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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

What are the current limits on determination of protonation state using neutron macromolecular crystallography?

The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. Here, we observe and discuss systematic map quality deterioration as result of data incompleteness.

Hydrogen bond↗
DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Streamlined engineering and mutational analysis

Natural transformation and homologous recombination in a soil bacterium, Acinetobacter baylyi ADP1, occur with exceptionally high efficiency. These genetic features can be harnessed to address a wide variety of fundamental and applied scientific topics. Recent advances in synthetic biology and laboratory evolution have led to renewed appreciation for the use of A. baylyi as a model organism. To complement several review articles that highlight new tool sets, this chapter focuses on simple protocols and examples of transformation assays that facilitate genetic analysis and engineering. Whole genome sequencing often reveals extensive genetic variation among closely related isolates that can confound the association of genotypic and phenotypic changes. In A. baylyi, such associations can be deciphered in unique ways by directly transforming cells with linear DNA fragments. The resulting allelic replacement, which occurs at high frequency, rapidly generates desired mutants via targeted chromosomal editing. Diverse screening and selection methods can be used to test hypotheses and streamline experimental strategies to reveal the significance of specific DNA sequences. Moreover, large procedural variations are well tolerated, and techniques can be readily adapted for new purposes. Furthermore, one goal of highlighting natural transformation methodology in A. baylyi is to expand the community of researchers using this versatile bacterial host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An additively manufactured near-eutectic Al-Ce-Ni-Mn-Zr alloy with high creep resistance

A new additively manufactured (AM) Al-7.5Ce-4.5Ni-0.4Mn-0.7Zr (wt.%) near-eutectic alloy is reported, which shows unprecedented creep resistance up to 400 °C (a homologous temperature of 0.72). The eutectic solidification microstructure comprises ~ 27 vol% of coarsening-resistant second phase network with an ultrafine (<100 nm) inter-phase spacing. Both Mn and Zr contribute to creep resistance of the alloy. Small amount of Mn addition promotes selection of coarsening resistant phases without compromising the alloy processability. Zr not only improves hot-tearing resistance, but further enhances the second phase coarsening resistance resulting in improved creep resistance. Neutron diffraction performed during creep deformation reveals that the underlying mechanism for creep resistance in this alloy is impedance to dislocation motion stemming from the ultrafine eutectic solidification microstructure, whereas load transfer strengthening becomes less effective as the creep temperature increases. The second phase forms a continuous network in the as-fabricated condition, which is maintained during long-term creep at 300 °C. However, this network is fragmented into fine dispersoids at higher temperatures. It is proposed that the rate-limiting deformation mechanism at 300–400 °C is (i) dislocation climb for the alloy with fragmented second phase dispersoids and (ii) Orowan looping for the alloy with a continuous second phase network. In conclusion, the present design of an AM-processable multicomponent eutectic alloy with high creep resistance can be applied to other metallic systems exhibiting eutectic reactions, with expected extreme creep resistance.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Microstructural modification of additively manufactured metals by electropulsing

Additive manufacturing (AM) promises rapid development cycles and fabrication of ready-to-use, geometrically-complex parts. The metallic parts produced by AM often contain highly non-equilibrium microstructures, e.g. chemical microsegregation and residual dislocation networks. While such microstructures can enhance some material properties, they are often undesirable. Many AM parts are thus heat-treated after fabrication, a process that significantly slows production. This study investigated if electropulsing, the process of sending high-current-density electrical pulses through a metallic part, could be used to modify the microstructures of AM 316 L stainless steel (SS) and AlSi10Mg parts fabricated by selective laser melting (SLM) more rapidly than thermal annealing. Electropulsing has shown promise as a rapid postprocessing method for materials fabricated using conventional methods, e.g. casting and rolling, but has never been applied to AM materials. For both the materials used in this study, as-fabricated SLM parts contained significant chemical heterogeneity, either chemical microsegregation (316 L SS) or a cellular interdendritic phase (AlSi10Mg). In both cases, annealing times on the order of hours at high homologous temperatures are necessary for homogenization. Using electropulsing, chemical microsegregation was eliminated in 316 L SS samples after 10, 16 ms electrical pulses. In AlSi10Mg parts, electropulsing produced spheroidized Si-rich particles after as few as 15, 16 ms electrical pulses with a corresponding increase in ductility. Finally, this study demonstrated that electropulsing can be used to modify the microstructures of AM metals.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Genomic adaptations of the green alga Dunaliella salina to life under high salinity

