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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

The semi-discrete Galerkin finite element modelling of compressible viscous flow past an airfoil

A method is developed to solve the two-dimensional, steady, compressible, turbulent boundary-layer equations and is coupled to an existing Euler solver for attached transonic airfoil analysis problems. The boundary-layer formulation utilizes the semi-discrete Galerkin (SDG) method to model the spatial variable normal to the surface with linear finite elements and the time-like variable with finite differences. A Dorodnitsyn transformed system of equations is used to bound the infinite spatial domain thereby permitting the use of a uniform finite element grid which provides high resolution near the wall and automatically follows boundary-layer growth. The second-order accurate Crank-Nicholson scheme is applied along with a linearization method to take advantage of the parabolic nature of the boundary-layer equations and generate a non-iterative marching routine. The SDG code can be applied to any smoothly-connected airfoil shape without modification and can be coupled to any inviscid flow solver. In this analysis, a direct viscous-inviscid interaction is accomplished between the Euler and boundary-layer codes, through the application of a transpiration velocity boundary condition. Results are presented for compressible turbulent flow past NACA 0012 and RAE 2822 airfoils at various freestream Mach numbers, Reynolds numbers, and angles of attack. All results show good agreement with experiment, and the coupled code proved to be a computationally-efficient and accurate airfoil analysis tool.

Meade, Andrew J., Jr.↗
NASA NTRS1993

Semi-discrete Galerkin solution of the compressible boundary-layer equations with viscous-inviscid interaction

A semi-discrete Galerkin (SDG) method is under development to model attached, turbulent, and compressible boundary layers for transonic airfoil analysis problems. For the boundary-layer formulation the method models the spatial variable normal to the surface with linear finite elements and the time-like variable with finite differences. A Dorodnitsyn transformed system of equations is used to bound the infinite spatial domain thereby providing high resolution near the wall and permitting the use of a uniform finite element grid which automatically follows boundary-layer growth. The second-order accurate Crank-Nicholson scheme is applied along with a linearization method to take advantage of the parabolic nature of the boundary-layer equations and generate a non-iterative marching routine. The SDG code can be applied to any smoothly-connected airfoil shape without modification and can be coupled to any inviscid flow solver. In this analysis, a direct viscous-inviscid interaction is accomplished between the Euler and boundary-layer codes through the application of a transpiration velocity boundary condition. Results are presented for compressible turbulent flow past RAE 2822 and NACA 0012 airfoils at various freestream Mach numbers, Reynolds numbers, and angles of attack.

Day, Brad A.↗
NASA NTRS2012

Causal Correlation Functions and Fourier Transforms: Application in Calculating Pressure Induced Shifts

By adopting a concept from signal processing, instead of starting from the correlation functions which are even, one considers the causal correlation functions whose Fourier transforms become complex. Their real and imaginary parts multiplied by 2 are the Fourier transforms of the original correlations and the subsequent Hilbert transforms, respectively. Thus, by taking this step one can complete the two previously needed transforms. However, to obviate performing the Cauchy principal integrations required in the Hilbert transforms is the greatest advantage. Meanwhile, because the causal correlations are well-bounded within the time domain and band limited in the frequency domain, one can replace their Fourier transforms by the discrete Fourier transforms and the latter can be carried out with the FFT algorithm. This replacement is justified by sampling theory because the Fourier transforms can be derived from the discrete Fourier transforms with the Nyquis rate without any distortions. We apply this method in calculating pressure induced shifts of H2O lines and obtain more reliable values. By comparing the calculated shifts with those in HITRAN 2008 and by screening both of them with the pair identity and the smooth variation rules, one can conclude many of shift values in HITRAN are not correct.

correlation function↗
NASA NTRSDate not supplied

Verifying PLC Programs via Monitors: Extending the Integration of FRET and PLCverif

