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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

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

Kinematics and dynamics of disclination lines in three-dimensional nematics

An exact kinematic law for the motion of disclination lines in nematic liquid crystals as a function of the tensor order parameter Q is derived. Unlike other order parameter fields that become singular at their respective defect cores, the tensor order parameter remains regular. Following earlier experimental and theoretical work, the disclination core is defined to be the line where the uniaxial and biaxial order parameters are equal, or equivalently, where the two largest eigenvalues of Q cross. This allows an exact expression relating the velocity of the line to spatial and temporal derivatives of Q on the line, to be specified by a dynamical model for the evolution of the nematic. By introducing a linear core approximation for Q, analytical results are given for several prototypical configurations, including line interactions and motion, loop annihilation, and the response to external fields and shear flows. Behaviour that follows from topological constraints or defect geometry is highlighted. Finally, the analytic results are shown to be in agreement with three-dimensional numerical calculations based on a singular Maier–Saupe free energy that allows for anisotropic elasticity.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Structure and stability of hydrous minerals at high pressure

The presence of even small amounts of hydrogen in the Earth's deep interior may have profound effects on mantle melting, rheology, and electrical conductivity. The recent discovery of a large class of high-pressure H-bearing silicates further underscores the potentially important role for hydrous minerals in the Earth's mantle. Hydrogen may also be a significant component of the Earth's core, as has been recently documented by studies of iron hydride at high pressure. In this study, we explore the role of H in crystal structures at high pressure through detailed Raman spectroscopic and x ray diffraction studies of hydrous minerals compressed in diamond anvil cells. Brucite, Mg(OH)2, has a simple structure and serves as an analogue for the more complex hydrous silicates. Over the past five years, this material has been studied at high pressure using shock-compression, powder x ray diffraction, infrared spectroscopy, Raman spectroscopy, and neutron diffraction. In addition, we have recently carried out single-crystal synchrotron x-ray diffraction on Mg(OH)2 and Raman spectroscopy on Mg(OD)2 at elevated pressure. From all these studies, an interesting picture of the crystal chemical behavior of this material at high pressure is beginning to emerge. Some of the primary conclusions are as follows: First, hydrogen bonding is enhanced by the application of pressure. Second, layered minerals which are elastically anisotropic at low pressure may not be so at high pressure. Furthermore, the brucite data place constraints on the effect of hydrogen on seismic velocities and density at very high pressure. Third, the stability of hydrous minerals may be enhanced at high P by subtle structural rearrangements that are difficult to detect using traditional probes and require detailed spectroscopic analyses. Finally, brucite appears to be unique in that it undergoes pressure-induced disordering that is confined solely to the H-containing layers of the structure.

Duffy, T. S.↗
NASA NTRS2004

Lunar and Planetary Science XXXV: Effects of Impacts: Shock and Awe

This document discusses the following topics: Zircon as a Shock Indicator in Impactites of Drill Core Yaxcopoil-1, Chicxulub Impact Structure, Mexico; Experimental Investigation of Shock Effects in a Metapelitic Granulite; Experimental Reproduction of Shock Veins in Single-Crystal Minerals; Post-Shock Crystal-Plastic Processes in Quartz from Crystalline Target Rocks of the Charlevoix Impact Structure; Shock Reequilibration of Fluid Inclusions; How Does Tektite Glass Lose Its Water?; Assessing the Role of Anhydrite in the KT Mass Extinction: Hints from Shock-loading Experiments; A Mineralogical and Geochemical Study of the Nonmarine Permian/Triassic Boundary in the Southern Karoo Basin, South Africa; Extraterrestrial Chromium in the Permian-Triassic Boundary at Graphite Peak, Antarctica; Magnetic Fe,Si,Al-rich Impact Spherules from the P-T Boundary Layer at Graphite Peak, Antarctica; A Newly Recognized Late Archean Impact Spherule Layer in the Reivilo Formation, Griqualand West Basin, South Africa; Initial Cr-Isotopic and Iridium Measurements of Concentrates from Late Eocene Cpx-Spherule Deposits; An Ordinary Chondrite Impactor Composition for the Bosumtwi Impact Structure, Ghana, West Africa: Discussion of Siderophile Element Contents and Os and Cr Isotope Data.

