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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Understanding nanoscale structural distortions in Pb(Zr 0.2 Ti 0.8 )O 3 by utilizing X-ray nanodiffraction and clustering algorithm analysis

Hard X-ray nanodiffraction provides a unique nondestructive technique to quantify local strain and structural inhomogeneities at nanometer length scales. However, sample mosaicity and phase separation can result in a complex diffraction pattern that can make it challenging to quantify nanoscale structural distortions. In this work, a k-means clustering algorithm was utilized to identify local maxima of intensity by partitioning diffraction data in a three-dimensional feature space of detector coordinates and intensity. This technique has been applied to X-ray nanodiffraction measurements of a patterned ferroelectric PbZr 0.2 Ti 0.8 O 3 sample. The analysis reveals the presence of two phases in the sample with different lattice parameters. A highly heterogeneous distribution of lattice parameters with a variation of 0.02 Å was also observed within one ferroelectric domain. This approach provides a nanoscale survey of subtle structural distortions as well as phase separation in ferroelectric domains in a patterned sample.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Multielectrode electrochemical cell for in situ structural characterization of amorphous thin-film catalysts using high-energy X-ray scattering

A multielectrode-based electrochemical cell allows the structural characterization of an amorphous thin-film water oxidation catalyst under various electrochemical potentials using high-energy X-ray scattering and atomic pair distribution function (PDF) techniques. A multielectrode with five electrodes provides a sufficiently low background signal to enable high-energy X-ray scattering (HEXS) measurements and amplifies the extremely low HEXS signals from samples for high-resolution PDF analysis of in situ data from thin-film catalysts. Glassy carbon (GC) creates a relatively low intensity HEXS pattern and is used as a working electrode. Instead of a three-dimensional (3D) porous electrode architecture, the flat geometry of the electrode enables various deposition techniques to be used for the preparation of a highly conductive metal oxide layer. PDF analysis demonstrates high spatial resolution for a 230 nm thick amorphous iridium oxide film deposited on two roughened 60 µm thick GC electrodes. The PDF analysis resolves the domain size and distinguishes changes in fine structure which are directly correlated with the structure and function of the catalysts. In conclusion, the results bring the opportunity to analyze the structure of nanometre-scale amorphous thin-film catalysts in an electrolyte-compatible and compact 3D-printed electrochemical cell in a three-electrode configuration.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural basis for intermodular communication in assembly-line polyketide biosynthesis

Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. Here, to investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain–domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Epitaxial strain tuning of Er 3+ in ferroelectric thin films

Er 3+ color centers are promising candidates for quantum science and technology due to their long electron and nuclear spin coherence times, as well as their desirable emission wavelength. By selecting host materials with suitable, controllable properties, we introduce new parameters that can be used to tailor the Er 3+ emission spectrum. PbTiO 3 is a well-studied ferroelectric material with known methods of engineering different domain configurations through epitaxial strain. By distorting the structure of Er 3+ -doped PbTiO 3 thin films, we can manipulate the crystal fields around the Er 3+ dopant. This is resolved through changes in the Er 3+ resonant fluorescence spectra, tying the optical properties of the defect directly to the domain configurations of the ferroelectic matrix. Additionally, we are able to resolve a second set of peaks for films with in-plane ferroelectric polarization. We hypothesize these results to be due to either the Er 3+ substituting different sites of the PbTiO 3 crystal, differences in charges between the Er 3+ dopant and the original substituent ion, or selection rules. Systematically studying the relationship between the Er 3+ emission and the epitaxial strain of the ferroelectric matrix lays the pathway for future optical studies of spin manipulation by altering ferroelectric order parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Tailoring Fibre Structure Enabled by X-ray Analytics for Targeted Biomedical Applications

The rising interest in designing fibres via spinning techniques combining the properties of various polymeric materials into advanced functionalised materials is directed towards targeted biomedical applications such as drug delivery, wearable sensors or tissue engineering. Understanding how these functional polymers exhibit multiscale structures ranging from the molecular level to nano-, micro-and millimetre scale is a key prerequisite for their challenging applications that can be addressed by a non-destructive X-ray based analytical approach. X-ray multimodalities combining X-ray imaging, scattering and diffraction allow the study of morphology, molecular structure, and the analysis of nano-domain size and shape, crystallinity and preferential orientation in 3D arrangements. The incorporation of X-ray analytics in the design process of polymeric fibers via their nanostructure under non-ambient conditions (i.e. temperature, mechanical load, humidity…) allows for efficient optimization of the fabrication process as well as quality control along the product lifetime under operating environmental conditions. Here, we demonstrate the successful collaboration between the laboratory of Biomimetic Textiles and Membranes and the Center of X-ray Analytics at Empa for the design, characterisation and optimisation of advanced functionalised polymeric fibrous material systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Automated characterization of spatial and dynamical heterogeneity in supercooled liquids via implementation of machine learning

