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At least 19 records

Preliminary observations on the effects of selenate on the development of the embryonic skate, Raja eglanteria

Morphogenesis of the clearnose skate, Raja eglanteria, was not significantly inhibited as a result of 7 days of exposure to 1-2 mM selenate in the sea water during Days 59-69 of embryonic development (hatching would normally have occurred at 82 +/- 4 days of incubation). Although corneal transparency appeared normal in the eye, preliminary measurements of the thickness of Bowman's layer of the cornea suggested that it was significantly thinner in the corneas of embryos exposed to 1-2 mM selenate. Selenate is an ion reported to inhibit sulfation of glycosaminoglycans in connective tissue.

NASA Discipline Number 93-10↗

Preliminary observations on the effects of selenate on the development of the embryonic skate, Raja eglanteria

Morphogenesis of the clearnose skate, Raja eglanteria, was not significantly inhibited as a result of 7 days of exposure to 1-2 mM selenate in the sea water during Days 59-69 of embryonic development (hatching would normally have occurred at 82 +/- 4 days of incubation). Although corneal transparency appeared normal in the eye, preliminary measurements of the thickness of Bowman's layer of the cornea suggested that it was significantly thinner in the corneas of embryos exposed to 1-2 mM selenate. Selenate is an ion reported to inhibit sulfation of glycosaminoglycans in connective tissue.

Non-NASA Center↗

Evolution of hematopoiesis: Three members of the PU.1 transcription factor family in a cartilaginous fish, Raja eglanteria

T lymphocytes and B lymphocytes are present in jawed vertebrates, including cartilaginous fishes, but not in jawless vertebrates or invertebrates. The origins of these lineages may be understood in terms of evolutionary changes in the structure and regulation of transcription factors that control lymphocyte development, such as PU.1. The identification and characterization of three members of the PU.1 family of transcription factors in a cartilaginous fish, Raja eglanteria, are described here. Two of these genes are orthologs of mammalian PU.1 and Spi-C, respectively, whereas the third gene, Spi-D, is a different family member. In addition, a PU.1-like gene has been identified in a jawless vertebrate, Petromyzon marinus (sea lamprey). Both DNA-binding and transactivation domains are highly conserved between mammalian and skate PU.1, in marked contrast to lamprey Spi, in which similarity is evident only in the DNA-binding domain. Phylogenetic analysis of sequence data suggests that the appearance of Spi-C may predate the divergence of the jawed and jawless vertebrates and that Spi-D arose before the divergence of the cartilaginous fish from the lineage leading to the mammals. The tissue-specific expression patterns of skate PU.1 and Spi-C suggest that these genes share regulatory as well as structural properties with their mammalian orthologs.

NASA Discipline Evolutionary Biology↗

Embryonic development of the cornea in the eye of the clearnose skate, Raja eglanteria: I. Stromal development in the absence of an endothelium

Embryos of the clearnose skate, Raja eglanteria, develop in sea water at 20-22 degrees C, hatching after 82 +/- 4 days (Luer and Gilbert, Environ. Biol. Fishes, 13:161-171, 1985). Eyes develop as steadily enlarging spheres whose corneas have the same radius of curvature as the sclera. The cornea begins development as a 2-cell thick epithelium beneath which by Day 12 there is only a basal lamina and a wispy matrix separating it from the underlying lens. This matrix, modified by Day 16, is displaced on Day 22 by a few orthogonal plies of fibrillar primary stroma. Ply number increases to at least 13 by Day 30, reaching the final number of 20 +/- 2 by Day 42. Stromal fibroblasts (keratocytes) appear at the corneal periphery by Day 22, and in increased numbers by Day 30, a time at which no keratocytes are seen in the central stroma. However, by Day 40, many fibroblasts are present at the corneal periphery, invading the primary stroma between plies, occasionally reaching even the central cornea. By Day 53, keratocytes are present between all plies, from corneal periphery to center. Thickness of each ply in this secondary stroma increases, but the number of plies remains the same as in the primary stroma. Bowman's layer, non-invaded matrix beneath the epithelial basal lamina, is not evident until Day 53. Sutural fibers, first seen on Day 22, originate in the corneal epithelial basal lamina, traversing perpendicularly the plies of the primary stroma. Sutural fibers persist throughout development of the secondary stroma and into adulthood. In contrast to chicks, skate corneas remain transparent throughout development, and never form an endothelium.