Kyte, F. T.↗
NASA NTRSDate not supplied

Location, location: deciphering the significance of in-situ hydrogen analyses of Martian meteorite phases

Understanding how inner planets acquired their volatiles such as hydrogen (H) is fundamental to constrain models of solar system formation [e.g. 1]. One avenue of estimating the H content and isotopic characteristics of differentiated planets is to analyze the samples we have from them as meteorites. Ideally, the H content and isotopic characteristic of the mantle sources of these igneous rocks should give insight into the volatile origin of each planetary body. The mantle H signatures can be estimated from that of the parent melt, which in turn may be derived from that of the first crystallized phases. However, we will illustrate the processes that can modify the H content and D/H ratios of pyroxene, olivine and feldspar in selected Martian meteorites relative to those of their mantle sources, with two key protocols for SIMS analysis. The first key is to put each analysis in textural context ("location, location"). In particular, of prime importance is whether an analysis is done at the center or the edge of a mineral grain, close or far from a shock disturbed area, and in a mineral crystallized at the beginning or late in the differentiation sequence. Accompanying the H analyses done by SIMS with major and trace element data at the same analysis locations allows to constrain the history of crystallization, cooling, alteration and shock of the meteorite. For example, volcanic degassing can be evidenced by decreasing water contents and increasing D/H ratios from core to edge of nakhlite pyroxenes [2]. Traverses of H analyses in pyroxene and maskelynite in shergottite LAR 06319 provide examples of H contents and D/H ratios modified during degassing following shock [3]. The second key is to assess if the area analyzed by SIMS has shock generated damage of the mineral structure, as will be shown in pyroxene and olivine from shergottite RBT 04262. Olivine in shergottites have too high water contents to be explained with an igneous origin and their D/H ratios are more consistent with terrestrial alteration, as observed before [4]. A review of all these processes shows how careful one has to be prior to using H measurements in meteorites to infer the origin and amount of water in differentiated planetary interiors.

A.H. Peslier↗
NASA NTRS1999

Geochemical Evidence for a Terrestrial Magma Ocean

The aftermath of phase separation and crystal-liquid fractionation in a magma ocean should leave a planet geochemically differentiated. Subsequent convective and other mixing processes may operate over time to obscure geochemical evidence of magma ocean differentiation. On the other hand, core formation is probably the most permanent, irreversible part of planetary differentiation. Hence the geochemical traces of core separation should be the most distinct remnants left behind in the mantle and crust, In the case of the Earth, core formation apparently coincided with a magma ocean that extended to a depth of approximately 1000 km. Evidence for this is found in high pressure element partitioning behavior of Ni and Co between liquid silicate and liquid iron alloy, and with the Ni-Co ratio and the abundance of Ni and Co in the Earth's upper mantle. A terrestrial magma ocean with a depth of 1000 km will solidify from the bottom up and first crystallize in the perovskite stability field. The largest effect of perovskite fractionation on major element distribution is to decrease the Si-Mg ratio in the silicate liquid and increase the Si-Mg ratio in the crystalline cumulate. Therefore, if a magma ocean with perovskite fractionation existed, then one could expect to observe an upper mantle with a lower than chondritic Si-Mg ratio. This is indeed observed in modern upper mantle peridotites. Although more experimental work is needed to fully understand the high-pressure behavior of trace element partitioning, it is likely that Hf is more compatible than Lu in perovskite-silicate liquid pairs. Thus, perovskite fractionation produces a molten mantle with a higher than chondritic Lu-Hf ratio. Arndt and Blichert-Toft measured Hf isotope compositions of Barberton komatiites that seem to require a source region with a long-lived, high Lu-Hf ratio. It is plausible that that these Barberton komatiites were generated within the majorite stability field by remelting a perovskite-depleted part of the upper mantle transition zone.

