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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Autoinhibition of a calmodulin-dependent calcium pump involves a structure in the stalk that connects the transmembrane domain to the ATPase catalytic domain

The regulation of Ca(2+)-pumps is important for controlling [Ca(2+)] in the cytosol and organelles of all eukaryotes. Here, we report a genetic strategy to identify residues that function in autoinhibition of a novel calmodulin-activated Ca(2+)-pump with an N-terminal regulatory domain (isoform ACA2 from Arabidopsis). Mutant pumps with constitutive activity were identified by complementation of a yeast (K616) deficient in two Ca(2+)-pumps. Fifteen mutations were found that disrupted a segment of the N-terminal autoinhibitor located between Lys(23) and Arg(54). Three mutations (E167K, D219N, and E341K) were found associated with the stalk that connects the ATPase catalytic domain (head) and with the transmembrane domain. Enzyme assays indicated that the stalk mutations resulted in calmodulin-independent activity, with V(max), K(mATP), and K(mCa(2+)) similar to that of a pump in which the N-terminal autoinhibitor had been deleted. A highly conservative substitution at Asp(219) (D219E) still produced a deregulated pump, indicating that the autoinhibitory structure in the stalk is highly sensitive to perturbation. In plasma membrane H(+)-ATPases from yeast and plants, similarly positioned mutations resulted in hyperactive pumps. Together, these results suggest that a structural feature of the stalk is of general importance in regulating diverse P-type ATPases.

NASA Discipline Plant Biology↗
DOE OSTI2020

Intrinsic Ion Transport Properties of Block Copolymer Electrolytes

Knowledge of intrinsic properties is of central importance for materials design and assessing suitability for specific applications. Self-assembling block copolymer electrolytes (BCEs) are of great interest for applications in solid-state energy storage devices. A fundamental understanding of ion transport properties, however, is hindered by the difficulty in deconvoluting extrinsic factors, such as defects, from intrinsic factors, such as the presence of interfaces between the domains. Here, we quantify the intrinsic ion transport properties of a model BCE system consisting of poly(styrene-block-ethylene oxide) (SEO) and lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt using a generalizable strategy of depositing thin films on interdigitated electrodes and self-assembling fully connected parallel lamellar structures throughout the films. Comparison between conductivity in homopolymer poly(ethylene oxide) (PEO)-LiTFSI electrolytes and the analogous conducting material in SEO over a range of salt concentrations (r, molar ratio of lithium ion to ethylene oxide repeat units) and temperatures reveals that between 20% and 50% of the PEO in SEO is inactive. Using mean-field theory calculations of the domain structure and monomer concentration profiles at domain interfaces-both of which vary substantially with salt concentration-the fraction of inactive PEO in the SEO, as derived from conductivity measurements, can be quantitatively reconciled with the fraction of PEO that is mixed with greater than a few volume percent of polystyrene. Despite the detrimental interfacial effects for ion transport in BCEs, the intrinsic conductivity of the SEO studied here (ca. 10 -3 S/cm at 90 degrees C, r = 0.085) is an order of magnitude higher than reported values from bulk samples of similar molecular weight SEO (ca. 10 -4 S/cm at 90 degrees C, r = 0.085). Finally, this work provides motivation and methods for pursuing improved BCE chemical design, interfacial engineering, and processing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2004

Structure Constraints in a Constraint-Based Planner

In this paper we report our work on a new constraint domain, where variables can take structured values. Earth-science data processing (ESDP) is a planning domain that requires the ability to represent and reason about complex constraints over structured data, such as satellite images. This paper reports on a constraint-based planner for ESDP and similar domains. We discuss our approach for translating a planning problem into a constraint satisfaction problem (CSP) and for representing and reasoning about structured objects and constraints over structures.