Verification of Programmable Logic Controller (PLC) programs requires reasoning about propositions qualified in terms of time. CERN’s PLCverif, an open-source tool for the analysis of safety-critical PLC systems, uses Linear Temporal Logic (LTL) for the specification of properties. Until now, PLCverif depended on third-party tools that accept LTL specifications to perform verification. However, our experience with industrial PLC programs shows that, to overcome analysis limitations, a wide range of techniques are needed to successfully verify complex properties. In this paper, we extend PLCverif to enable PLC program verification of pure-past LTL (PLTL) safety properties with assertion-based verification tools. To this end, we take an algorithm from the runtime-monitoring domain, apply it to bounded model checking of PLC programs, and implement it in PLCverif. We extend the integration of NASA’s Formal Requirements Elicitation Tool (FRET) into PLCverif to use PLTL properties generated with FRET. In addition, we leverage the program structure induced by the PLC scan-cycle for a state-space reduction. Finally, we expose the algorithm to a real-world case study of critical systems at CERN.

Formal verification↗
DOE OSTI2021

Scaled boundary cubature scheme for numerical integration over planar regions with affine and curved boundaries

This paper introduces the scaled boundary cubature (SBC) scheme for accurate and efficient integration of functions over polygons and two-dimensional regions bounded by parametric curves. Over two-dimensional domains, the SBC method reduces integration over a region bounded by m curves to integration over m regions (referred to as curved triangular regions), where each region is bounded by two line segments and a curve. With proper (counterclockwise) orientation of the boundary curves, the scheme is applicable to convex and nonconvex domains. Additionally, for star-convex domains, a tensor-product cubature rule with positive weights and integration points in the interior of the domain is obtained. If the integrand is homogeneous, we show that this new method reduces to the homogeneous numerical integration scheme; however, the SBC scheme is more versatile since it is equally applicable to both homogeneous and non-homogeneous functions. This paper also introduces several methods for smoothing integrands with point singularities and near-singularities. When these methods are used, highly efficient integration of weakly singular functions is realized. Finally, the SBC method is applied to a number of benchmark problems, which reveal its broad applicability and superior performance (in terms of time to generate a rule and accuracy per cubature point) when compared to existing methods for integration.

42 ENGINEERING↗
DOE OSTI2021

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants

The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme–HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively. The calculated sequence similarity networks between HISN2 analogs from prokaryotes and eukaryotes suggest that the plant enzymes are closest relatives of those in the class of Deltaproteobacteria. In this work, we obtained crystal structures of HISN2 enzyme from Medicago truncatula (MtHISN2) and described its architecture and interactions with AMP. The AMP molecule bound to the PRA-PH domain shows positioning of the N1-phosphoribosyl relevant to catalysis. AMP bound to the PRA-CH domain mimics a part of the substrate, giving insights into the reaction mechanism. The latter interaction also arises as a possible second-tier regulatory mechanism of the HBP flux, as indicated by inhibition assays and isothermal titration calorimetry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation

Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ~250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L–P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Coherent lidar design and performance verification

The verification of LAWS beam alignment in space can be achieved by a measurement of heterodyne efficiency using the surface return. The crucial element is a direct detection signal that can be identified for each surface return. This should be satisfied for LAWS but will not be satisfied for descoped LAWS. The performance of algorithms for velocity estimation can be described with two basic parameters: the number of coherently detected photo-electrons per estimate and the number of independent signal samples per estimate. The average error of spectral domain velocity estimation algorithms are bounded by a new periodogram Cramer-Rao Bound. Comparison of the periodogram CRB with the exact CRB indicates a factor of two improvement in velocity accuracy is possible using non-spectral domain estimators. This improvement has been demonstrated with a maximum-likelihood estimator. The comparison of velocity estimation algorithms for 2 and 10 micron coherent lidar was performed by assuming all the system design parameters are fixed and the signal statistics are dominated by a 1 m/s rms wind fluctuation over the range gate. The beam alignment requirements for 2 micron are much more severe than for a 10 micron lidar. The effects of the random backscattered field on estimating the alignment error is a major problem for space based lidar operation, especially if the heterodyne efficiency cannot be estimated. For LAWS, the biggest science payoff would result from a short transmitted pulse, on the order of 0.5 microseconds instead of 3 microseconds. The numerically errors for simulation of laser propagation in the atmosphere have been determined as a joint project with the University of California, San Diego. Useful scaling laws were obtained for Kolmogorov atmospheric refractive turbulence and an atmospheric refractive turbulence characterized with an inner scale. This permits verification of the simulation procedure which is essential for the evaluation of the effects of refractive turbulence on coherent Doppler lidar systems. The analysis of 2 micron Doppler lidar data from Coherent Technologies, Inc. (CTI) has demonstrated many of the advantages of doppler lidar measurements of boundary layer winds. The effects of wind shear and wind turbulence over the pulse volume are probably the dominant source of the reduced performance. The effects of wind shear and wind turbulence on the statistical description of doppler lidar data has been derived and calculated.

