. As key virulence factors of C. difficile, toxin A (TcdA) and toxin B (TcdB) act by glucosylating and inactivating Rho and Ras family small GTPases in host cells, which leads to actin cytoskeleton disruption, cell rounding, and ultimately cell death. Here we present the co-crystal structure of the glucosyltransferase domain (GTD) of TcdA in complex with its substrate human RhoA at 2.60-angstrom resolution. This structure reveals that TcdA GTD grips RhoA mainly through its switch I and switch II regions, which is complemented by interactions involving RhoA’s pre-switch I region. Comprehensive structural comparisons between the TcdA GTD–RhoA complex and the structures of TcdB GTD in complex with Cdc42 and R-Ras reveal both the conserved and divergent features of these two toxins in terms of substrate recognition. Taken together, these findings establish the structural basis for TcdA recognition of small GTPases and advance our understanding of the substrates selectivity of large clostridial toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A novel hardmask-to-substrate pattern transfer method for creating 3D, multi-level, hierarchical, high aspect-ratio structures for applications in microfluidics and cooling technologies

Abstract This letter solves a major hurdle that mars photolithography-based fabrication of micro-mesoscale structures in silicon. Conventional photolithography is usually performed on smooth, flat wafer surfaces to lay a 2D design and subsequently etch it to create single-level features. It is, however, unable to process non-flat surfaces or already etched wafers and create more than one level in the structure. In this study, we have described a novel cleanroom-based process flow that allows for easy creation of such multi-level, hierarchical 3D structures in a substrate. This is achieved by introducing an ultra-thin sacrificial silicon dioxide hardmask layer on the substrate which is first 3D patterned via multiple rounds of lithography. This 3D pattern is then scaled vertically by a factor of 200–300 and transferred to the substrate underneath via a single shot deep etching step. The proposed method is also easily characterizable—using features of different topographies and dimensions, the etch rates and selectivities were quantified; this characterization information was later used while fabricating specific target structures. Furthermore, this study comprehensively compares the novel pattern transfer technique to already existing methods of creating multi-level structures, like grayscale lithography and chip stacking. The proposed process was found to be cheaper, faster, and easier to standardize compared to other methods—this made the overall process more reliable and repeatable. We hope it will encourage more research into hybrid structures that hold the key to dramatic performance improvements in several micro-mesoscale devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Magnetic anisotropy and GGG substrate stray field in YIG films down to millikelvin temperatures

Abstract Quantum magnonics investigates the quantum-mechanical properties of magnons, such as quantum coherence or entanglement for solid-state quantum information technologies at the nanoscale. The most promising material for quantum magnonics is the ferrimagnetic yttrium iron garnet (YIG), which hosts magnons with the longest lifetimes. YIG films of the highest quality are grown on a paramagnetic gadolinium gallium garnet (GGG) substrate. The literature has reported that ferromagnetic resonance (FMR) frequencies of YIG/GGG decrease at temperatures below 50 K despite the increase in YIG magnetization. We investigated a 97 nm-thick YIG film grown on 500 μm-thick GGG substrate through a series of experiments conducted at temperatures as low as 30 mK, and using both analytical and numerical methods. Our findings suggest that the primary factor contributing to the FMR frequency shift is the stray magnetic field created by the partially magnetized GGG substrate. This stray field is antiparallel to the applied external field and is highly inhomogeneous, reaching up to 40 mT in the center of the sample. At temperatures below 500 mK, the GGG field exhibits a saturation that cannot be described by the standard Brillouin function for a paramagnet. Including the calculated GGG field in the analysis of the FMR frequency versus temperature dependence allowed the determination of the cubic and uniaxial anisotropies. We find that the total crystallographic anisotropy increases more than three times with the decrease in temperature down to 2 K. Our findings enable accurate predictions of the YIG/GGG magnetic systems behavior at low and ultralow millikelvin temperatures, crucial for developing quantum magnonic devices.

Serha, Rostyslav O.↗
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 OSTI2020

Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases

Glycosylation of secondary metabolites involves plant UDP-dependent glycosyltransferases (UGTs). UGTs have shown promise as catalysts in the synthesis of glycosides for medical treatment. However, limited understanding at the molecular level due to insufficient biochemical and structural information has hindered potential applications of most of these UGTs. In the absence of experimental crystal structures, we employed advanced molecular modeling and simulations in conjunction with biochemical characterization to design a workflow to study five Group H Arabidopsis thaliana (76E1, 76E2, 76E4, 76E5, 76D1) UGTs. Based on our rational structural manipulation and analysis, we identified key amino acids (P129 in 76D1; D374 in 76E2; K275 in 76E4), which when mutated improved donor substrate recognition than wildtype UGTs. Molecular dynamics simulations and deep learning analysis identified structural differences, which drive substrate preferences. The design of these UGTs with broader substrate specificity may play important role in biotechnological and industrial applications. These findings can also serve as basis to study other plant UGTs and thereby advancing UGT enzyme engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Influence of substrate misorientation on the optical properties of Mg-doped GaN

The GaN substrate miscut angle has a significant effect on the optical properties of Mg-doped GaN grown by metal-organic chemical vapor deposition. We have studied the optical properties of epilayers grown on c-plane GaN wafers with nominal miscut angles of 0.3° and 4° toward the [11¯00] direction. Periodic surface steps are observed in thin films grown on 0.3° miscut substrates. The step separation and height, as well as the surface roughness, increase with layer thickness, leading to a decrease in Mg doping efficiency. For films grown on 4° miscut substrates, step bunching causes the formation of visually observable wavy features on the film surface with strong spatial variations in cathodoluminescence characteristics, indicating a significant effect of surface morphology on the nature of Mg incorporation and p-type characteristics.

