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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Designing and defining dynamic protein cage nanoassemblies in solution

Central challenges in the design of large and dynamic macromolecular assemblies for synthetic biology lie in developing effective methods for testing design strategies and their outcomes, including comprehensive assessments of solution behavior. Here, we created and validated an advanced design of a 600-kDa protein homododecamer that self-assembles into a symmetric tetrahedral cage. The monomeric unit is composed of a trimerizing apex-forming domain genetically linked to an edge-forming dimerizing domain. Enhancing the crystallographic results, high-throughput small-angle x-ray scattering (SAXS) comprehensively contrasted our modifications under diverse solution conditions. To generate a phase diagram associating structure and assembly, we developed force plots that measure dissimilarity among multiple SAXS data sets. These new tools, which provided effective feedback on experimental constructs relative to design, have general applicability in analyzing the solution behavior of heterogeneous nanosystems and have been made available as a web-based application. Specifically, our results probed the influence of solution conditions and symmetry on stability and structural adaptability, identifying the dimeric interface as the weak point in the assembly. Force plots comparing SAXS data sets further reveal more complex and controllable behavior in solution than captured by our crystal structures. Lastly, these methods for objectively and comprehensively comparing SAXS profiles for systems critically affected by solvent conditions and structural heterogeneity provide an enabling technology for advancing the design and bioengineering of nanoscale biological materials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

HIV-1 vaccine design through minimizing envelope metastability

Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41 ECTO ) is the main source of envelope metastability by replacing wild-type gp41 ECTO with BG505 gp41 ECTO of the uncleaved prefusion-optimized (UFO) design. These gp41 ECTO -swapped trimers can be produced in CHO cells with high yield and high purity. The crystal structure of a gp41 ECTO -swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder viruses and UFO trimers containing a consensus-based ancestral gp41 ECTO suggest an evolutionary root of metastability. The gp41 ECTO -stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer, I3-01. In mice and rabbits, these gp140 nanoparticles induced tier 2 neutralizing antibody responses more effectively than soluble trimers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microsecond dynamics control the HIV-1 Envelope conformation

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel

The region consisting of the first and second variable regions (V1V2) of gp120 plays vital roles in the functioning of the HIV-1 envelope (Env). V1V2, which harbors multiple glycans and is highly sequence diverse, is located at the Env apex and stabilizes the trimeric gp120 spike on the virion surface. It shields V3 and the coreceptor binding sites in the prefusion state and exposes them upon CD4 binding. Data from the RV144 human HIV-1 vaccine trial suggested that antibody responses targeting the V1V2 region inversely correlated with the risk of infection; thus, understanding the antigenic structure of V1V2 can contribute to vaccine design. We have determined a crystal structure of a V1V2 scaffold molecule (V1V2 ZM109 -1FD6) in complex with 830A, a human monoclonal antibody that recognizes a V1V2 epitope overlapping the integrin-binding motif in V2. The structure revealed that V1V2 assumes a five-stranded beta barrel structure with the region of the integrin-binding site (amino acids [aa] 179 to 181) included in a “kink” followed by an extra beta strand. The complete barrel structure naturally presents the glycans on its outer surface and packs into its core conserved hydrophobic residues, including the Ile at position 181 which was highly correlated with vaccine efficacy in RV144. The epitope of monoclonal antibody 830A is discontinuous and composed of three segments: (i) Thr 175 , Tyr 177 , Leu 179 , and Asp 180 at the kink overlapping the integrin-binding site; (ii) Arg 153 and Val 154 in V1; and (iii) Ile 194 at the C terminus of V2. Here, this report thus provides the atomic details of the immunogenic “V2i epitope.”