Agee, Carl B.↗
NASA NTRS1992

Space Station Furnace Facility Core. Requirements definition and conceptual design study. Volume 2: Technical report. Appendix 6: Technical summary reports

The Space Station Furnace Facility (SSFF) is a modular facility for materials research in the microgravity environment of the Space Station Freedom (SSF). The SSFF is designed for crystal growth and solidification research in the fields of electronic and photonic materials, metals and alloys, and glasses and ceramics and will allow for experimental determination of the role of gravitational forces in the solidification process. The facility will provide a capability for basic scientific research and will evaluate the commercial viability of low-gravity processing of selected technologically important materials. The facility is designed to support a complement of furnace modules as outlined in the Science Capabilities Requirements Document (SCRD). The SSFF is a three rack facility that provides the functions, interfaces, and equipment necessary for the processing of the furnaces and consists of two main parts: the SSFF Core Rack and the two Experiment Racks. The facility is designed to accommodate two experimenter-provided furnace modules housed within the two experiment racks, and is designed to operate these two furnace modules simultaneously. The SCRD specifies a wide range of furnace requirements and serves as the basis for the SSFF conceptual design. SSFF will support automated processing during the man-tended operations and is also designed for crew interface during the permanently manned configuration. The facility is modular in design and facilitates changes as required, so the SSFF is adept to modifications, maintenance, reconfiguration, and technology evolution.

Source record↗
DOE OSTI2022

Uncertainty Quantification Framework for Predicting Material Response with Large Number of Parameters: Application to Creep Prediction in Ferritic-Martensitic Steels Using Combined Crystal Plasticity and Grain Boundary Models

This paper presents an uncertainty quantification (UQ) framework for the physics-based model prediction of material response with a large number of parameters. The application problem presented in this work is that of predicting creep in Grade 91 steel at 600°C. The material response is defined with a physically based microstructural model with constitutive equations emulating several observed phenomena in Grade 91 and embodied into an explicit geometry mesoscale finite element model for prior austenite grains and grain boundaries. Creep within the grains and in grain boundaries are represented by crystal plasticity for dislocation motion and a physics-based model for cavity growth and nucleation, respectively. The creep behavior of this material is influenced by several parameters, some of which have a wide range of variation based on experimental data. UQ combined with microstructural modeling can discover the core microstructural causes of experimental variability, leading to improved materials with lower variability in critical long-term material properties. In this study, we investigate the model's uncertainty to identify material properties that may be modified during production to increase creep life and analyze different components of the crystal plasticity model for improvements. For this purpose, a quantity of interest is defined as time to minimum creep rate, which correlates well to the creep failure of the material. A deep neural network model was trained and validated to be used as a surrogate for the finite element model. Then, a variance-based sensitivity analysis is performed on the surrogate model to find the Sobol indices of the input parameters in respect to the output quantity of interest. The Sobol indices are used to reduce the dimensionality of the model. Generalized polynomial chaos expansion is used on the reduced basis models to propagate the uncertainty from the input parameters to the quantity of interest using the deep neural network surrogate model. These results are benchmarked against uncertainty propagation using Monte Carlo simulations. In conclusion, the UQ performed through the reduced basis model captures almost all the uncertainty in the model with significantly fewer simulations, making it possible to perform the UQ directly via simulations with the finite element model rather than surrogate machine-learned models.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Electrically Pumped Epitaxially Regrown GaSb-Based Type-I Quantum-Well Surface-Emitting Lasers with Buried High-Index-Contrast Photonic Crystal Layer

Epitaxially regrown electrically pumped photonic crystal surface-emitting lasers (PCSELs) emitting near 2 and 2.6 μm are designed, fabricated, and characterized. A high-index-contrast photonic crystal layer is incorporated into the GaSb-based laser heterostructure by air-hole-retaining epitaxial regrowth. A square lattice of triangular holes is etched in the top waveguide core layer of the incomplete laser heterostructure. The nanopatterned surface is subsequently cleaned and regrown with AlGaAsSb p-cladding material. Transmission electron microscopy studies demonstrate uniform regrowth over the nanopatterned GaSb surface. The selected regrowth regimes yield a buried 2D array of elongated air-holes. The diode PCSELs based on moderately etched nanopatterns demonstrate band-edge lasing near 2 μm up to room temperatures. The cascade diode PCSELs operate near 2.6 μm with minimum threshold current densities of about 500 A cm -2 achieved at 180 K. The devices generate mW level output in narrow divergence beam emitted from the window in substrate contact. The angle-resolved electroluminescence measurements reveal a four-sub-band band structure with an apparent photonic bandgap corresponding to the buried high-index-contrast square photonic crystal layer. Finally, the PCSELs made of heterostructures supporting two modes in the vertical direction demonstrate two sets of sub-bands showing anti-crossing-like interaction.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