Non-NASA Center↗

EQSIM and RAJA: Enabling Exascale Predictions of Earthquake Effects on Critical Infrastructure

Nearly 120 years ago, the great “San Francisco” earthquake of 1906 provided a stark and sobering view of the havoc that can be caused by the sudden and violent movement of Earth’s tectonic plates. According to USGS, the rupture along the San Andreas fault extended 296 miles (447 kilometers) and shook so violently that the motion could be felt as far north as Oregon and east into Nevada. The estimated 7.9-magnitude quake and subsequent fires decimated the major metropolis and surrounding areas: buildings turned to ruins, hundreds of thousands of people left homeless, and a death toll exceeding 3,000. Today, as evidenced by the catastrophic 7.8-magnitude earthquake that struck Turkey in February of 2023, large earthquakes still present a significant potential danger to life and economic security as researchers work to develop ways to better understand earthquake phenomena and quantify associated risks.

42 ENGINEERING↗

Toward performance-portable PETSc for GPU-based exascale systems

The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization. The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. Furthermore, a blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.

97 MATHEMATICS AND COMPUTING↗

Performance Portable Graphics Processing Unit Acceleration of a High-Order Finite Element Multiphysics Application

The Lawrence Livermore National Laboratory (LLNL) will soon have in place the El Capitan exascale supercomputer, based on advanced micro devices (AMD) graphics processing units (GPUs). As part of a multiyear effort under the National Nuclear Security Administration (NNSA) Advanced Simulation and Computing (ASC) program, we have been developing marbl, a next generation, performance portable multiphysics application based on high-order finite elements. In previous years, we successfully ported the Arbitrary Lagrangian–Eulerian (ALE), multimaterial, compressible flow capabilities of marbl to nvidia GPUs as described in Vargas et al. Here, in this paper, we describe our ongoing effort in extending marbl's GPU capabilities with additional physics, including multigroup radiation diffusion and thermonuclear burn for high energy density physics (HEDP) and fusion modeling. We also describe how our portability abstraction approach based on the raja Portability Suite and the mfem finite element discretization library has enabled us to achieve high performance on AMD based GPUs with minimal effort in hardware-specific porting. Throughout this work, we highlight numerical and algorithmic developments that were required to achieve GPU performance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SW4 Curvilinear Kernels

Five computationally expensive stencil evaluation routines from SW4(https://github.com/geodynamics/sw4 GPL license) have been extracted and packaged with a driver to create a mini-app for evaluating compiler and GPU performance. The kernels can executed on AMD and Nvidia GPUs with and without RAJA. The kernel driver generates synthetic inputs, checks for correctness and measures kernel run times.

Pankajakshan, Ramesh↗

Complex expression patterns of lymphocyte-specific genes during the development of cartilaginous fish implicate unique lymphoid tissues in generating an immune repertoire

Cartilaginous fish express canonical B and T cell recognition genes, but their lymphoid organs and lymphocyte development have been poorly defined. Here, the expression of Ig, TCR, recombination-activating gene (Rag)-1 and terminal deoxynucleosidase (TdT) genes has been used to identify roles of various lymphoid tissues throughout development in the cartilaginous fish, Raja eglanteria (clearnose skate). In embryogenesis, Ig and TCR genes are sharply up-regulated at 8 weeks of development. At this stage TCR and TdT expression is limited to the thymus; later, TCR gene expression appears in peripheral sites in hatchlings and adults, suggesting that the thymus is a source of T cells as in mammals. B cell gene expression indicates more complex roles for the spleen and two special organs of cartilaginous fish-the Leydig and epigonal (gonad-associated) organs. In the adult, the Leydig organ is the site of the highest IgM and IgX expression. However, the spleen is the first site of IgM expression, while IgX is expressed first in gonad, liver, Leydig and even thymus. Distinctive spatiotemporal patterns of Ig light chain gene expression also are seen. A subset of Ig genes is pre-rearranged in the germline of the cartilaginous fish, making expression possible without rearrangement. To assess whether this allows differential developmental regulation, IgM and IgX heavy chain cDNA sequences from specific tissues and developmental stages have been compared with known germline-joined genomic sequences. Both non-productively rearranged genes and germline-joined genes are transcribed in the embryo and hatchling, but not in the adult.