Pang, Wan-Lin↗
DOE OSTI2023

Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230

Pfs230 is essential for Plasmodium falciparum transmission to mosquitoes and is the protein targeted by the most advanced malaria-transmission-blocking vaccine candidate. Prior understanding of functional epitopes on Pfs230 is based on two monoclonal antibodies (mAbs) with moderate transmission-reducing activity (TRA), elicited from subunit immunization. Here, we screened the B cell repertoire of two naturally exposed individuals possessing serum TRA and identified five potent mAbs from sixteen Pfs230 domain-1-specific mAbs. Structures of three potent and three low-activity antibodies bound to Pfs230 domain 1 revealed four distinct epitopes. Highly potent mAbs from natural infection recognized a common conformational epitope that is highly conserved across P. falciparum field isolates, while antibodies with negligible TRA derived from natural infection or immunization recognized three distinct sites. Our study provides molecular blueprints describing P. falciparum TRA, informed by contrasting potent and non-functional epitopes elicited by natural exposure and vaccination.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Tetrahedral Trees: A Family of Hierarchical Spatial Indexes for Tetrahedral Meshes

In this work, we address the problem of performing efficient spatial and topological queries on large tetrahedral meshes with arbitrary topology and complex boundaries. Such meshes arise in several application domains, such as 3D Geographic Information Systems (GISs), scientific visualization, and finite element analysis. To this aim, we propose Tetrahedral trees, a family of spatial indexes based on a nested space subdivision (an octree or a kD-tree) and defined by several different subdivision criteria. We provide efficient algorithms for spatial and topological queries on Tetrahedral trees and compare to state-of-the-art approaches. Our results indicate that Tetrahedral trees are an improvement over R*-trees for querying tetrahedral meshes; they are more compact, faster in many queries, and stable at variations of construction thresholds. They also support spatial queries on more general domains than topological data structures, which explicitly encode adjacency information for efficient navigation but have difficulties with domains with a non-trivial geometric or topological shape.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1987

Methodology for testing and validating knowledge bases

A test and validation toolset developed for artificial intelligence programs is described. The basic premises of this method are: (1) knowledge bases have a strongly declarative character and represent mostly structural information about different domains, (2) the conditions for integrity, consistency, and correctness can be transformed into structural properties of knowledge bases, and (3) structural information and structural properties can be uniformly represented by graphs and checked by graph algorithms. The interactive test and validation environment have been implemented on a SUN workstation.

Krishnamurthy, C.↗
NASA NTRS1988

The onset of plume dynamics in the spectral space

Time-dependent convection for infinite Prandtl number fluids has been investigated hitherto in the physical domain. Dynamics of plumelike structures resulting from boundary-layer instabilities can be interpreted in the spectral domain as having both direct and inverse cascades of energy taking place. In the physical domain only a small part of the spectrum is discernible. But the rest of the spectrum is needed for properly describing the nonlinear process. Only a relatively few modes, fewer than ten, are actually required for describing the essential features associated with the onset of plume dynamics.

Vincent, Alain P.↗
DOE OSTI2025

Slender-body approach for computing second-order wave loads in the frequency domain

This work presents a slender-body approach to evaluate the second-order wave loads acting on a floating structure in the frequency domain. The approach is in the same spirit as the common use of Morison’s equation to approximate the wave loads without solving the radiation/diffraction problem. To do so, we employ Rainey’s equation, which can be seen as an extension of the inertial part of Morison’s equation to include nonlinear effects. We introduce modifications to Rainey’s formulation in order to evaluate wave kinematics at the mean body position instead of the original approach of considering instantaneous displacements. We also propose a simple approximation to partially account for wave scattering effects on the second-order loads based on the analytical solution of a surface-piercing bottom-mounted vertical circular cylinder. Though limited to structures composed of cylinders, this slender-body approach is orders of magnitude faster than computing second-order wave coefficients with a radiation/diffraction code. We implemented this approach for difference-frequency (slow drift) loads in an open-source frequency-domain floating wind turbine model. We present comparisons against results obtained with radiation/diffraction theory for three reference floating wind turbine designs: the OC3-Hywind spar, the OC4-DeepCwind semisubmersible, and the VolturnUS-S semisubmersible. In general, the results show that the proposed slender-body approach with the correction to approximate wave scattering effects provides useful estimations of the difference-frequency wave loads and the resulting motions of the floater.