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL

The V3 region of HIV-1 gp120 is important for virus-coreceptor interaction and highly immunogenic. Although most anti-V3 antibodies neutralize only the sensitive tier 1 viruses, anti-V3 antibodies effective against the more resistant viruses exist, and a better understanding of these antibodies and their epitopes would be beneficial for the development of novel vaccine immunogens against HIV. The HIV-1 isolate JRFL with its cryptic V3 is resistant to most V3-specific monoclonal antibodies (MAbs). However, the V3 MAb 2424 achieves 100% neutralization against JRFL. 2424 is encoded by IGHV3-53 and IGLV2-28 genes, a pairing rarely used by the other V3 MAbs. 2424 also has distinct binding and neutralization profiles. Studies of 2424-mediated neutralization of JRFL produced with a mannosidase inhibitor further revealed that its neutralizing activity is unaffected by the glycan composition of the virus envelope. To understand the distinct activity of 2424, we determined the crystal structure of 2424 Fab in complex with a JRFL V3 peptide and showed that the 2424 epitope is located at the tip of the V3 crown ( 307 IHIGPGRAFYT 319 ), dominated by interactions with His P308 , Pro P313 , and Arg P315 . The binding mode of 2424 is similar to that of the well-characterized MAb 447-52D, although 2424 is more side chain dependent. The 2424 epitope is focused on the very apex of V3, away from nearby glycans, facilitating antibody access. Lastly, this feature distinguishes the 2424 epitope from the other V3 crown epitopes and indicates that the tip of V3 is a potential site to target and incorporate into HIV vaccine immunogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effect of Passive Administration of Monoclonal Antibodies Recognizing Simian Immunodeficiency Virus (SIV) V2 in CH59-Like Coil/Helical or β -Sheet Conformations on Time of SIV mac251 Acquisition

The monoclonal antibodies (MAbs) NCI05 and NCI09, isolated from a vacci nated macaque that was protected from multiple simian immunodeficiency virus (SIV) chal lenges, both target an overlapping, conformationally dynamic epitope in SIV envelope vari able region 2 (V2). Here, we show that NCI05 recognizes a CH59-like coil/helical epitope, whereas NCI09 recognizes a b-hairpin linear epitope. In vitro, NCI05 and, to a lesser extent, NCI09 mediate the killing of SIV-infected cells in a CD4-dependent manner. Compared to NCI05, NCI09 mediates higher titers of antibody-dependent cellular cytotoxicity (ADCC) to gp120-coated cells, as well as higher levels of trogocytosis, a monocyte function that contributes to immune evasion. We also found that passive administration of NCI05 or NCI09 to macaques did not affect the risk of SIV mac251 acquisition compared to controls, demonstrating that these anti-V2 antibodies alone are not protective. However, NCI05 but not NCI09 mucosal levels strongly correlated with delayed SIV mac251 acquisition, and functional and structural data suggest that NCI05 targets a transient state of the viral spike apex that is partially opened, compared to its prefusion-closed conformation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Polymorphism and structure of Nd{sub 2}MоO{sub 6} single crystals

The tetragonal and monoclinic modifications of Nd{sub 2}MoO{sub 6} single crystals have been investigated by X-ray diffraction. The analysis has been on laboratory sources (2D CCD diffractometers: Xcalibur S (Shared Research Center, Institute of Crystallography, Russian Academy of Sciences) and BRUKER Smart APEX 2 (Shared Research Center, Institute of General and Inorganic Chemistry, Russian Academy of Sciences)) and on a synchrotron radiation source (ESRF, Grenoble, PILATUS@SNBL diffractometer). Local displacements of all atoms in the oxymolybdate structure have been revealed for the first time using electron density difference maps. Possible violation of the translational periodicity in the distribution of Mo and Nd atoms over types is indirectly confirmed, and statistical disorder of oxygen atoms is revealed. The results of the study confirm the previous suggestion that polymorphic transformations occur in oxymolybdates at a very low rate and, apparently, continuously in a wide temperature range. With an increase in temperature, layers undergo ordering according to the cation type as a result of the phase transition from the monoclinic to the tetragonal phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Temperature quenching of spontaneous emission in tunnel-injection nanostructures

The spontaneous-emission spectra in the near-IR range (0.8–1.3 μm) from inverted tunnel-injection nanostructures are measured. These structures contain an InAs quantum-dot layer and an InGaAs quantum-well layer, separated by GaAs barrier spacer whose thickness varies in the range 3–9 nm. The temperature dependence of this emission in the range 5–295 K is investigated, both for optical excitation (photoluminescence) and for current injection in p–n junction (electroluminescence). At room temperature, current pumping proves more effective for inverted tunnel-injection nanostructures with a thin barrier (<6 nm), when the apexes of the quantum dots connect with the quantum well by narrow InGaAs straps (nanobridges). In that case, the quenching of the electroluminescence by heating from 5 to 295 K is slight. The quenching factor S{sub T} of the integrated intensity I is S{sub T} = I{sub 5}/I{sub 295} ≈ 3. The temperature stability of the emission from inverted tunnel-injection nanostructures is discussed on the basis of extended Arrhenius analysis.