Life in high salinity environments poses challenges to cells in a variety of ways: maintenance of ion homeostasis and nutrient acquisition, often while concomitantly enduring saturating irradiances. Dunaliella salina has an exceptional ability to thrive even in saturated brine solutions. This ability has made it a model organism for studying responses to abiotic stress factors. Here we describe the occurrence of unique gene families, expansion of gene families, or gene losses that might be linked to osmoadaptive strategies. We discovered multiple unique genes coding for several of the homologous superfamily of the Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family and of the glycolipid 2-alpha-mannosyltransferase family, suggesting that such components on the cell surface are essential to life in high salt. Gene expansion was found in families that participate in sensing of abiotic stress and signal transduction in plants. One example is the patched family of the Sonic Hedgehog receptor proteins, supporting a previous hypothesis that plasma membrane sterols are important for sensing changes in salinities in D. salina. We also investigated genome-based capabilities regarding glycerol metabolism and present an extensive map for core carbon metabolism. We postulate that a second broader glycerol cycle exists that also connects to photorespiration, thus extending the previously described glycerol cycle. Further genome-based analysis of isoprenoid and carotenoid metabolism revealed duplications of genes for 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and phytoene synthase (PSY), with the second gene copy of each enzyme being clustered together. Moreover, we identified two genes predicted to code for a prokaryotic-type phytoene desaturase (CRTI), indicating that D. salina may have eukaryotic and prokaryotic elements comprising its carotenoid biosynthesis pathways. In brief, our genomic data provide the basis for further gene discoveries regarding sensing abiotic stress, the metabolism of this halophilic alga, and its potential in biotechnological applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fracton phases via exotic higher-form symmetry-breaking

We study p-string condensation mechanisms for fracton phases from the viewpoint of higher-form symmetry, focusing on the examples of the X-cube model and the rank-two symmetric-tensor scalar charge theory. This work is motivated by questions of the relationship between fracton phases and continuum quantum field theories, and also provides general principles to describe p-string condensation independent of specific lattice model constructions. We give a perspective on higher-form symmetry in lattice models in terms of cellular homology. Applying this perspective to the coupled-layer construction of the X-cube model, we identify a foliated 1-form symmetry that is broken in the X-cube phase, but preserved in the phase of decoupled toric code layers. Similar considerations for the scalar charge theory lead to a framed 1-form symmetry. These symmetries are distinct from standard 1-form symmetries that arise, for instance, in relativistic quantum field theory. Here, we also give a general discussion on interpreting p-string condensation, and related constructions involving gauging of symmetry, in terms of higher-form symmetry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Spectroscopic insight into carbon speciation and removal on a Cu/BEA catalyst during renewable high-octane hydrocarbon synthesis

Conversion of methanol and dimethyl ether (DME) to high-octane gasoline catalyzed by beta zeolite (BEA) provides an opportunity for the production of high-quality fuels from renewable carbon sources (e.g., gasified biomass). Recent research demonstrated that a Cu-modified BEA zeolite catalyst (Cu/BEA) offered advantages over the unmodified BEA catalyst due to multifunctional Cu species that enabled incorporation of co-fed H2, reactivation of light alkanes, and reduction of products from the aromatic hydrocarbon pool. The shift in hydrocarbon pool chemistry has the potential to influence the identity and relative composition of surface carbon species that are often linked to deactivation. A detailed understanding of these carbon species is important to develop an effective and efficient regeneration procedure that can enable the transition from fundamental catalyst development to commercial application. Here, we applied complementary ex situ and in situ characterization techniques to compare the structures of surface carbon species on post-reaction Cu/BEA and unmodified BEA catalysts. Both catalysts contained acyclic and aromatic hydrocarbons along with graphitic carbon species. However, the post-reaction Cu/BEA catalyst had a lower polycyclic aromatic content, and further, the graphitic species were more hydrogenated and defective. It was also found that the presence of Cu promoted carbon removal at lower temperatures than for unmodified BEA through activation of O2 by Cu oxide during thermal oxidation. The fundamental insight into the composition of surface carbon species enabled the design of an effective and efficient regeneration strategy for the DME homologation reaction over Cu/BEA, resulting in full recovery of the catalyst activity.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

Powders and pellets – Extrusion engineering for a Cu/BEA syngas-to-hydrocarbons catalyst