Abstract A computational approach by an implementation of the principle component analysis (PCA) with K -means and Gaussian mixture (GM) clustering methods from machine learning algorithms to identify structural and dynamical heterogeneities of supercooled liquids is developed. In this method, a collection of the average weighted coordination numbers ( W C N s ‾ ) of particles calculated from particles’ positions are used as an order parameter to build a low-dimensional representation of feature (structural) space for K -means clustering to sort the particles in the system into few meso-states using PCA. Nano-domains or aggregated clusters are also formed in configurational (real) space from a direct mapping using associated meso-states’ particle identities with some misclassified interfacial particles. These classification uncertainties can be improved by a co-learning strategy which utilizes the probabilistic GM clustering and the information transfer between the structural space and configurational space iteratively until convergence. A final classification of meso-states in structural space and domains in configurational space are stable over long times and measured to have dynamical heterogeneities. Armed with such a classification protocol, various studies over the thermodynamic and dynamical properties of these domains indicate that the observed heterogeneity is the result of liquid–liquid phase separation after quenching to a supercooled state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Molecular basis for polysaccharide recognition and modulated ATP hydrolysis by the O antigen ABC transporter

O antigens are ubiquitous protective extensions of lipopolysaccharides in the extracellular leaflet of the Gram-negative outer membrane. Following biosynthesis in the cytosol, the lipid-linked polysaccharide is transported to the periplasm by the WzmWzt ABC transporter. Often, O antigen secretion requires the chemical modification of its elongating terminus, which the transporter recognizes via a carbohydrate-binding domain (CBD). Here, using components from A. aeolicus, we identify the O antigen structure with methylated mannose or rhamnose as its cap. Crystal and cryo electron microscopy structures reveal how WzmWzt recognizes this cap between its carbohydrate and nucleotide-binding domains in a nucleotide-free state. ATP binding induces drastic conformational changes of its CBD, terminating interactions with the O antigen. ATPase assays and site directed mutagenesis reveal reduced hydrolytic activity upon O antigen binding, likely to facilitate polymer loading into the ABC transporter. Our results elucidate critical steps in the recognition and translocation of polysaccharides by ABC transporters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Potential-induced wetting and dewetting in pH-responsive block copolymer membranes for mass transport control

Wetting and dewetting behavior in channel-confined hydrophobic volumes is used in biological membranes to effect selective ion/molecular transport. Artificial biomimetic hydrophobic nanopores have been devised utilizing wetting and dewetting, however, tunable mass transport control utilizing multiple transport modes is required for applications such as controllable release/transport, water separation/purification and energy conversion. Here, we investigate the potential-induced wetting and dewetting behavior in a pH-responsive membrane composed of a polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) block copolymer (BCP) when fabricated as a hierarchically-organized sandwich structure on a nanopore electrode array (NEA), i.e. BCP@NEA. At pH < pK a (P4VP) (pK a ~ 4.8), the BCP acts as an anion-exchange membrane due to the hydrophilic, protonated P4VP cylindrical nanodomains, but at pH > pK a (P4VP), the P4VP domains exhibit charge-neutral, hydrophobic and collapsed structures, blocking mass transport via the hydrophobic membrane. However, when originally prepared in a dewetted condition, mass transport in the BCP membrane may be switched on if sufficiently negative potentials are applied to the BCP@NEA architecture. When the hydrophobic BCP membrane is introduced on top of 2-electrode-embedded nanopore arrays, electrolyte solution in the nanopores is introduced, then isolated, by exploiting the potential-induced wetting and dewetting transitions in the BCP membrane. The potential-induced wetting/dewetting transition and the effect on cyclic voltammetry in the BCP@NEA structures is characterized as a function of the potential, pH and ionic strength. Additionally chronoamperometry and redox cycling experiments are used to further characterize the potential response. The multi-modal mass transport system proposed in this work will be useful for ultrasensitive sensing and single-molecule studies, which require long-time monitoring to explore reaction dynamics as well as molecular heterogeneity in nanoconfined volumes.