17 WIND ENERGY↗
DOE OSTI2020

Tandem sialoglycan-binding modules in a Streptococcus sanguinis serine-rich repeat adhesin create target dependent avidity effects

Sialic acid–binding immunoglobulin-like lectins (Siglec)–like domains of streptococcal serine-rich repeat (SRR) adhesins recognize sialylated glycans on human salivary, platelet, and plasma glycoproteins via a YTRY sequence motif. The SRR adhesin from Streptococcus sanguinis strain SK1 has tandem sialoglycan-binding domains and has previously been shown to bind sialoglycans with high affinity. However, both domains contain substitutions within the canonical YTRY motif, making it unclear how they interact with host receptors. To identify how the S. sanguinis strain SK1 SRR adhesin affects interactions with sialylated glycans and glycoproteins, we determined high-resolution crystal structures of the binding domains alone and with purified trisaccharides. These structural studies determined that the ligands still bind at the noncanonical binding motif, but with fewer hydrogen-bonding interactions to the protein than is observed in structures of other Siglec-like adhesins. Complementary biochemical studies identified that each of the two binding domains has a different selectivity profile. Interestingly, the binding of SK1 to platelets and plasma glycoproteins identified that the interaction to some host targets is dominated by the contribution of one binding domain, whereas the binding to other host receptors is mediated by both binding domains. These results provide insight into outstanding questions concerning the roles of tandem domains in targeting host receptors and suggest mechanisms for how pathogens can adapt to the availability of a range of related but nonidentical host receptors. They further suggest that the definition of the YTRY motif should be changed to ΦTRX, a more rigorous description of this sialic acid–recognition motif given recent findings.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Domain modeling and grid generation for multi-block structured grids with application to aerodynamic and hydrodynamic configurations

About five years ago, a joint development was started of a flow simulation system for engine-airframe integration studies on propeller as well as jet aircraft. The initial system was based on the Euler equations and made operational for industrial aerodynamic design work. The system consists of three major components: a domain modeller, for the graphical interactive subdivision of flow domains into an unstructured collection of blocks; a grid generator, for the graphical interactive computation of structured grids in blocks; and a flow solver, for the computation of flows on multi-block grids. The industrial partners of the collaboration and NLR have demonstrated that the domain modeller, grid generator and flow solver can be applied to simulate Euler flows around complete aircraft, including propulsion system simulation. Extension to Navier-Stokes flows is in progress. Delft Hydraulics has shown that both the domain modeller and grid generator can also be applied successfully for hydrodynamic configurations. An overview is given about the main aspects of both domain modelling and grid generation.

Spekreijse, S. P.↗
DOE OSTI2021

Osmosensing by WNK Kinases

With No Lysine (K) WNK kinases regulate electro-neutral cotransporters that are controlled by osmotic stress and chloride. We showed previously that autophosphorylation of WNK1 is inhibited by chloride, raising the possibility that WNKs are activated by osmotic stress. Here we demonstrate that unphosphorylated WNK isoforms 3 and 1 autophosphorylate in response to osmotic pressure in vitro, applied with the crowding agent polyethylene glycol (PEG)400 or osmolyte ethylene glycol (EG), and that this activation is opposed by chloride. Small angle x-ray scattering of WNK3 in the presence and absence of PEG400, static light scattering in EG, and crystallography of WNK1 were used to understand the mechanism. Osmosensing in WNK3 and WNK1 appears to occur through a conformational equilibrium between an inactive, unphosphorylated, chloride-binding dimer and an autophosphorylation-competent monomer. An improved structure of the inactive kinase domain of WNK1, and a comparison with the structure of a monophosphorylated form of WNK1, suggests that large cavities, greater hydration, and specific bound water may participate in the osmosensing mechanism. Our prior work showed that osmolytes have effects on the structure of phosphorylated WNK1, suggestive of multiple stages of osmotic regulation in WNKs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Terrace‐Edge‐Induced Domain Nucleation in Room‐Temperature 2D Magnetic Van Der Waals Heterostructures

Abstract Terrace‐edges, which are step‐like height discontinuities formed during layer stacking or exfoliation, can locally modify magnetic characteristics. Magnetic domain behavior and its structural dependence in a 2D van der Waals (vdW) heterostructure composed of two distinct room‐temperature ferromagnets: Fe 3 GaTe 2 , an intrinsic vdW ferromagnet, and vanadium‐doped WSe 2 , a transition metal dichalcogenide exhibiting defect‐induced magnetism, is investigated. Using magnetic transmission X‐ray microscopy, the formation and annihilation of magnetic domains are directly observed and it is found that domains preferentially form at terrace‐edges of the heterostructure. Micromagnetic simulations reveal that in‐plane magnetization tilting near the terrace‐edge results in a localized maximum in total magnetic energy that promotes domain formation. The findings highlight the significant role of structural edge features and interfacial magnetic interactions in determining domain formation in hybrid 2D vdW magnetic systems, offering a new route to spatially controlled magnetization at room temperature.

