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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Fast Butterfly-Compressed Hadamard–Babich Integrator for High-Frequency Helmholtz Equations in Inhomogeneous Media with Arbitrary Sources

Here we present a butterfly-compressed representation of the Hadamard-Babich (HB) ansatz for the Green's function of the high-frequency Helmholtz equation in smooth inhomogeneous media. For a computational domain discretized with Nv discretization cells, the proposed algorithm first solves and tabulates the phase and HB coefficients via eikonal and transport equations with observation points and point sources located at the Chebyshev nodes using a set of much coarser computation grids, and then butterfly compresses the resulting HB interactions from all Nv cell centers to each other. The overall CPU time and memory requirement scale as O(Nv log2 Nv) for any bounded two-dimensional (2D) domains with arbitrary excitation sources. A direct extension of this scheme to bounded 3D domains yields an O(Nv4/3) CPU complexity, which can be further reduced to quasi-linear complexities with proposed remedies. The scheme can also efficiently handle scattering problems involving inclusions in inhomogeneous media. Although the current construction of our HB integrator does not accommodate caustics, the resulting HB integrator itself can be applied to certain sources, such as concave-shaped sources, to produce caustic effects. Compared to finite-difference frequency domain methods, the proposed HB integrator is free of numerical dispersion and requires fewer discretization points per wavelength. As a result, it can solve wave propagation problems well beyond the capability of existing solvers. Remarkably, the proposed scheme can accurately model wave propagation in 2D domains with 640 wavelengths per direction and in 3D domains with 54 wavelengths per direction on a state-of-the-art supercomputer at Lawrence Berkeley National Laboratory.

Hadamard--Babich ansatz↗
NASA NTRS1980

Finite difference grid generation by multivariate blending function interpolation

The General Interpolants Method (GIM) code which solves the multidimensional Navier-Stokes equations for arbitrary geometric domains is described. The geometry module in the GIM code generates two and three dimensional grids over specified flow regimes, establishes boundary condition information and computes finite difference analogs for use in the GIM code numerical solution module. The technique can be classified as an algebraic equation approach. The geometry package uses multivariate blending function interpolation of vector-values functions which define the shapes of the edges and surfaces bounding the flow domain. By employing blending functions which conform to the cardinality conditions the flow domain may be mapped onto a unit square (2-D) or unit cube (3-D), thus producing an intrinsic coordinate system for the region of interest. The intrinsic coordinate system facilitates grid spacing control to allow for optimum distribution of nodes in the flow domain.

Anderson, P. G.↗
DOE OSTI2020

Investigation of Indigoidine Synthetase Reveals a Conserved Active-Site Base Residue of Nonribosomal Peptide Synthetase Oxidases

Nonribosomal peptide synthetase (NRPS) oxidase (Ox) domains oxidize protein-bound intermediates to install crucial structural motifs in bioactive natural products. The mechanism of this domain remains elusive. Here, by studying indigoidine synthetase, a single-module NRPS involved in the biosynthesis of indigoidine and several other bacterial secondary metabolites, we demonstrate that its Ox domain utilizes an active-site base residue, tyrosine 665, to deprotonate a protein-bound l-glutaminyl residue. In this work, we further validate the generality of this active-site residue among NRPS Ox domains. These findings not only resolve the biosynthetic pathway mediated by indigoidine synthetase but enable mechanistic insight into NRPS Ox domains.

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

X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain

Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear. Here we present a high-resolution X-ray crystal structure of ADP-bound Escherichia coli RadD, revealing a zinc-ribbon element that was not modelled in a previous RadD crystal structure. Insights into the mode of nucleotide binding and additional structure refinement afforded by the new RadD model will help to drive investigations into the activity of RadD as a genome stability and repair factor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conservative numerical schemes with optimal dispersive wave relations: Part I. Derivation and analysis

An energy-conserving and an energy-and-enstrophy conserving numerical schemes are derived by approximating the Hamiltonian formulation of the inviscid shallow water flows based on the vorticity-divergence variables. These schemes also conserve the first-order moments such as mass and vorticity, as usual. The conservative properties of the schemes stem from the skew-symmetry and singularities of the Poisson brackets, which are carefully retained in the discrete approximations. Here, the schemes operate on unstructured orthogonal dual meshes, over bounded or unbounded domains, and they are also shown to possess the same optimal dispersive wave relations as those of the Z-grid scheme, which is a consequence of the use of the vorticity and divergence variables.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A moment-conserving discontinuous Galerkin representation of the relativistic Maxwellian distribution

Kinetic simulations of relativistic gases and plasmas are critical for understanding diverse astrophysical and terrestrial systems, but the accurate construction of the relativistic Maxwellian, the Maxwell–Jüttner distribution, on a discrete simulation grid is challenging. Difficulties arise from the finite velocity bounds of the domain, which may not capture the entire distribution function, as well as errors introduced by projecting the function onto a discrete grid. Here, we present a novel scheme for iteratively correcting the moments of the projected distribution applicable to all grid-based discretizations of the relativistic kinetic equation. In addition, we describe how to compute the needed nonlinear quantities, such as Lorentz boost factors, in a discontinuous Galerkin scheme through a combination of numerical quadrature and weak operations. The resulting method accurately captures the distribution function and ensures that the moments match the desired values to machine precision.