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

Unexpected symmetry breaking in ferroelectric wurtzite thin films on silicon observed by optical second harmonic generation

Optical second harmonic generation (SHG) exists as a popular tool for probing materials with broken inversion symmetry in the physical and biological sciences. SHG polarimetry can reveal material anisotropy with high sensitivity, including point group and phase transitions. Here, we probe ferroelectric wurtzite films with a nominal 6 mm symmetry under a normal reflection geometry using SHG microscopy and discover an unexpected symmetry breaking. Symmetry considerations would normally forbid the detection of the SHG signal when light propagates along the polar 6-fold rotation axis. Yet a uniquely anisotropic SHG response is observed in this geometry in Al 1-x B x N, Al 1-x Sc x N, Zn 1-x Mg x O, and AlN/Al 1-x Sc x N heterostructures grown on silicon that can be modeled by an average monoclinic symmetry of point group m. A significant enhancement of the SHG signal corresponding to up to a 5.3× increase in the SHG intensity (hence ∼2.3 × in effective SHG tensor coefficient) is observed at antiparallel polar domain walls, suggesting local cooperative alignment of symmetry-breaking structural distortions. Namely, it is found that the monoclinic mirror plane is oriented predominantly perpendicular to the walls. Such increases in domain wall SHG thus reveal that subtle symmetry breaking can be a pathway to large property enhancements.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Small-angle neutron scattering solution structures of NADPH-dependent sulfite reductase

Sulfite reductase (SiR), a dodecameric complex of flavoprotein reductase subunits (SiRFP) and hemoprotein oxidase subunits (SiRHP), reduces sulfur for biomass incorporation. Electron transfer within SiR requires intra- and inter-subunit interactions that are mediated by the relative position of each protein, governed by flexible domain movements. Using small-angle neutron scattering, we report the first solution structures of SiR heterodimers containing a single copy of each subunit. These structures show how the subunits bind and how both subunit binding and oxidation state impact SiRFP’s conformation. Neutron contrast matching experiments on selectively deuterated heterodimers allow us to define the contribution of each subunit to the solution scattering. SiRHP binding induces a change in the position of SiRFP’s flavodoxin-like domain relative to its ferredoxin-NADP + reductase domain while compacting SiRHP’s N-terminus. Reduction of SiRFP leads to a more open structure relative to its oxidized state, re-positioning SiRFP’s N-terminal flavodoxin-like domain towards the SiRHP binding position. These structures show, for the first time, how both SiRHP binding to, and reduction of, SiRFP positions SiRFP for electron transfer between the subunits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Deep Learning and Structural Imaging of Materials

Deep learning has had a transformative effect on numerous domains and is actively utilized by many scientists in data-intensive fields such as high-energy physics and cosmology. Materials science, and in particular, the structural imaging of materials with electrons and X-rays are projected to enter the age of scientific data torrents, positioning them as new application spaces for modern artificial intelligence. In this contribution, we provide a synopsis on the foundations and latest progress in deep learning and present an in-depth application of utilizing modern deep artificial neural networks in scanning transmission electron microscopy to extract structural material properties. We use this case study to expose the strengths of deep learning-based models and discuss their current limitations, in the process highlighting their potential use in other data-intensive structural imaging modalities.

Laanait, Nouamane↗
DOE OSTI2023

Identification of a carbonic anhydrase–Rubisco complex within the alpha-carboxysome

Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO 2 fixation—Rubisco and carbonic anhydrase—and are the centerpiece of the bacterial CO 2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO 2 by carbonic anhydrase, producing a high CO 2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus . We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of a tripartite protein complex that targets toxins to the type VII secretion system

Type VII secretion systems are membrane-embedded nanomachines used by Gram-positive bacteria to export effector proteins from the cytoplasm to the extracellular environment. Many of these effectors are polymorphic toxins comprised of an N-terminal Leu-x-Gly (LXG) domain of unknown function and a C-terminal toxin domain that inhibits the growth of bacterial competitors. In recent work, it was shown that LXG effectors require two cognate Lap proteins for T7SS-dependent export. Here, we present the 2.6 Å structure of the LXG domain of the TelA toxin from the opportunistic pathogen Streptococcus intermedius in complex with both of its cognate Lap targeting factors. The structure reveals an elongated α-helical bundle within which each Lap protein makes extensive hydrophobic contacts with either end of the LXG domain. Remarkably, despite low overall sequence identity, we identify striking structural similarity between our LXG complex and PE–PPE heterodimers exported by the distantly related ESX type VII secretion systems of Mycobacteria implying a conserved mechanism of effector export among diverse Gram-positive bacteria. Overall, our findings demonstrate that LXG domains, in conjunction with their cognate Lap targeting factors, represent a tripartite secretion signal for a widespread family of T7SS toxins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain

Abstract SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5′-TCGGAT-3′) of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Temporal dynamics of large-scale structures for turbulent Rayleigh–Bénard convection in a moderate aspect-ratio cylinder

We investigate the spatial organization and temporal dynamics of large-scale, coherent structures in turbulent Rayleigh–Bénard convection via direct numerical simulation of a 6.3 aspect-ratio cylinder with Rayleigh and Prandtl numbers of 9.6×10 7 and 6.7, respectively. Fourier modal decomposition is performed to investigate the structural organization of the coherent turbulent motions by analysing the length scales, time scales and the underlying dynamical processes that are ultimately responsible for the large-scale structure formation and evolution. We observe a high level of rotational symmetry in the large-scale structure in this study and that the structure is well described by the first four azimuthal Fourier modes. Two different large-scale organizations are observed during the duration of the simulation and these patterns are dominated spatially and energetically by azimuthal Fourier modes with frequencies of 2 and 3. Studies of the transition between these two large-scale patterns, radial and vertical variations in the azimuthal energy spectra, as well as the spatial and modal variations in the system's correlation time are conducted. Rotational dynamics are observed for individual Fourier modes and the global structure with strong similarities to the dynamics that have been reported for unit aspect-ratio domains in prior works. It is shown that the large-scale structures have very long correlation time scales, on the order of hundreds to thousands of free-fall time units, and that they are the primary source for a horizontal inhomogeneity within the system that can be observed during a finite, but a very long-time simulation or experiment.

42 ENGINEERING↗
DOE OSTI2020

Structure and function of a flavin-dependent S-monooxygenase from garlic ( Allium sativum )

Allicin is a component of the characteristic smell and flavor of garlic ( Allium sativum ). A flavin-containing monooxygenase (FMO) produced by A. sativum (AsFMO) was previously proposed to oxidize S-allyl- L -cysteine (SAC) to alliin, an allicin precursor. In this paper, we present a kinetic and structural characterization of AsFMO that suggests a possible contradiction to this proposal. Results of steady-state kinetic analyses revealed that AsFMO exhibited negligible activity with SAC; however, the enzyme was highly active with L -cysteine, N-acetyl- L -cysteine, and allyl mercaptan. We found that allyl mercaptan with NADPH was the preferred substrate-cofactor combination. Rapid-reaction kinetic analyses showed that NADPH binds tightly ($K_D$ of ~2 μM) to AsFMO and that the hydride transfer occurs with pro-R stereospecificity. We detected the formation of a long-wavelength band when AsFMO was reduced by NADPH, probably representing the formation of a charge-transfer complex. In the absence of substrate, the reduced enzyme, in complex with NADP + , reacted with oxygen and formed an intermediate with a spectrum characteristic of C4a-hydroperoxyflavin, which decays several orders of magnitude more slowly than the $k$ cat . The presence of substrate enhanced C4a-hydroperoxyflavin formation and, upon hydroxylation, oxidation occurred with a rate constant similar to the $k$ cat . The structure of AsFMO complexed with FAD at 2.08-Å resolution features two domains for binding of FAD and NADPH, representative of class B flavin monooxygenases. These biochemical and structural results are consistent with AsFMO being an S-monooxygenase involved in allicin biosynthesis through direct formation of sulfenic acid and not SAC oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Re-investigation of moment direction in a Kitaev material α -RuCl 3

Abstract We report x-ray diffraction and resonant elastic x-ray scattering studies on two α -RuCl 3 crystals with distinct magnetic transition temperatures: T N = 7.3 K and 6.5 K. We find that the sample with T N = 6.5 K exhibits a high degree of stacking faults and structural twinning at low temperature, whereas the T N = 7.3 K sample primarily comprises a single domain of R 3 ¯ . Notwithstanding, both samples exhibit an identical zigzag magnetic structure, with magnetic moments pointing away from the honeycomb plane by α = 31 ( 2 ) ∘ . We argue that the identical ordered moment directions in these samples suggest that the intralayer magnetic interactions remain mostly unchanged regardless of T N .

2D magnetism↗