36 MATERIALS SCIENCE↗
DOE OSTI2025

GRinding Automated Classification Engine

This work is an ML-driven framework for automated surface analysis of microscopy images. We create a training dataset by imaging stainless steel samples to benchmark four developed deep neural network architectures. These models, based on a YOLOv8n-cls backend, integrate image features and process metadata using various fusion methods to distinguish between acceptable and unacceptable surface finishes. This code is associated with publication "Classifying Alloy Surface Preparation Quality with Metadata-Infused Machine Learning for Rapid Alloy Discovery" for project APEX LDRD-ER (25-ERD-039)

Gongora, AldairE [Lawrence Livermore National Labo↗
DOE OSTI2016

Mathematical model for burden distribution in blast furnace

Burden distribution in a blast furnace is vital to its smooth running. However, it is difficult to directly measure the burden distribution for an operating blast furnace. Therefore, mathematical models have been applied to guide the charging process to achieve the desired burden distribution. The accuracies of such models depend on the prediction of falling curve, stockline profile formation, and burden descent mode. Here, a new stockline profile formation model is proposed in which new equations have been developed for the inner and outer repose angle by considering the influence of the burden flow's vertical and horizontal velocity at the apex of the stockline profile. Furthermore, validation of this new stockline profile formation model is provided through comparison between calculated results and experimental data for stockline profile. A stepped burden descending strategy, in which the burden would descend through a specified distance after each ring charging process, is proposed corresponding to the successive charging process. The influence of the burden descending strategy on the falling point, the final burden profile and radial depth ratio of ore to coke is also analysed. Our results show that the burden descending strategy greatly affects the final burden distribution, especially in the peripheral region.

42 ENGINEERING↗
DOE OSTI2019

Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal

Bengal tigers (Panthera tigris tigris) serve a pivotal role as an apex predator in forest ecosystems. To increase our knowledge on factors impacting the viability and health of this endangered species, we studied the gut microbiota in 32 individual Bengal tigers from three geographically separated areas (Chitwan National Park (CNP), Bardia National Park (BNP) and Suklaphanta Wildlife Reserve (SWR)) in Nepal, using noninvasive genetic sampling methods. Gut microbiota influence the immune system, impact various physiological functions, and modulates metabolic reactions, that ultimately impact the host health, behavior and development. Across the tiger populations in Nepal, we found significant differences in the composition of microbial communities based on their geographic locations. Specifically, we detected significant differences between CNP and the other two protected areas (CNP vs BNP: pseudo t = 1.944, P = 0.006; CNP vs SWR: pseudo t = 1.9942, P = 0.0071), but no differences between BNP and SWR. This mirrors what has been found for tiger gene flow in the same populations, suggesting gut microbiota composition and host gene flow may be linked. Furthermore, predictive metagenome functional content analysis (PICRUSt) revealed a higher functional enrichment and diversity for significant gut microbiota in the Chitwan tiger population and the lowest enrichment and diversity in Suklaphanta. The CNP tiger population contained higher proportions of microbiota that are associated with predicted functions relevant for metabolism of amino acid, lipid, xenobiotics biodegradation, terpenoides and polyketides than the SWR population. We conclude the tiger population structure, gut microbiota profile and associated functional metabolic categories are correlated, with geographically most separated CNP and SWR tiger population having the most distinct and different host genotype and microbiota profiles. Our work dramatically expands the understanding of tiger microbiota in wild populations and provides a valuable case study on how to investigate genetic diversity at different hierarchical levels, including hosts as well as their microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Structure and Recognition of a Novel HIV-1 gp120-gp41 Interface Antibody that Caused MPER Exposure through Viral Escape