astrophysical plasmas↗
DOE OSTI2022

A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases

The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an “induced fit” model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

SHP2 genetic variants in NSML-associated RASopathies disrupt the PZR–IRX transcription factor signaling axis

Noonan syndrome with multiple lentigines (NSML) is a rare autosomal dominant disorder caused by mutations inPTPN11(protein tyrosine phosphatase nonreceptor type 11) which encodes for the protein tyrosine phosphatase, SHP2. Approximately 85% of NSML patients develop hypertrophic cardiomyopathy (HCM). Here, we show that SHP2 is recruited to tyrosyl phosphorylated protein-zero related (PZR) in NSML mice. This recruitment is required for the Iroquois homeobox (IRX) transcription factors 3 and 5 to suppress BMP10 which negatively regulates postnatal cardiac growth. The protein expression of IRX3 and IRX5 was elevated in hypertrophied NSML hearts. IRX3 and IRX5 upregulation was rescued in NSML mice harboring a knock-in mutation of PZR that fails to become tyrosyl phosphorylated and recruit SHP2. NSML mice treated with low-dose dasatinib also exhibited normalized IRX3 and IRX5 expression levels. Consistent with this, BMP10 expression levels were reduced in NSML mice and rescued in PZR tyrosyl phosphorylation-deficient and low-dose dasatinib-treated NSML mice. A crystal structure of the tandem SH2 domains of SHP2 bound to tyrosyl phosphorylated PZR reveals that recruitment constrains the open SHP2 conformation to facilitate cellular-Src (c-Src) binding. Disruption of c-Src binding to SHP2 abolished IRX activation and failure to suppress BMP10. Hence, NSML-associated SHP2 genetic variants disrupt IRX transcription factor signaling to BMP10, implicating this axis as a target for RASopathy-associated HCM.

Science & Technology - Other Topics↗
DOE OSTI2020

Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition

Abstract Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1992

Modal element method for scattering of sound by absorbing bodies

The modal element method for acoustic scattering from 2-D body is presented. The body may be acoustically soft (absorbing) or hard (reflecting). The infinite computational region is divided into two subdomains - the bounded finite element domain, which is characterized by complicated geometry and/or variable material properties, and the surrounding unbounded homogeneous domain. The acoustic pressure field is represented approximately in the finite element domain by a finite element solution, and is represented analytically by an eigenfunction expansion in the homogeneous domain. The two solutions are coupled by the continuity of pressure and velocity across the interface between the two subdomains. Also, for hard bodies, a compact modal ring grid system is introduced for which computing requirements are drastically reduced. Analysis for 2-D scattering from solid and coated (acoustically treated) bodies is presented, and several simple numerical examples are discussed. In addition, criteria are presented for determining the number of modes to accurately resolve the scattered pressure field from a solid cylinder as a function of the frequency of the incoming wave and the radius of the cylinder.

Baumeister, Kenneth J.↗
NASA NTRS1993

Three-dimensional supersonic vortex breakdown

Three-dimensional supersonic vortex-breakdown problems in bound and unbound domains are solved. The solutions are obtained using the time-accurate integration of the unsteady, compressible, full Navier-Stokes (NS) equations. The computational scheme is an implicit, upwind, flux-difference splitting, finite-volume scheme. Two vortex-breakdown applications are considered in the present paper. The first is for a supersonic swirling jet which is issued from a nozzle into a supersonic uniform flow at a lower Mach number than that of the swirling jet. The second is for a supersonic swirling flow in a configured circular duct. In the first application, an extensive study of the effects of grid fineness, shape and grid-point distribution on the vortex breakdown is presented. Four grids are used in this study and they show a substantial dependence of the breakdown bubble and shock wave on the grid used. In the second application, the bubble-type and helix-type vortex breakdown have been captured.

Kandil, Osama A.↗
NASA NTRS1993

Numerical simulation and physical aspects of supersonic vortex breakdown

Existing numerical simulations and physical aspects of subsonic and supersonic vortex-breakdown modes are reviewed. The solution to the problem of supersonic vortex breakdown is emphasized in this paper and carried out with the full Navier-Stokes equations for compressible flows. Numerical simulations of vortex-breakdown modes are presented in bounded and unbounded domains. The effects of different types of downstream-exit boundary conditions are studied and discussed.

Liu, C. H.↗
NASA NTRS1993

Modal element method for scattering and absorbing of sound by two-dimensional bodies

The modal element method for acoustic scattering from a 2-D body is presented. The body may be acoustically soft (absorbing) or hard (reflecting). The infinite computational region is divided into two subdomains - the bounded finite element domain, which is characterized by complicated geometry and/or variable material properties, and the surrounding unbounded homogeneous domain. The acoustic pressure field is represented approximately in the finite element domain by a finite element solution, and is represented analytically by an eigenfunction expansion in the homogeneous domain. The two solutions are coupled by the continuity of pressure and velocity across the interface between the two subdomains. Also, for hard bodies, a compact modal ring grid system is introduced for which computing requirements are drastically reduced. Analysis for 2-D scattering from solid and coated (acoustically treated) bodies is presented, and several simple numerical examples are discussed. In addition, criteria are presented for determining the number of modes to accurately resolve the scattered pressure field from a solid cylinder as a function of the frequency of the incoming wave and the radius of the cylinder.