Converting high-performing powder catalysts from the laboratory reactor scale into effective extruded catalysts at the industrial scale remains a hurdle for advancing sustainable catalytic processes, such as the conversion of biogenic syngas into high octane gasoline. Recently, a process-intensified syngas-to-hydrocarbons (STH) reaction in a single reactor under relatively mild conditions (220–250 ºC, 0.75–2.0 MPa) was reported, enabled by the development of a dimethyl ether (DME) homologation catalyst, Cu-modified H-BEA (Cu/BEA) zeolite. In this study, we explore approaches for synthesizing engineered Cu/BEA catalysts for use in the STH reaction to retain the high performance observed with the powder catalyst. We demonstrate that changes to the order of manufacturing steps (i.e., Cu deposition, alumina binder addition, and extrusion) result in observable changes to key active sites (Brønsted acid sites and zeolitic Cu + species), and ultimately, catalyst performance. When the Cu precursor was added directly to BEA before extrusion, both types of active sites were stabilized, preserving the activity of the powder catalyst. However, when the Cu precursor was added after extrusion, the resulting Cu species were mobile, destabilizing Brønsted acid sites and leading to near-zero activity.

09 BIOMASS FUELS↗
DOE OSTI2026

Localization and functional exploration of leiomodin-2’s C-terminal binding sites

Striated muscle contraction occurs through interactions between overlapping myosin-based thick and actin-based thin filaments within the sarcomere. For effective contraction to occur, the length of the thin filament must be maintained to allow for sufficient overlap with the thick filament. The proteins leiomodin and tropomodulin compete for binding at the pointed end of thin filaments to regulate their length, utilizing their homologous N-terminal actin and tropomyosin binding sites. Leiomodin also has a region called the C-terminal extension, absent in tropomodulin. In this region, the cardiac isoform (leiomodin-2) contains additional actin-binding sites that enable it to bind along the sides of thin filaments in a Ca2+-dependent manner. Here, using nuclear magnetic resonance spectroscopy, we localize the regions of the C-terminal extension that contain residues involved in thin filament side-binding. Using co-sedimentation assays, we reveal that these regions can independently bind thin filaments and discover that the poly-proline region plays a role as a linker, maintaining an adequate distance between two of the regions required for effective interaction to occur. In addition to its role in side-binding, we provide direct evidence that the poly-proline region interacts with profilin and propose a new mechanism by which leiomodin-2 may assist in the polymerization of profilin-bound actin at thin filament pointed ends.

ACTIN-BINDING PROTEINS↗
DOE OSTI2024

Functional plasticity of HCO 3 – uptake and CO 2 fixation in Cupriavidus necator H16

Despite its prominence, the ability to engineer Cupriavidus necator H16 for inorganic carbon uptake and fixation is underexplored. We tested the roles of endogenous and heterologous genes on C. necator inorganic carbon metabolism. Deletion of β-carbonic anhydrase can had the most deleterious effect on C. necator autotrophic growth. Replacement of this native uptake system with several classes of dissolved inorganic carbon (DIC) transporters from Cyanobacteria and chemolithoautotrophic bacteria recovered autotrophic growth and supported higher cell densities compared to wild-type (WT) C. necator in batch culture. Strains expressing Halothiobacillus neopolitanus DAB2 (hnDAB2) and diverse rubisco homologs grew in CO 2 similarly to the wild-type strain. Our experiments suggest that the primary role of carbonic anhydrase during autotrophic growth is to support anaplerotic metabolism, and an array of DIC transporters can complement this function. This work demonstrates flexibility in HCO 3 - uptake and CO 2 fixation in C. necator, providing new pathways for CO 2 -based biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Locking out water at 100°C

We report that thermophilic proteins, present in organisms that live at high temperatures, denature at much higher temperatures compared with their mesophilic counterparts. How these proteins stand the heat has long been researched and is particularly interesting because homologous pairs of thermophilic and mesophilic proteins show a high degree of structural and sequence similarity. In early studies of thermophilic proteins, the proportion of solvent-accessible charged residues was found to be increased at the expense of polar residues. Further analyses confirmed this and also noted strengthening of hydrophobic cores by branched apolar residues. At the same time, whether thermophilic proteins actually need to be more or less flexible than their mesophilic counterparts and the potential usefulness of surface loop deletion has been debated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Generative $β$-hairpin design using a residue-based physicochemical property landscape

De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the -hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial -hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.