Frehlich, Rod↗
DOE OSTI2020

A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi

Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Lepto-axiogenesis and the scale of supersymmetry

If the Peccei-Quinn field containing the QCD axion undergoes rotations in the early universe, the dimension-five operator responsible for neutrino masses can generate a lepton asymmetry that ultimately gives rise to the observed baryon asymmetry of the Universe. This lepto-axiogenesis scenario requires a flat potential for the radial direction of the Peccei-Quinn field, naturally realized in supersymmetric models. We carefully compute the efficiency of this mechanism for the Dine-Fischler-Srednicki-Zhitnitsky (DFSZ) and Kim-Shifman-Vainshtein-Zakharov (KSVZ) axion models and place lower bounds on the masses of scalar superpartners required to reproduce the observed baryon asymmetry. For the KSVZ model, we find an efficiency for generation of the asymmetry six times larger than the previously extant computation after including scattering channels involving superpartners. In this case, the superpartner scale should be above 30 TeV for a domain wall number of one; the lower bound weakens for larger domain wall numbers. We find that the superpartner mass scale may also be as low as ~ 30 TeV for the DFSZ model. In all cases, the lower bound on the superpartner masses is inversely proportional to the sum of the squares of the neutrino masses and so can strengthen as the upper bound on the neutrino mass improves. We identify the parameter space where the axion rotation can simultaneously produce axion dark matter via kinetic misalignment; in this case it is possible to put an upper bound of order PeV on the masses of scalar superpartners.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1994

Performance of mean-frequency estimators for Doppler radar and lidar

The performance of mean-frequency estimators for Doppler radar and lidar measurements of winds is presented in terms of two basic parameters: Phi, the ratio of the average signal energy per estimate to the spectral noise level; and Omega, which is proportional to the number of independent samples per estimate. For fixed Phi and Omega, the Cramer-Rao bound (CRB) (theoretical best performance) for unbiased estimators of mean frequency (normalized by the spectral width of the signal), signal power, and spectral width are essentially independent of the number of data samples M. For large Phi, the estimators of mean frequency are unbiased and the performance is independent of M. The spectral domain estimators and covariance based estimators are bounded by the approximate period of M. The spectral domain estimators and covariance based estimators are bounded by the approximate periodogram CRB. The standard deviation of the maximum-likelihood estimator approaches the exact CRB, which can be more than a factor of 2 better than the performance of the spectral domain estimators or covariance-based estimators for typical Omega. For small Phi, the estimators are biased due to the effects of the uncorrelated noise (white noise), which results in uniformly distributed 'bad' estimates. The fraction of bad estimates is a function of Phi and M with weak dependence on the parameter Omega. Simple empirical models describe the standard deviation of the good estimates and the fraction of bad estimates. For Doppler lidar and for large Phi, better performance is obtained by using many low-energy pulses instead of one pulse with the same total energy. For small Phi, the converse is true.