The yeast ALA synthase C‐terminus positively controls enzyme structure and function

Abstract 5‐Aminolevulinic acid synthase (ALAS) is a pyridoxal 5′‐phosphate (PLP)‐dependent enzyme that catalyzes the first and rate‐limiting step of heme biosynthesis in α‐proteobacteria and several non‐plant eukaryotes. All ALAS homologs contain a highly conserved catalytic core, but eukaryotes also have a unique C‐terminal extension that plays a role in enzyme regulation. Several mutations in this region are implicated in multiple blood disorders in humans. In Saccharomyces cerevisiae ALAS (Hem1), the C‐terminal extension wraps around the homodimer core to contact conserved ALAS motifs proximal to the opposite active site. To determine the importance of these Hem1 C‐terminal interactions, we determined the crystal structure of S. cerevisiae Hem1 lacking the terminal 14 amino acids (Hem1 ΔCT). With truncation of the C‐terminal extension, we show structurally and biochemically that multiple catalytic motifs become flexible, including an antiparallel β‐sheet important to Fold‐Type I PLP‐dependent enzymes. The changes in protein conformation result in an altered cofactor microenvironment, decreased enzyme activity and catalytic efficiency, and ablation of subunit cooperativity. These findings suggest that the eukaryotic ALAS C‐terminus has a homolog‐specific role in mediating heme biosynthesis, indicating a mechanism for autoregulation that can be exploited to allosterically modulate heme biosynthesis in different organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein

The molecular basis for the severity and rapid spread of the COVID-19 disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04-Å resolution by X-ray crystallography. The structure reveals a ~60-residue core similar to SARS-CoV-2 ORF7a, with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate noncovalent interface is formed by another SARS-CoV-2-specific sequence, 73 YIDI 76 . Together, the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

Diffraction Studies of the Atomic Vibrations of Bulk and Surface Atoms in the Reciprocal and Real Spaces of Nanocrystalline SiC

To describe and evaluate the vibrational properties of nanoparticles it is necessary to distinguish between the surface and the core of the particles. Theoretical calculations show that vibrational density of states of the inner atoms of nanograins is similar to bulk material but shifted to higher energies which can be explained by the fact that the gain core is stressed (hardened) due to the presence of internal pressure. Theoretical calculations also show that there is a difference between vibrational properties of a crystal lattice of the grain interior in isolated particles and in a dense (sintered) nanocrystalline material. This is probably due to a coupling of the modes inside the grains via the grain boundaries in dense nanocrystalline bodies. We examined strains present in the surface shell based on examination of diamond and Sic nanocrystals in reciprocal (Bragg-type scattering) and real (PDF analysis) space analysis of neutron diffraction data. Recently we examined the atomic thermal motions in nanocrystalline Sic based on the assumption of a simple Einstein model for uncorrelated atomic notions. According to this model, the Bragg intensity is attenuated as a function of scattering angle by the Debye-Waller factor. Based on this assumption overall temperature factors were determined from the Wilson plots.

Stelmakh, S.↗
NASA NTRS1997

Auger Spectroscopy of Hydrogenated Diamond Surfaces

An energy shift and a change of the line shape of the carbon core-valence-valence Auger spectra are observed for diamond surfaces after their exposure to an electron beam, or annealing at temperatures higher then 950 C. The effect is studied for both natural diamond crystals and chemical-vapor-deposited diamond films. A theoretical model is proposed for Auger spectra of hydrogenated diamond surfaces. The observed changes of the carbon Auger line shape are shown to be related to the redistribution of the valence-band local density of states caused by the hydrogen desorption from the surface. One-electron calculation of Auger spectra of diamond surfaces with various hydrogen coverages are presented. They are based on self-consistent wave functions and matrix elements calculated in the framework of the local-density approximation and the self-consistent linear muffin-tin orbital method with static core-hole effects taken into account. The major features of experimental spectra are explained.