A comprehensive understanding of the regions on HIV-1 envelope trimers targeted by broadly neutralizing antibodies may contribute to rational design of an HIV-1 vaccine. We previously identified a participant in the CAPRISA cohort, CAP248, who developed trimer-specific antibodies capable of neutralizing 60% of heterologous viruses at three years post-infection. Here, we report the isolation by B cell culture of monoclonal antibody CAP248-2B, which targets a novel membrane proximal epitope including elements of gp120 and gp41. Despite low maximum inhibition plateaus, often below 50% inhibitory concentrations, the breadth of CAP248-2B significantly correlated with donor plasma. Site-directed mutagenesis, X-ray crystallography, and negative-stain electron microscopy 3D reconstructions revealed how CAP248-2B recognizes a cleavage-dependent epitope that includes the gp120 C terminus. While this epitope is distinct, it overlapped in parts of gp41 with the epitopes of broadly neutralizing antibodies PGT151, VRC34, 35O22, 3BC315, and 10E8. CAP248-2B has a conformationally variable paratope with an unusually long 19 amino acid light chain third complementarity determining region. Two phenylalanines at the loop apex were predicted by docking and mutagenesis data to interact with the viral membrane. Neutralization by CAP248-2B is not dependent on any single glycan proximal to its epitope, and low neutralization plateaus could not be completely explained by N- or O-linked glycosylation pathway inhibitors, furin co-transfection, or pre-incubation with soluble CD4. Viral escape from CAP248-2B involved a cluster of rare mutations in the gp120-gp41 cleavage sites. Simultaneous introduction of these mutations into heterologous viruses abrogated neutralization by CAP248-2B, but enhanced neutralization sensitivity to 35O22, 4E10, and 10E8 by 10-100-fold. Altogether, this study expands the region of the HIV-1 gp120-gp41 quaternary interface that is a target for broadly neutralizing antibodies and identifies a set of mutations in the gp120 C terminus that exposes the membrane-proximal external region of gp41, with potential utility in HIV vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Engineering well-expressed, V2-immunofocusing HIV-1 envelope glycoprotein membrane trimers for use in heterologous prime-boost vaccine regimens

HIV-1 vaccine immunofocusing strategies may be able to induce broadly-reactive neutralizing antibodies (NAbs). Here, we engineered a panel of diverse, membrane-resident native HIV-1 trimers vulnerable to two broad targets—the V2 apex and fusion peptide (FP). Selection criteria included i) high expression and ii) infectious function, so that trimer neutralization sensitivity can be profiled in pseudovirus (PV) assays. Initially, we boosted the expression of 17 candidate trimers by truncating gp41 and introducing a gp120-gp41 SOS disulfide to prevent gp120 shedding. "Repairs" were made to fill glycan holes and eliminate other strain-specific aberrations. A new neutralization assay allowed PV infection when our standard assay was insufficient. Trimers with exposed V3 loops, a target of non-NAbs, were discarded. To try to increase V2-sensitivity, we removed clashing glycans and modified the C-strand. Notably, a D167N mutation improved V2-sensitivity in several cases. Glycopeptide analysis of JR-FL trimers revealed near complete sequon occupation and that filling the N197 glycan hole was well-tolerated. In contrast, sequon optimization and inserting/removing glycans at other positions frequently had global "ripple" effects on glycan maturation and sequon occupation throughout the gp120 outer domain and gp41. V2 MAb CH01 selectively bound to trimers with small high mannose glycans near the base of the V1 loop, thereby avoiding clashes. Knocking in a rare N49 glycan was found to perturb gp41 glycans, increasing FP NAb sensitivity—and sometimes improving expression. Finally, a biophysical analysis of VLPs revealed that i) ~25% of particles bear Env spikes, ii) spontaneous particle budding is high and only increases 4-fold upon Gag transfection, and iii) Env+ particles express ~30–40 spikes. Taken together, we identified 7 diverse trimers with a range of sensitivities to two targets to allow rigorous testing of immunofocusing vaccine concepts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

High-pressure phase transitions of clinoenstatite

Clinoenstatite (Mg 2 Si 2 O 6 ) undergoes a well-known phase transition from a low-pressure form (LPCEN, space group P2 1 /c ) to a high-pressure form (HPCEN, space group C2/c ) at similar to ~ 6 GPa. High-pressure structure refinements of HPCEN were carried out based on single-crystal X-ray diffraction experiments between 9.5 and 35.5 GPa to determine its P-V equation of state and structural evolution over an expanded pressure range relevant to pyroxene metastability. The best-fit isothermal equation of state to our data combined with the five data points between 5.34 and 7.93 GPa from Angel and Hugh-Jones (1994) yields a second-order Birch-Murnaghan equation with K T0 = 121(2) GPa and V 0 = 403.9(5) Å 3 (with $K^{'}_{T0}$ = 4 implied). Further reduction of misfit upon fitting a third-order Birch-Murnaghan equation is not significant at the 90% confidence level. At ~45 GPa, a transition from HPCEN to a P21/c -structured polymorph (HPCEN2) was observed in our study, which is isostructural to the P2 1 /c phase recently observed in diopside (CaMgSi 2 O 6 ) at 50 GPa (Plonka et al. 2012) and in clinoferrosilite (Fe 2 Si 2 O 6 ) at 30–36 GPa (Pakhomova et al. 2017). Observation of HPCEN2 in Mg 2 Si 2 O 6 completes the third apex of the pyroxene quadrilateral wherein HPCEN2 is found, facilitating a broader view of clinopyroxene crystal chemistry at conditions relevant to metastability in the Earth’s mantle along cold subduction geotherms.