Liu, Hanxiao (ORCID:0000000331067542)↗
DOE OSTI2020

Ligand structure and adsorption free energy of nanocrystals on solid substrates

In this paper, we present an investigation on the absorption of alkylthiolated nanocrystals on a solid substrate. We calculate adsorption free energies and report a number of effects induced by the substrate. Nearest neighbor distances and bonding free energies are significantly different than for a free floating case, there is a weakening of bonding free energies among nanocrystals, and the adsorption is manifestly anisotropic, i.e., stronger along certain directions of the nanocrystal core. We contend that this last result accounts for the Bain transition (fcc → bcc) observed in experimental results. We report the presence of vortices induced by the substrate, which explain the increased nearest neighbor distance among nanocrystals, which is in excellent quantitative agreement with experimental results and with the predictions of the Orbifold Topological Model. Implications for the assembly of nanostructures and future experiments are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Record >10 MV/cm mesa breakdown fields in Al 0.85 Ga 0.15 N/Al 0.6 Ga 0.4 N high electron mobility transistors on native AlN substrates

The ultra-wide bandgap of Al-rich AlGaN is expected to support a significantly larger breakdown field compared to GaN, but the reported performance thus far has been limited by the use of foreign substrates. In this Letter, the material and electrical properties of Al 0.85 Ga 0.15 N/Al 0.6 Ga 0.4 N high electron mobility transistors (HEMT) grown on a 2-in. single crystal AlN substrate are investigated, and it is demonstrated that native AlN substrates unlock the potential for Al-rich AlGaN to sustain large fields in such devices. We further study how Ohmic contacts made directly to a Si-doped channel layer reduce the knee voltage and increase the output current density. High-quality AlGaN growth is confirmed via scanning transmission electron microscopy, which also reveals the absence of metal penetration at the Ohmic contact interface and is in contrast to established GaN HEMT technology. Two-terminal mesa breakdown characteristics with 1.3 μm separation possess a record-high breakdown field strength of ~11.5 MV/cm for an undoped Al 0.6 Ga 0.4 N-channel layer. The breakdown voltages for three-terminal devices measured with gate-drain distances of 4 and 9 μm are 850 and 1500 V, respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Molecular beam homoepitaxy of N-polar AlN on bulk AlN substrates

N-polar AlN epilayers were grown on the N-face of single-crystal bulk AlN substrates by plasma-assisted molecular beam epitaxy. A combination of in situ thermal deoxidation and Al-assisted thermal desorption at high temperature aided in removing native surface oxides and impurities from the N-polar surface of the substrate enabling successful homoepitaxy. Subsequent epitaxial growth of the AlN layer on the in situ cleaned substrates, grown in a sufficiently high Al droplet regime, exhibited smooth surface morphologies with clean and wide atomic steps. KOH etch studies confirmed the N-polarity of the homoepitaxial films. Secondary ion mass spectrometry profiles show Si and H impurity concentrations below the noise levels, whereas O and C impurity concentrations of [Formula: see text] and [Formula: see text] atoms/cm 3 are observed, respectively. Although the structural defect densities are low, they interestingly appear as inversion domains of different dimensionalities.

Singhal, Jashan↗
DOE OSTI2022

Synthesis of antiferromagnetic Weyl semimetal Mn 3 Ge on insulating substrates by electron beam assisted molecular beam epitaxy

The antiferromagnetic kagome semimetals Mn 3 X (X = Ge, Sn, Ga) are of great interest due to properties arising from their Berry curvature, such as large anomalous Nernst and anomalous Hall coefficients, and spin to charge conversion efficiencies at ambient temperatures. However, the synthesis of epitaxial thin films of Mn 3 Ge in the desired hexagonal phase has been challenging because they do not wet insulating substrates, necessitating the use of a metallic buffer layer. Furthermore, a ferrimagnetic tetragonal phase also forms readily under typical growth conditions, interfering with hexagonal phase properties. We have synthesized atomically smooth and continuous epitaxial thin films of hexagonal Mn 3 Ge directly on insulating LaAlO 3 (111) substrates using electron beam assisted molecular beam epitaxy, using a three-step process that mitigates the formation of the tetragonal phase. The anomalous Nernst coefficient is found to be more than six times larger in our films than in sputtered thin films of Mn 3 Ge and significantly larger than that of Fe. Our approach can be used to grow thin layers of kagome materials, without interference from a buffer layer in transport properties, and may be applicable to a broader range of materials with large surface energies that do not grow readily on insulating substrates.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Carbon nanotube substrates enhance SARS-CoV-2 spike protein ion yields in matrix-assisted laser desorption–ionization mass spectrometry

