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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
NASA NTRS1998

Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

Lietzke, Susan E↗
DOE OSTI2022

A Single Application of Compost Can Leave Lasting Impacts on Soil Microbial Community Structure and Alter Cross-Domain Interaction Networks

Our current understanding suggests that nutrient management strategies applied to agricultural soils over multiple years are required to cause major and stable shifts in soil microbial communities. However, some studies suggest that agricultural soils can benefit even from sporadic, single additions of organic matter. Here we investigate how single additions of high-quality organic matter can cause significant shifts in microbial soil communities over multiple cropping cycles. We grew radishes in a tropical Oxisol soil for six crop cycles after a single application of a high-nitrogen compost or urea. At planting and before biomass harvest, we sampled soils influenced by the radish rhizosphere and sequenced bacterial and archaeal 16S and fungal ITS rDNA marker genes. We measured microbial richness and diversity, community composition and structure, and constructed correlation networks to predict cross-domain microbial interactions. We found that a single application of compost, compared to urea or control, resulted in a persistent improved plant biomass response and led to sustained changes in the soil microbial community throughout the duration of the 227-day study. Compost altered the structure of both the fungal and prokaryotic microbial communities, introduced new microorganisms that persisted in the resident soil system, and altered soil microbial correlation network structure and hub taxa. In contrast, fertilization with urea did not significantly alter the structure of soil microbial communities compared to the control but reduced network complexity and altered hub taxa. This study highlights the significant impacts that high-quality organic matter fertilization can exert on agricultural soil microbiomes and adds to the growing body of knowledge on using organic fertilizers as a way to steer the soil microbiome toward a healthier soil.

Heisey, Steven↗
DOE OSTI2020

Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation

SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determine the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain. The structure reveals that CV30 binds to an epitope that overlaps with the human ACE2 receptor binding motif providing a structural basis for its neutralization. CV30 also induces shedding of the S1 subunit, indicating an additional mechanism of neutralization. A germline reversion of CV30 results in a substantial reduction in both binding affinity and neutralization potential indicating the minimal somatic mutation is needed for potently neutralizing antibodies against SARS-CoV-2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural diversity and clustering of bacterial flagellar outer domains

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

Science & Technology - Other Topics↗
DOE OSTI2023

Domain-dependent strain and stacking in two-dimensional van der Waals ferroelectrics

Van der Waals (vdW) ferroelectrics have attracted significant attention for their potential in next-generation nano-electronics. Two-dimensional (2D) group-IV monochalcogenides have emerged as a promising candidate due to their strong room temperature in-plane polarization down to a monolayer limit. However, their polarization is strongly coupled with the lattice strain and stacking orders, which impact their electronic properties. Here, we utilize four-dimensional scanning transmission electron microscopy (4D-STEM) to simultaneously probe the in-plane strain and out-of-plane stacking in vdW SnSe. Specifically, we observe large lattice strain up to 4% with a gradient across ~50 nm to compensate lattice mismatch at domain walls, mitigating defects initiation. Additionally, we discover the unusual ferroelectric-to-antiferroelectric domain walls stabilized by vdW force and may lead to anisotropic nonlinear optical responses. Our findings provide a comprehensive understanding of in-plane and out-of-plane structures affecting domain properties in vdW SnSe, laying the foundation for domain wall engineering in vdW ferroelectrics.

42 ENGINEERING↗
DOE OSTI2024

Contact-dependent growth inhibition (CDI) systems deploy a large family of polymorphic ionophoric toxins for inter-bacterial competition

Contact-dependent growth inhibition (CDI) is a widespread form of inter-bacterial competition mediated by CdiA effector proteins. CdiA is presented on the inhibitor cell surface and delivers its toxic C-terminal region (CdiA-CT) into neighboring bacteria upon contact. Inhibitor cells also produce CdiI immunity proteins, which neutralize CdiA-CT toxins to prevent auto-inhibition. Here, we describe a diverse group of CDI ionophore toxins that dissipate the transmembrane potential in target bacteria. These CdiA-CT toxins are composed of two distinct domains based on AlphaFold2 modeling. The C-terminal ionophore domains are all predicted to form five-helix bundles capable of spanning the cell membrane. The N-terminal "entry" domains are variable in structure and appear to hijack different integral membrane proteins to promote toxin assembly into the lipid bilayer. The CDI ionophores deployed by E. coli isolates partition into six major groups based on their entry domain structures. Comparative sequence analyses led to the identification of receptor proteins for ionophore toxins from groups 1 & 3 (AcrB), group 2 (SecY) and groups 4 (YciB). Using forward genetic approaches, we identify novel receptors for the group 5 and 6 ionophores. Group 5 exploits homologous putrescine import proteins encoded by puuP and plaP, and group 6 toxins recognize di/tripeptide transporters encoded by paralogous dtpA and dtpB genes. Finally, we find that the ionophore domains exhibit significant intra-group sequence variation, particularly at positions that are predicted to interact with CdiI. Accordingly, the corresponding immunity proteins are also highly polymorphic, typically sharing only ~30% sequence identity with members of the same group. Competition experiments confirm that the immunity proteins are specific for their cognate ionophores and provide no protection against other toxins from the same group. The specificity of this protein interaction network provides a mechanism for self/nonself discrimination between E. coli isolates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A 3.4-Å cryo-electron microscopy structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family Coronaviridae that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV-1 and SARS-CoV-2. Here we present the in situ structure of HCoV-NL63 spike (S) trimer at 3.4-Å resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other sites, as well as different glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. Overall, this structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Spin orbit torque in ferromagnet/topological-quantum-material heterostructures