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

A Zika virus mutation enhances transmission potential and confers escape from protective dengue virus immunity

Zika virus (ZIKV) and dengue virus (DENV) are arthropod-borne pathogenic flaviviruses that co-circulate in many countries. To understand some of the pressures that influence ZIKV evolution, we mimic the natural transmission cycle by repeating serial passaging of ZIKV through cultured mosquito cells and either DENV-naive or DENV-immune mice. Compared with wild-type ZIKV, the strains passaged under both conditions exhibit increased pathogenesis in DENV-immune mice. Application of reverse genetics identifies an isoleucine-to-valine mutation (I39V) in the NS2B proteins of both passaged strains that confers enhanced fitness and escape from pre-existing DENV immunity. Introduction of I39V or I39T, a naturally occurring homologous mutation detected in recent ZIKV isolates, increases the replication of wild-type ZIKV in human neuronal precursor cells and laboratory-raised mosquitoes. Our data indicate that ZIKV strains with enhanced transmissibility and pathogenicity can emerge in DENV-naive or -immune settings, and that NS2B-I39 mutants may represent ZIKV variants of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Caulobacter lipid A is conditionally dispensable in the absence of fur and in the presence of anionic sphingolipids

Lipid A, the membrane-anchored portion of lipopolysaccharide (LPS), is an essential component of the outer membrane (OM) of nearly all Gram-negative bacteria. Here we identify regulatory and structural factors that together render lipid A nonessential in Caulobacter crescentus. Mutations in the ferric uptake regulator fur allow Caulobacter to survive in the absence of either LpxC, which catalyzes an early step of lipid A synthesis, or CtpA, a tyrosine phosphatase homolog we find is needed for wild-type lipid A structure and abundance. Alterations in Fur-regulated processes, rather than iron status per se, underlie the ability to survive when lipid A synthesis is blocked. Fitness of lipid A-deficient Caulobacter requires an anionic sphingolipid, ceramide phosphoglycerate (CPG), which also mediates sensitivity to the antibiotic colistin. Our results demonstrate that, in an altered regulatory landscape, anionic sphingolipids can support the integrity of a lipid A-deficient OM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis of selective TRPM7 inhibition by the anticancer agent CCT128930

TRP channels are implicated in various diseases, but high structural similarity between them makes selective pharmacological modulation challenging. Here, we study the molecular mechanism underlying specific inhibition of the TRPM7 channel, which is essential for cancer cell proliferation, by the anticancer agent CCT128930 (CCT). Using cryo-EM, functional analysis, and MD simulations, we show that CCT binds to a vanilloid-like (VL) site, stabilizing TRPM7 in the closed non-conducting state. Similar to other allosteric inhibitors of TRPM7, NS8593 and VER155008, binding of CCT is accompanied by displacement of a lipid that resides in the VL site in the apo condition. Moreover, we demonstrate the principal role of several residues in the VL site enabling CCT to inhibit TRPM7 without impacting the homologous TRPM6 channel. Hence, our results uncover the central role of the VL site for the selective interaction of TRPM7 with small molecules that can be explored in future drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Biochemical and structural characterization of enzymes in the 4-hydroxybenzoate catabolic pathway of lignin-degrading white-rot fungi

White-rot fungi (WRF) are the most efficient lignin-degrading organisms in nature. However, their capacity to use lignin-related aromatic compounds, such as 4-hydroxybenzoate, as carbon sources has only been described recently. Previously, the hydroxyquinol pathway was proposed for the bioconversion of these compounds in fungi, but gene- and structure-function relationships of the full enzymatic pathway remain uncharacterized in any single fungal species. Here, we characterize seven enzymes from two WRF, Trametes versicolor and Gelatoporia subvermispora, which constitute a four-enzyme cascade from 4-hydroxybenzoate to β-ketoadipate via the hydroxyquinol pathway. Furthermore, we solve the crystal structure of four of these enzymes and identify mechanistic differences with the closest bacterial and fungal structural homologs. Overall, this research expands our understanding of aromatic catabolism by WRF and establishes an alternative strategy for the conversion of lignin-related compounds to the valuable molecule β-ketoadipate, contributing to the development of biological processes for lignin valorization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mucus-derived glycans are inhibitory signals for Salmonella Typhimurium SPI-1-mediated invasion

Mucus forms a critical barrier against enteric pathogens like Salmonella enterica serovar Typhimurium. While in vivo studies indicate that secreted, gel-forming mucins and specifically core 3 glycosylation are protective against S. Typhimurium, the molecular mechanisms involved remain unclear. Here, we demonstrate that native intestinal mucins inhibit Salmonella invasion of colonic epithelial cells by downregulating the type 3 secretion system through suppression of the key virulence regulator, HilD. Our study identifies mucin glycans and specific mucin sugars, namely N-acetyl galactosamine and N-acetyl glucosamine, as the components responsible for mucin’s anti-virulence effect, likely via functional or direct interaction with HilD’s putative carbohydrate-binding domain. Notably, we find that the native presentation of these sugars is important for activity. These insights provide a mechanistic foundation for mucin-based strategies to combat enteric infections and, given the prevalence of homologous AraC-type regulators in other pathogens, suggest mucins’ potential as broad-spectrum anti-virulence agents.

60 APPLIED LIFE SCIENCES↗