Krainsky, I. L.↗
NASA NTRS2003

Melt Redistribution in Dynamic Systems: Applications to Core Formation

Samples of olivine + Fe-S were fabricated by hot-pressing a mechanical mixture of the two phases. Olivine powders with a starting grain size of approx. 10 microns were prepared by crushing crystals of San Carlos olivine followed by pulverization in a fluid energy mill. Iron sulfide powder with a particle size of approx. 5 microns was prepared from a 2:1 mixture of reagent grade iron sulfide (FeS) plus iron. Rods 20 mm in length by 10 mm in diameter were cold-pressed into iron capsules with a uniaxial stress of approx. 200 MPa. These rods were then hot-pressed at 1523 K and 300 MPa for 4 h to obtain a starting material with <2% porosity. Samples for shear experiments were cut perpendicular to the long axis of these rods. The discs were shaped into ellipses approx. 6 mm by approx. 8 mm with a thickness ranging from 0.6 to 1.0 mm. An iron foil strain marker was inserted into a cut made along the minor axis. The sample was placed between two thoriated tungsten pistons cut at 45 deg to the long axis and then placed into an iron sleeve capped by alumina discs. The sample was then sheared in a gas pressure-medium apparatus at a temperature of 1523 K and a confining pressure of 300 MPa.

Hustoft, J. W.↗
NASA NTRS1993

Isotopic and trace element characteristics of an unusual refractory inclusion from Essebi

The isotopic and chemical properties of Ca-Al-rich inclusions (CAI) provide important clues to the early solar nebula environment. While the abundances of refractory major and trace elements are similar to those expected for high temperature condensates, the variety of textural, chemical, and isotopic signatures indicate most CAI experienced complex, multi-stage histories involving repeated episodes of condensation, evaporation, and metamorphism. Evidence of multiple processes is especially apparent in an unusual refractory inclusion from Essebi (URIE) described by El Goresy et al. The melilite (mel)-rich core of URIE contains polygonal framboids of spinel (sp) and hibonite (hb) or sp and fassaite (fas) and is surrounded by a rim sequence consisting of five layers. In contrast to rims on Allende, the mineralogy of the URIE rim layers becomes increasingly refractory from the core outwards, ending in a layer of spinel-Al2O3 solid solution + Sc-rich fassaite. The chemical and mineralogical features of URIE are inconsistent with crystallization from a homogeneous melt, and El Goresy et al. proposed a multi-step history involving condensation of sp + hb and aggregation into framboids, capture of framboids by a refractory silicate melt droplet, condensation of rim layers, and alteration of mel to calcite and feldspathoid. The PANURGE ion probe was used to investigate the isotopic and trace element characteristics of URIE to develop a more complete picture of the multiple processes leading to formation and metamorphism.

Deloule, E.↗
DOE OSTI2024

A parallel and performance portable implementation of a full-field crystal plasticity model

We have developed a parallel implementation of an Elasto-Viscoplastic Fast Fourier Transform-based (EVPFFT) micromechanical solver to enable computationally efficient crystal plasticity modeling for polycrystalline materials. Our primary focus lies in achieving performance portability, allowing a single EVPFFT implementation to run optimally on various homogeneous architectures, including multi-core Central Processing Units (CPUs), as well as on heterogeneous computer architectures comprising multi-core CPUs and Graphics Processing Units (GPUs) from different vendors. To accomplish this goal, we have leveraged MATAR, a C++ software library that simplifies the creation and utilization of multidimensional dense or sparse matrix and array data structures. These data structures are designed to be portable across diverse architectures through the use of Kokkos, a performance-portable library. Additionally, we have employed the Message Passing Interface (MPI) to efficiently distribute the computational workload among processors. The heFFTe (Highly Efficient FFT for Exascale) library is used to facilitate the performance portability of the fast Fourier transforms (FFTs) computation. The computational performance of EVPFFT is evaluated and presented in terms of parallel scalability and simulation runtime on different high-performance computing (HPC) architectures. As a result, the utility of the developed framework to efficiently simulate the micro-mechanical fields in polycrystalline microstructures in engineering applications is discussed.

36 MATERIALS SCIENCE↗