Baumeister, K. J.↗
NASA NTRS1994

Modal element method for potential flow in non-uniform ducts: Combining closed form analysis with CFD

An analytical procedure is presented, called the modal element method, that combines numerical grid based algorithms with eigenfunction expansions developed by separation of variables. A modal element method is presented for solving potential flow in a channel with two-dimensional cylindrical like obstacles. The infinite computational region is divided into three subdomains; the bounded finite element domain, which is characterized by the cylindrical obstacle and the surrounding unbounded uniform channel entrance and exit domains. The velocity potential is represented approximately in the grid based domain by a finite element solution and is represented analytically by an eigenfunction expansion in the uniform semi-infinite entrance and exit domains. The calculated flow fields are in excellent agreement with exact analytical solutions. By eliminating the grid surrounding the obstacle, the modal element method reduces the numerical grid size, employs a more precise far field boundary condition, as well as giving theoretical insight to the interaction of the obstacle with the mean flow. Although the analysis focuses on a specific geometry, the formulation is general and can be applied to a variety of problems as seen by a comparison to companion theories in aeroacoustics and electromagnetics.

Baumeister, Kenneth J.↗
NASA NTRS1992

Shock/vortex interaction and vortex-breakdown modes

Computational simulation and study of shock/vortex interaction and vortex-breakdown modes are considered for bound (internal) and unbound (external) flow domains. The problem is formulated using the unsteady, compressible, full Navier-Stokes (NS) equations which are solved using an implicit, flux-difference splitting, finite-volume scheme. For the bound flow domain, a supersonic swirling flow is considered in a configured circular duct and the problem is solved for quasi-axisymmetric and three-dimensional flows. For the unbound domain, a supersonic swirling flow issued from a nozzle into a uniform supersonic flow of lower Mach number is considered for quasi-axisymmetric and three-dimensional flows. The results show several modes of breakdown; e.g., no-breakdown, transient single-bubble breakdown, transient multi-bubble breakdown, periodic multi-bubble multi-frequency breakdown and helical breakdown.

Kandil, Osama A.↗
DOE OSTI2021

Visualization of large-scale charged domain Walls in hexagonal manganites

A ferroelectric charged domain wall (CDW) carries bound charges, originating from the variation of the normal components of polarization across the domain boundary, leading to a possible two-dimensional conductive interface in insulating materials. The ferroelectric CDW can be precisely created, erased, and manipulated, therefore offering an intriguing pathway toward the design of nano-devices. However, due to rather large energy costs, the size of the CDW is usually on the nanoscale. Here, taking flux-grown ferroelectric hexagonal manganites (h-RMnO 3 ) as an example, we creatively adopted an accessible inclined polishing process to reveal the domain evolution of stripe, loop, and vortex domain patterns by depth profiling. Interestingly, we observed an unexpected large-scale straight CDW in as-grown LuMnO 3 with length up to a millimeter size, which may result from the “polar catastrophe” during the flux growth. The large-scale CDW has a residual influence on the formation of the loop domain when the crystal anneals below the ferroelectric transition temperature, but completely disappears as the topological vortices emerge. The observed large-scale CDWs make h-RMnO 3 a potential candidate for advanced electronic devices, leading to a panoply of desired properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Theoretical analysis of key factors achieving reversed magnetic shear q-profiles sustained with lower hybrid waves on EAST

The phase space analysis technique is applied to provide new insights into the fully non-inductive lower hybrid current driven (LHCD) discharges on EAST (Garofalo et al 2017 Nucl. Fusion 57 076037). The analysis shows that there are bounded and unbounded topologies of lower hybrid (LH) waves in phase space. For typical parameters on EAST, the propagation domain for 4.6 GHz LH waves is bounded, while unbounded for 2.45 GHz LH waves and one of the conditions is recognized to be good for achieving an off-axis current profile driven by 4.6 GHz LH waves on EAST. The parametric analysis on the potential power deposition (PPD) region for those experiments demonstrates that the reversed magnetic shear dominates the wave behavior, and confines the LH power absorption to the far off-axis region as long as it occurs in the 4.6 GHz dominated LHCD discharge. GENRAY/CQL3D simulations also confirm this effect of reversed shear on the power absorption of 4.6 GHz waves. A bounded propagation domain and a positive feedback loop between magnetic shear reversal and off-axis LHCD profile could explain the LH-only-sustained strong reversed magnetic shear observed in experiments on multiple machines. In contrast, there is no such effect for 2.45 GHz waves on EAST since the PPD region is less sensitive to the change of reversed shear due to the unbounded propagation domain.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