The main objective of this proposal was to investigate the spin-orbital driven phenomena in topological insulator (TI)/ferromagnet (FM) or transition metal (TM) heterostructures. In particularly, we tried to utilize the spin-momentum locking properties on the surface of TIs to achieve ideal spin-orbit torques (SOTs). In practice, we found that the surface properties have been greatly modified, resulting in much more complicated magneto-transport behaviors than what is expected in SOT-driven magnetotransport. Through systematic and extended investigations, we start to unravel that the nonlinear magnetotransport properties, which was, in the past, mainly attributed to SOT-driven phenomena, can be used to infer the modification of the electronic band structures of TIs and spin textures in FMs which are closely related with charge-spin interconversion phenomena. Regarding the band structures In TIs, we find under electrostatic perturbations imposed by deposition of nonmagnetic TMs, the quantum well states formed on the surface of TIs develop substantial Rashba spin-splitting, which is detected as a bilinear magnetoresistance (BMR). Under magnetic perturbations, the nonlinear planar Hall effect (NPHE) in the topological surface states is greatly enhanced, possibly reflecting the modified surface band structure due to time-reversal symmetry breaking. In a double HM/FM heterostructure where the magnetic anisotropy can be robustly tuned, we observed second-harmonic Hall voltage responses corresponding to domain wall structures with fixed chirality, stabilized by interfacial Dzyaloshinskii–Moriya interaction (DMI). In addition, in the linear transport regime, we utilized inverse-SHE-induced anomalous Hall effect in Pt to probe the exchange bias on the surface of a doped magnetic insulator Tm 3 Fe 5 O 12 .

36 MATERIALS SCIENCE↗
NASA NTRS1990

Grid generation for computational CFD of full aerodynamic configurations

It is now possible to compute flow about very complex three-dimensional aerodynamic configurations. Grid generation is an essential part of such computations and a basic capability has been demonstrated. The present problems are: (1) choosing among the competing approaches (structured, unstructured or rectangular); (2) automating and packaging software for grid generation; (3) assessing and assuring grid quality; (4) solid boundary-surface representation and grid generation on solid boundaries; (5) automated domain decomposition (structured grids); (6) grid adaption during the flow solution process. This paper discusses some of the capabilities in the computation of complex three-dimensional grids and addresses some of he current challenges.

Smith, Robert E.↗
DOE OSTI2026

Discovery of spontaneous mesoscopic strain waves in nematic domains using dark-field x-ray microscopy

Electronic nematic order arises when correlated electrons spontaneously break the rotational symmetry of a crystal lattice. When electronic nematic order couples bilinearly to symmetry-breaking lattice strain, both appear together at a single ferroelastic phase transition, producing structural twin domains with distinct orientations of the nematic director. While the effects of applied strain on these domains are well established, the intrinsic behavior of spontaneous subdomain strain fields has remained unexplored. Here, we report the discovery of spontaneous mesoscopic strain waves within individual nematic domains of an iron-based superconductor, observed using dark-field x-ray microscopy (DFXM). Using this advanced full-field imaging technique, we visualize subdomain strain modulations emerging concurrently with nematic order. Elastic compatibility relations governing inhomogeneous strains provide a natural mechanism for the strain waves. Our findings reveal a broadly relevant form of strain self-organization and position DFXM as a powerful probe of the local interplay between lattice strain and electronic order.

36 MATERIALS SCIENCE↗
NASA NTRS1991

Automated on-orbit frequency domain identification for large space structures

Recent experiences in the field of flexible structure control in space have indicated a need for on-orbit system identification to support robust control redesign to avoid in-flight instabilities and maintain high spacecraft performance. This paper highlights an automated frequency domain system identification methodology recently developed to fulfill this need. The methodology is focused to support (1) the estimation of system quantities useful for robust control analysis and design; (2) experiment design tailored to performing system identification in a typically constrained on-orbit environment; and (3) the automation of operations to reduce 'human in the loop' requirements.