Non-NASA Center↗

Acceleration Modes and Transitions in Pulsed Plasma Accelerators

Pulsed plasma accelerators typically operate by storing energy in a capacitor bank and then discharging this energy through a gas, ionizing and accelerating it through the Lorentz body force. Two plasma accelerator types employing this general scheme have typically been studied: the gas-fed pulsed plasma thruster and the quasi-steady magnetoplasmadynamic (MPD) accelerator. The gas-fed pulsed plasma accelerator is generally represented as a completely transient device discharging in approximately 1-10 microseconds. When the capacitor bank is discharged through the gas, a current sheet forms at the breech of the thruster and propagates forward under a j (current density) by B (magnetic field) body force, entraining propellant it encounters. This process is sometimes referred to as detonation-mode acceleration because the current sheet representation approximates that of a strong shock propagating through the gas. Acceleration of the initial current sheet ceases when either the current sheet reaches the end of the device and is ejected or when the current in the circuit reverses, striking a new current sheet at the breech and depriving the initial sheet of additional acceleration. In the quasi-steady MPD accelerator, the pulse is lengthened to approximately 1 millisecond or longer and maintained at an approximately constant level during discharge. The time over which the transient phenomena experienced during startup typically occur is short relative to the overall discharge time, which is now long enough for the plasma to assume a relatively steady-state configuration. The ionized gas flows through a stationary current channel in a manner that is sometimes referred to as the deflagration-mode of operation. The plasma experiences electromagnetic acceleration as it flows through the current channel towards the exit of the device. A device that had a short pulse length but appeared to operate in a plasma acceleration regime different from the gas-fed pulsed plasma accelerators was developed by Cheng, et al. The Coaxial High ENerGy (CHENG) thruster operated on the 10-microseconds timescales of pulsed plasma thrusters, but claimed high thrust density, high efficiency and low electrode erosion rates, which are more consistent with the deflagration mode of acceleration. Separate work on gas-fed pulsed plasma thrusters (PPTs) by Ziemer, et al. identified two separate regimes of performance. The regime at higher mass bits (termed Mode I in that work) possessed relatively constant thrust efficiency (ratio of jet kinetic energy to input electrical energy) as a function of mass bit. In the second regime at very low mass bits (termed Mode II), the efficiency increased with decreasing mass bit. Work by Poehlmann et al. and by Sitaraman and Raja sought to understand the performance of the CHENG thruster and the Mode I / Mode II performance in PPTs by modeling the acceleration using the Hugoniot Relation, with the detonation and deflagration modes representing two distinct sets of solutions to the relevant conservation laws. These works studied the proposal that, depending upon the values of the various controllable parameters, the accelerator would operate in either the detonation or deflagration mode. In the present work, we propose a variation on the explanation for the differences in performance between the various pulsed plasma accelerators. Instead of treating the accelerator as if it were only operating in one mode or the other during a pulse, we model the initial stage of the discharge in all cases as an accelerating current sheet (detonation mode). If the current sheet reaches the exit of the accelerator before the discharge is completed, the acceleration mode transitions to the deflagration mode type found in the quasi-steady MPD thrusters. This modeling method is used to demonstrate that standard gas-fed pulsed plasma accelerators, the CHENG thruster, and the quasi-steady MPD accelerator are variations of the same device, with the overall acceleration of the plasma depending upon the behavior of the plasma discharge during initial transient phase and the relative lengths of the detonation and deflagration modes of operation.

Polzin, Kurt A.↗

Porting the Nonlinear Optimization Library HiOp to Accelerator-Based Hardware Architectures

While interior point method has been the centerpiece of nonlinear programming tools used in science and engineering, its reliance on linear solvers that can tackle sparse symmetric indefinite and highly ill-conditioned problems made it difficult to implement it effectively on hardware accelerators. HiOp optimization package attempts to provide an implementation of the interior point method suitable for hardware accelerators by compressing the original sparse problem to produce an underlying linear problem that is dense and of manageable size. Implementations of dense linear solvers are more mature and utilize hardware accelerators better than their sparse counterparts. There is a number of important domain problems, such as optimal power flow analysis for power grids, where the sparse problem can be effectively compressed and deploying dense linear solver within the interior point method can improve performance. Here we describe a portable implementation of HiOp optimization engine, which uses a linear solver from Magma library and runs entirely on hardware accelerators. To compress the problem, HiOp uses customized mixed dense-sparse linear algebra. All HiOp kernels are implemented using Umpire and RAJA portability libraries. We describe details of the implementation and discuss trade-offs between performance, portability and development cost.