Lee, Jieun↗
NASA NTRS1990

Finite element analysis and optimization of composite structures

Linearly elastic fiber reinforced composite discs and laminates in plane stress with variable local orientation and concentration of one or two fiber fields embedded in the matrix material, are considered. The thicknesses and the domain of the discs or laminates are assumed to be given, together with prescribed boundary conditions and in-plane loading along the edge. The problem under study consists in determining throughout the structural domain the optimum orientations and concentrations of the fiber fields in such a way as to maximize the integral stiffness of the composite disc or laminate under the seven loading. Minimization of the integral stiffness can also be performed. The optimization is performed subject to a prescribed bound on the total cost or weight of the composite that for given unit cost factors or specific weights determines the amounts of fiber and matrix materials in the structure. Examples are presented.

Thomsen, Jan↗
DOE OSTI2023

A VOI Web Application for Distinct Geothermal Domains: Statistical Evaluation of Different Data Types within the Great Basin

The Great Basin region contains different domains that have different structural and hydrothermal flow patterns. Depending on the characteristics of these patterns, certain data types may be more successful at detecting hidden geothermal resources. In this paper, we quantitatively evaluate if certain data types are more successful in certain domains. Given different aquifer, strain and structural conditions, we explore which data types statistically reveal positively labeled geothermal sites. We utilize value of information (VOI) metrics to help quantify the reliability of data types to discriminate against "positive" and "negative" labeled geothermal sites. We also evaluate how kernel density estimation can help generalize the statistics that inform VOI, which is necessary given the limited data in geothermal exploration. Except for the Carbonate Aquifer, the highest ranking of the Vimperfect is the Local Structural Setting. Next, the slip and dilation tendency is first for Carbonate Aquifer and second for Central Nevada Seismic Belt and Western Great Basin. For the Carbonate Aquifer, heat flow is has the lowest Vimperfect value compared to the other three domains, which is consistent with the understanding of how heat flow measurements are masked by regional groundwater flow.

Bayesian analysis↗
DOE OSTI2023

Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis

Deubiquitination of cellular substrates by viral proteases is a mechanism used to interfere with host cellular signaling processes, shared between members of the coronavirus- and arterivirus families. In the case of Arteriviruses, deubiquitinating and polyprotein processing activities are accomplished by the virus-encoded papain-like protease 2 (PLP2). Several studies have implicated the deubiquitinating activity of the porcine reproductive and respiratory syndrome virus (PRRSV) PLP2 in the downregulation of cellular interferon production, however to date, the only arterivirus PLP2 structure described is that of equine arteritis virus (EAV), a distantly related virus. Here we describe the first crystal structure of the PRRSV PLP2 domain both in the presence and absence of its ubiquitin substrate, which reveals unique structural differences in this viral domain compared to PLP2 from EAV. To probe the role of PRRSV PLP2 deubiquitinating activity in host immune evasion, we selectively removed this activity from the domain by mutagenesis and found that the viral domain could no longer downregulate cellular interferon production. Interestingly, unlike EAV, and also unlike the situation for MERS-CoV, we found that recombinant PRRSV carrying PLP2 DUB-specific mutations faces significant selective pressure to revert to wild-type virus in MARC-145 cells, suggesting that the PLP2 DUB activity, which in PRRSV is present as three different versions of viral protein nsp2 expressed during infection, is critically important for PRRSV replication.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
DOE OSTI2022

The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation

Yeast Cadmium Factor 1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically-disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4 Å and 4.0 Å resolution in inward-facing open conformations that capture previously unobserved ordered states of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the Lasso motif. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide insights into how R-domains control ABCC transporter activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Serodominant SARS-CoV-2 Nucleocapsid Peptides Map to Unstructured Protein Regions

The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern.

60 APPLIED LIFE SCIENCES↗