Bayard, D. S.↗
DOE OSTI2020

Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. In this work, we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Probing the Structure and Dynamics of Fluid Mixtures in Porous Materials Through Ultrafast Vibrational Spectro-Microscopy and Many-Body Molecular Dynamics

This research program focused on the characterization of both molecular structure and dynamics of aqueous solutions in various metal-organic frameworks (MOFs) and organic polymers that have recently been proposed for applications in water treatment technologies. This was accomplished by integrating ultrafast vibrational spectroscopy and microscopy, which are sensitive to local environments, molecular orientation, and dynamical couplings, with many-body molecular dynamics (MB-MD) simulations, which enable realistic modeling of aqueous systems and porous materials under different thermodynamic conditions. Our studies allowed for identifying the physical mechanisms and characterizing the underlying molecular interactions between water and host materials that determine the adsorption and transport processes of water in various MOFs and β-cyclodextrin polymers – prototypical examples of porous materials and polymers, that have recently been proposed for technological applications in water purification. By combining bulk- and surface-sensitive, spatially resolved ultrafast vibrational spectroscopy with MB-MD simulations, it was possible to gain broad insight into the structure and mobility of water under heterogeneous confinement at various length scales. In particular, measurements of surface- and bulk-sensitive vibrational spectra at single crystal level, integrated with MB-MD simulations were used to characterize domain-specific, structure–binding affinity relationships. Besides providing specific information about the behavior of aqueous solutions in prototypical MOFs and organic polymers for potential applications in water treatment technologies, our studies also provided fundamental insights into the properties of aqueous solutions in confined heterogeneous environments, which have broad implications in many areas, ranging from heterogeneous catalysis to oil recovery, ion transport processes, and reaction-diffusion processes in crowded systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1990

A middle man approach to knowledge acquisition in expert systems

The Weed Control Advisor (WCA) is a robust expert system that has been successfully implemented on an IBM AT class microcomputer in CLIPS. The goal of the WCA was to demonstrate the feasibility of providing an economical, efficient, user friendly system through which Texas rice producers could obtain expert level knowledge regarding herbicide application for weed control. During the development phase of the WCA, an improved knowledge acquisition method which we call the Middle Man Approach (MMA) was applied to facilitate the communication process between the domain experts and the knowledge engineer. The MMA served to circumvent the problems associated with the more traditional forms of knowledge acquisition by placing the Middle Man, a semi-expert in the problem domain with some computer expertise, at the site of system development. The middle man was able to contribute to system development in two major ways. First, the Middle Man had experience working in rice production and could assume many of the responsibilities normally performed by the domain experts such as explaining the background of the problem domain and determining the important relations. Second, the Middle Man was familiar with computers and worked closely with the system developers to update the rules after the domain experts reviewed the prototype, contribute to the help menus and explanation portions of the expert system, conduct the testing that is required to insure that the expert system gives the expected results answer questions in a timely way, help the knowledge engineer structure the domain knowledge into a useable form, and provide insight into the end user's profile which helped in the development of the simple user friendly interface. The final results were not only that both time expended and costs were greatly reduced by using the MMA, but the quality of the system was improved. This papa will introduce the WCA system and then discuss traditional knowledge acquisition along with some of the problems often associated with it, the MMA methodology, and its application to the WCA development.