Frehlich, R. G.↗
DOE OSTI2022

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes, including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD structures reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated operator DNA binding activation. Biochemical and in vivo studies support the structural model. Our data thus reveal the molecular mechanism underpinning an SOS-independent DNA damage repair pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sensitivity Analysis for Solutions to Heterogeneous Nonlocal Systems. Theoretical and Numerical Studies

The paper presents a collection of results on continuous dependence for solutions to nonlocal problems under perturbations of data and system parameters. The integral operators appearing in the systems capture interactions via heterogeneous kernels that exhibit different types of weak singularities, space dependence, even regions of zero-interaction. Here, the stability results showcase explicit bounds involving the measure of the domain and of the interaction collar size, nonlocal Poincaré constant, and other parameters. In the nonlinear setting, the bounds quantify in different L p norms the sensitivity of solutions under different nonlinearity profiles. The results are validated by numerical simulations showcasing discontinuous solutions, varying horizons of interactions, and symmetric and heterogeneous kernels.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation

SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective inhibition of these domains has been challenging due to the multitude of homologous proteins in the proteome. Here, we developed a monobody, synthetic binding protein, that bound to and inhibited the SHP2 PTP domain. It was selective to SHP2 PTP over close homologs. A crystal structure of the monobody-PTP complex revealed that the monobody bound both highly conserved residues in the active site and less conserved residues in the periphery, rationalizing its high selectivity. Its epitope overlapped with the interface between the PTP and N-terminal SH2 domains that is formed in auto-inhibited SHP2. By using the monobody as a probe for the accessibility of the PTP active site, we developed a simple, nonenzymatic assay for the allosteric regulation of SHP2. The assay showed that, in the absence of an activating phospho-Tyr ligand, wild-type SHP2 and the “PTP-dead” C459E mutant were predominantly in the closed state in which the PTP active site is inaccessible, whereas the E76K and C459S mutants were in the open, active state. It also revealed that previously developed monobodies to the SH2 domains, ligands lacking a phospho-Tyr, weakly favored the open state. These results provide corroboration for a conformational equilibrium underlying allosteric regulation of SHP2, provide powerful tools for characterizing and controlling SHP2 functions, and inform drug discovery against SHP2.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2024

A Convexification-Based Outer-Approximation Method for Convex and Nonconvex MINLP

The advancement of domain reduction techniques has significantly enhanced the performance of solvers in mathematical programming. This paper delves into the impact of integrating convexification and domain reduction techniques within the Outer-Approximation method. We propose a refined convexification-based Outer-Approximation method alongside a Branch-and-Bound method for both convex and nonconvex Mixed-Integer Nonlinear Programming problems. These methods have been developed and incorporated into the open-source Mixed-Integer Nonlinear Decomposition Toolbox for Pyomo-MindtPy. Comprehensive benchmark tests were conducted, validating the effectiveness and reliability of our proposed algorithms. These tests highlight the improvements achieved by incorporating convexification and domain reduction techniques into the Outer-Approximation and Branch-and-Bound methods.

Optimization↗
DOE OSTI2025

Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, "pipe strap" conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.

Fenwick, Michael K↗
DOE OSTI2023

Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS‐CoV‐2

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) enters the host cell by binding to angiotensin‐converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS‐CoV‐2 viruses impact species specificity. Reverse zoonoses led to SARS‐CoV‐2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink‐associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio‐layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink‐derived S glycoproteins of SARS‐CoV‐2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo‐electron microscopy (cryo‐EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor‐binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S‐ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS‐CoV‐2 entry.

Virology↗
DOE OSTI2023

Structural basis for flagellin-induced NAIP5 activation

The NAIP (NLR family apoptosis inhibitory protein)/NLRC4 (NLR family CARD containing protein 4) inflammasome senses Gram-negative bacterial ligand. In the ligand-bound state, the winged helix domain of NAIP forms a steric clash with NLRC4 to open it up. However, how ligand binding activates NAIP is less clear. Here, we investigated the dynamics of the ligand-binding region of inactive NAIP5 and solved the cryo-EM structure of NAIP5 in complex with its specific ligand, FliC from flagellin, at 2.9-Å resolution. The structure revealed a “trap and lock” mechanism in FliC recognition, whereby FliC-D0 C is first trapped by the hydrophobic pocket of NAIP5, then locked in the binding site by ID (insertion domain) and C-terminal tail of NAIP5. The FliC-D0 N domain further inserts into ID to stabilize the complex. According to this mechanism, FliC triggers the conformational change of NAIP5 by bringing multiple flexible domains together.

60 APPLIED LIFE SCIENCES↗