97 MATHEMATICS AND COMPUTING↗

Giant low-field magnetocaloric effect and refrigerant capacity in reduced dimensionality EuTiO 3 multiferroics

Engineering magnetic materials into a thin film form while preserving its excellent magnetocaloric response is essential in the development of miniature magnetic coolers. We demonstrate how this can be achieved in the case of EuTiO 3 - an emerging multiferroic material. Unlike conventional cases where reduced dimensionality considerably decreased the magnetic entropy change (ΔS M ) and hence the refrigerant capacity (RC), we show the large low-field enhancements of ΔS M and RC in a ~100 nm thick nanocrystalline EuTiO 3 film (ΔS M ~ 24 J kg -1 K -1 and RC = 152 J kg -1 for μ 0 ΔH = 2T) relative to its single crystal counterpart (ΔS M ~ 17 J kg -1 K -1 and RC ~ 107 J kg -1 for μ 0 ΔH = 2T). The nanocrystalline EuTiO 3 film is an excellent candidate for cryogenic magnetic refrigeration. From our study, a new approach for improving both MCE and RC in magnetic nanomaterials is proposed, which will stimulate further research on magnetocaloric thin films and related cooling devices.

36 MATERIALS SCIENCE↗

Evaluation of residual stresses in isothermal friction stir welded 304L stainless steel plates

Friction stir welding was performed on 304L SS plates in order to heal simulated cracks created by electrical discharge machining. Two different tool temperatures (825 and 725 °C) were chosen for this study. Both neutron diffraction and X-ray diffraction techniques were employed to evaluate the residual stresses along two orthogonal reference directions, longitudinal (syy) and transverse (sxx). The former technique was also used to measure residual stresses at various depths. It was found that, at 1 mm depth from the top surface inside the stir zone (SZ), the longitudinal component was tensile in nature while the transverse component was compressive. The nature and magnitude of the residual stress fields, and the position of the peak residual stresses were found to vary with the weld depth. The SZ of the 725 °C weld exhibited higher peak stress than 825 °C weld mainly due to a lack of stress relief at the lower temperature.

Friction stir welding, Steel↗

Particle-in-cell Monte Carlo-collision modeling of non-ideal effects in wave-heated dense microplasmas

A computational model for non-ideal plasma effects during the time evolution of a second-stage laser-heated discharge at high pressures is presented. The model extends a classical one-dimensional particle-in-cell Monte Carlo-collision (PIC-MCC) approach coupled with Maxwell's equations for the laser-heating process of a xenon plasma at 300 K temperature and 10–100 bar pressure. Plasma non-ideality resulting from Coulomb coupling at high plasma densities is manifested as a depression in the effective ionization potential of atoms and enhanced collision cross sections. These non-ideal effects are represented using the Ecker–Kröll model in the context of the PIC-MCC approach. We find that full ionization of the plasma is obtained on the picosecond timescale, starting from the skin layer and quickly expanding throughout the domain through an anomalous extension of the skin depth. More critically, we show that the inclusion of the non-ideal plasma effects results in more rapid ionization compared to an ideal plasma, especially at higher pressures. The ionization delay reduction is of the order of a fraction of a picosecond, corresponding to a 16% decrease at 100 bar. As the amplitude of the wave field is lowered, the ionization rate is lowered, making the plasma non-ideality effects more prominent.

Solmaz, Evrim (ORCID:0000000211830881)↗

Kramers nodal line in the charge density wave state of YTe 3 and the influence of twin domains

Recent studies have focused on the relationship between charge density wave (CDW) collective electronic ground states and nontrivial topological states. YTe 3 , a nonmagnetic quasi-two-dimensional chalcogenide, has been reported to exhibit a CDW state below 334 K. Using angle-resolved photoemission spectroscopy (ARPES) and density functional theory (DFT), we establish that YTe 3 is a CDW-induced Kramers nodal line (KNL) metal, a recently proposed topological state of matter. Scanning tunneling microscopy and low energy electron diffraction reveal two orthogonal domains, each with a unidirectional CDW and a similar wave vector (𝐪 CDW ). When the influence of twin domains is considered, the effective band structure (EBS) computations that utilize DFT-calculated bands using a noncentrosymmetric structure determined by x-ray crystallography, show excellent agreement with ARPES. The noncentrosymmetry of YTe 3 is established by Raman spectroscopy. The Fermi surface and ARPES intensity plots show weak shadow bands displaced by 𝐪 CDW from the main bands. Furthermore, these are linked to CDW modulation, as the EBS calculation confirms. Bilayer split main and shadow bands suggest the existence of crossings, according to theory and experiment. DFT bands, including spin-orbit coupling, indicate existence of a KNL along the Σ direction from multiple crossings of bands dispersing perpendicular to it. Additionally, doubly degenerate bands are only found along the KNL at all energies, with some bands dispersing through the Fermi level.

Angle-resolved photoemission spectroscopy↗