Jordan, Janice A.↗
DOE OSTI2024

Improving and Automating Building Model Data Exchange

There are many instances throughout a project’s lifecycle where there arises a need for quick and accurate risk assessment of building designs. For example, an unexpected design change during construction may necessitate structural engineers to perform a seismic risk assessment on analytical models of the updated building design using high fidelity structural analysis software, such as ANSYS or Abaqus. However, the efficiency of such workflows often depends upon the interoperability of architectural design software and structural analysis software. When the quality of this interoperability is lacking or even non-existent, the efficiency of virtual engineering workflows is hampered, which increases project costs. A McGraw Hill industry survey of professional users of Building Information Modeling (BIM) technologies found that there is high demand for BIM interoperability for structural analysis, but that the value/difficulty ratio is currently too low for practical use. There have been efforts by the academic community to facilitate model data exchange between the architectural design and structural analysis domains, but such solutions have not been widely adopted by industry, face technical challenges, and oftentimes are limited in applicability for users of various BIM software. Therefore, INL is developing capabilities to improve, automate, and generalize model data exchange between architectural BIM software (e.g., Revit) and structural analysis software (e.g., SAP2000, ANSYS). The goal is to help expedite and automate as much of the pre-processing step for creating analytical models in finite element analysis software as reasonably as possible. Such a "BIM-to-FEA" conversion tool should provide direct benefit to end-users through accuracy, automation, quick turn-around, and wide applicability. To generalize the application of this BIM-to-FEA conversion tool and increase its useability among the many different commercial BIM software currently used by industry, the program is being developed with the concept of openBIM. OpenBIM is the application of non-proprietary, open data standards that allow for BIM model data exchange in a format that is accessible, retainable, and useable for all users. The most widely used open, non-proprietary data exchange format for BIM is the Industry Foundation Classes (IFC) schema. IFC is developed by buildingSMART international and is ISO certified (ISO 16739-1:2018). The BIM-to-FEA conversion tool is being developed for compatibility with typical commercial building designs of steel framed structures. The tool is currently capable of importing architectural BIM data of framed building structures, recognizing and extracting the aspects of the model that are required for structural analysis, adjusting the connectivity of frame members, and finally exporting to an analytical model stored in the IFC format. The exported IFC analytical model can then be imported into various openBIM compliant software, such as SAP2000. Such capabilities have already been tested on commercial software, as shown above, and continue to be improved. Work is underway to test the conversion on various commercial BIM software, develop a user-friendly interface, incorporate the program into the broader DeepLynx data warehouse project being developed by INL, and to eventually open-source the tool for the benefit of the community. Future development of the tool envisions the ability for efficient iterative risk assessment of generative building designs, all within a workflow utilizing open-source tools. One such open-source tool will be MOOSE, an advanced finite element analysis tool developed at INL. The conversion tool will also branch out from typical commercial building designs and will aim to incorporate nuclear construction. The aim will be to convert both structural and non-structural components of nuclear facilities, such as curved concrete containment structures and piping systems, respectively.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Exceptional Cycling Performance Enabled by Local Structural Rearrangements in Disordered Rocksalt Cathodes

The capacity of lithium transition-metal (TM) oxide cathodes is directly linked to the magnitude and accessibility of the redox reservoir associated with TM cations and/or oxygen anions, which traditionally decreases with cycling as a result of chemical, structural, or mechanical fatigue. Here, it is shown that a capacity increase over 125% can be achieved upon cycling of high-energy Mn- and F-rich cation-disordered rocksalt oxyfluoride cathodes. This study reveals that in Li 1.2 Mn 0.7 Nb 0.1 O 1.8 F 0.2 , repeated Li extraction/reinsertion utilizing Mn 3+ /Mn 4+ redox along with some degree of O-redox participation leads to local structural rearrangements and formation of domains with off-stoichiometry spinel-like features. The effective integration of these local “structure-domains” within the cubic disordered rocksalt framework promotes better Li diffusion and improves material utilization, consequently increased capacity upon cycling. Finally, this study provides important new insights into materials design strategies to further exploit the rich compositional and structural space of Mn chemistry for developing sustainable, high-energy cathode materials.

25 ENERGY STORAGE↗
NASA NTRS1980

Investigation of multilayer magnetic domain lattice file

The feasibility of the self structured multilayered bubble domain memory as a mass memory medium for satellite applications is examined. Theoretical considerations of multilayer bubble supporting materials are presented, in addition to the experimental evaluation of current accessed circuitry for various memory functions. The design, fabrication, and test of four device designs is described, and a recommended memory storage area configuration is presented. Memory functions which were demonstrated include the current accessed propagation of bubble domains and stripe domains, pinning of stripe domain ends, generation of single and double bubbles, generation of arrays of coexisting strip and bubble domains in a single garnet layer, and demonstration of different values of the strip out field for single and double bubbles indicating adequate margins for data detection. All functions necessary to develop a multilayer self structured bubble memory device were demonstrated in individual experiments.

Torok, E. J.↗
DOE OSTI2023

Real-Space Infrared Spectroscopy of Ferroelectric Domain Walls in Multiferroic h -(Lu,Sc)FeO 3

Herein we employ synchrotron-based near-field infrared spectroscopy to image the phononic properties of ferroelectric domain walls in hexagonal ( h ) Lu 0.6 Sc 0.4 FeO 3 , and we compare our findings with a detailed symmetry analysis, lattice dynamics calculations, and prior models of domain-wall structure. Rather than metallic and atomically thin as observed in the rare-earth manganites, ferroelectric walls in h -Lu 0.6 Sc 0.4 FeO 3 are broad and semiconducting, a finding that we attribute to the presence of an A -site substitution-induced intermediate phase that reduces strain and renders the interior of the domain wall nonpolar. Mixed Lu/Sc occupation on the A site also provides compositional heterogeneity over micron-sized length scales, and we leverage the fact that Lu and Sc cluster in different ratios to demonstrate that the spectral characteristics at the wall are robust even in different compositional regimes. This work opens the door to broadband imaging of physical and chemical heterogeneity in ferroics and represents an important step toward revealing the rich properties of these flexible defect states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