58 GEOSCIENCES↗
DOE OSTI2013

Characterization and Computer Modeling for Brunelleschi's Dome of Santa Maria del Fiore in Florence

In 1420 Brunelleschi began construction on the enormous dome of Santa Maria del Fiore church in Florence Italy. Of special interest was the fact that his design did not require temporary supports from below (the distance from the ground level to the dome was too high to build such scaffolding/centering). Instead he made use of the stabilizing effect of compressive hoop stresses. As the dome went up, it was always in balance since no part extended beyond the other. Thus, the compressive forces were distributed both radially from the apex of the dome, and circumferentially about the center of the dome providing a stable configuration.

Accelerator Design, Technology, and Operations↗
DOE OSTI2015

An Improved Refractive Focusing Optic

A diamond optic that can both dissipate the heat load while reducing phase profile errors of the beam will allow a more full realization of the benefits of the previous investments in light sources by allowing experiments that depend on high resolution imaging or spacial resolution. Reducing the x-ray spot size on samples will improve the quality of this information leading to better understanding of materials properties. During Phase I, we explored techniques for characterizing and improving the accuracy of the shape of diamond lenses, particularly in the apex of the parabolic curve, in order to make an optic whose optical performance exceeds what is currently available. We made efforts to reduce the lens surface roughness through a variety of dry etching methods. Additional work sought to make compound lenses with shorter focal lengths and to mount the lenses on copper supports by a variety of methods. Lastly, lenses were made and tested on the 1-BM beamline at APS.

42 ENGINEERING↗
DOE OSTI2016

A High-Efficiency, Low Cost, High-Temperature Nanocomposite Soft Magnetic Materials for Vehicle Power Electronics.

The charge components for each gas atomization experiment (GA-1-230, GA-1-232, and GA-1-238) was provided by Aegis and consisted of elemental materials, while MPC provided the master alloy arc melted button castings that were added to yield a charge composition of (Co35Fe65)88Zr7B4Cu. The atmosphere in the melting chamber and connected atomization system was evacuated with a mechanical pump prior to backfilling with ultrahigh purity (UHP grade) Ar. The melt was contained in a bottom tapped zirconia crucible with an alumina stopper rod to seal the exit while heating to a pouring temperature of 1550 – 1575oC. When the desired superheat was reached, the stopper rod was lifted and melt flowed through a yttria stabilized zirconia (YSZ) pour tube with a 3.2 mm orifice and was atomized with Ar from a 45-22-052-409 gas atomization nozzle (or atomization die), having a jet apex angle of 45 degrees with 22 cylindrical gas jets (each with diameter of 1.32 mm or 0.052 inches) arrayed around the axis of a 10.4 mm central bore. The Ar atomization gas supply regulator pressure was set to produce nozzle manifold pressures for the series of runs at a pressure of 450 psi. Secondary gas halos of Ar and He also were added to the interior of the spray chamber at various downstream locations for additional cooling of the atomized droplets and to prevent coalescence of the resulting powder. Powder size analysis and size classification were performed with a full set of ASTM sieves, starting with the 106 µm screen and proceeding down through the 20 µm screen. A Microtrac particle size analyzer was used to verify the size classification results of the particulate resulting from the runs. The resulting powder size distribution results are provided with this report labeled with their respective run numbers (GA-1-230, GA-1-232, and GA-1-238). It should be noted that the size distribution results of the first atomization run were quite acceptable and the same parameters were used for the second and third runs to test the reproducibility for technology transfer purposes.

33 ADVANCED PROPULSION SYSTEMS↗