Nanostructured surfaces enhance ion yields in matrix-assisted laser desorption–ionization mass spectrometry (MALDI-MS). The spike protein complex, S1, is one fingerprint signature of Sars-CoV-2 with a mass of 75 kDa. Here, we show that MALDI-MS yields of Sars-CoV-2 spike protein ions in the 100 kDa range are enhanced 50-fold when the matrix–analyte solution is placed on substrates that are coated with a dense forest of multi-walled carbon nanotubes, compared to yields from uncoated substrates. Nanostructured substrates can support the development of mass spectrometry techniques for sensitive pathogen detection and environmental monitoring.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Origins of epitaxial macro-terraces and macro-steps on GaN substrates

Localized lattice distortions in GaN substrates can serve as nucleation sites for epitaxial macro-steps and macro-terraces. These detrimental macro-scale features give rise to optically hazy homoepitaxial GaN surfaces. After nucleating, these macro-features grow laterally along the surface and coalesce, leading to significant coverage of the wafer surface. Dot-core GaN substrates consisting of a periodic array of cores were used as a defect-engineered system, where dislocations are intentionally concentrated at the cores. The high density of threading dislocations at the cores induced localized lattice distortions. Here, these distortions are associated predominantly with lattice tilt on the order of hundreds of arcsec across ~0.5 mm laterally along the wafer surface. The resulting macro-features that nucleated at these localized distorted sites were made up of macro-terraces with lengths ranging ~30–~150 μm and macro-step heights ranging ~200–~400 nm. Another source of localized distortion was threading screw dislocations or GaN nanopipes that resulted in spiral growth and hillock formation. Based on x-ray topography and optical microscopy measurements, we speculate that the coalescence of hillocks evolves into macro-terraces and macro-steps. While previous studies focused on the substrate miscut as a means to control macro-feature formation, we show that localized lattice tilt from defects is another important contributor to macro-feature formation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Interband cascade light-emitting diodes grown on silicon substrates using GaSb buffer layer

Interband cascade light-emitting diodes (ICLEDs) offer attractive advantages for infrared applications, which would greatly expand if high-quality growth on silicon substrates could be achieved. Here, this work describes the formation of threading dislocations in ICLEDs grown monolithically on GaSb-on-Silicon wafers. The epitaxial growth is done in two stages: the GaSb-on-Silicon buffer is grown first, followed by the ICLED growth. The buffer growth involves the nucleation of a 10-nm-thick AlSb buffer layer on the silicon surface, followed by the GaSb growth. The AlSb nucleation layer promotes the formation of 90° and 60° interfacial misfit dislocations, resulting in a highly planar morphology for subsequent GaSb growth that is almost 100% relaxed. The resulting GaSb buffer for growth of the ICLED has a threading dislocation density of ~10 7 /cm 2 after ~3 μm of growth. The fabricated LEDs showed variations in device performance, with some devices demonstrating comparable light–current–voltage curves to those for devices grown on GaSb substrates, while other devices showed somewhat reduced relative performance. Cross-sectional transmission electron microscopy observations of the inferior diodes indicated that the multiplication of threading dislocations in the active region had most likely caused the increased leakage current and lower output power. Enhanced defect filter layers on the GaSb/Si substrates should provide more consistent diode performance and a viable future growth approach for antimonide-based ICLEDs and other infrared devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Superconducting (Ba,K)Fe 2 As 2 epitaxial films on single and bicrystal SrTiO 3 substrates

The realization of single crystal and bicrystal films of superconducting materials is of great interest because they allow the investigation of the intragrain performance as well as the understanding of potential limitations in the grain boundary transparency. For many years, the realization of a high-quality (Ba,K)Fe 2 As 2 film has been challenging. Here, the realization of (Ba,K)Fe 2 As 2 epitaxial thin films on single crystal SrTiO 3 (001) and [001]-tilt-type SrTiO 3 bicrystal substrates with high superconducting properties is demonstrated. The epitaxial growth of (Ba,K)Fe 2 As 2 was enabled by implementing an undoped BaFe 2 As 2 buffer layer between the SrTiO 3 substrate and (Ba,K)Fe 2 As 2 film. The film exhibits a high T c of 38.0 K and an extremely high J c of 14.3 MA/cm 2 at 4.2 K. Artificial grain boundaries of (Ba,K)Fe 2 As 2 were also successfully achieved on bicrystals with misorientation angles up to 36.8° by the same preparation methods. The artificial grain boundaries exhibited an identical T c of 38.0 K and an excellent transfer of the grain orientation from the bicrystal substrates with high crystallinity comparable to that of the high-quality Ba(Fe,Co) 2 As 2 films. Furthermore, this enables the investigation of the intrinsic (Ba,K)Fe 2 As 2 grain boundary nature, which will clarify its potential for superconducting applications, like Josephson junctions, wires, and magnets.

(Ba,K)Fe2As2↗