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At least 379 records · Page 21

Analysis of the Pore Structures of Shale Using Neutron and X-Ray Small Angle Scattering

Analysis of the multi-scale pore structures of shale is of critical importance to understanding their role as caprocks and oil/gas reservoirs, as well as their contribution to global elemental cycles because of weathering. While several techniques have been employed to understand these structures, small angle neutron and X-ray scattering, which can quantify several features of the pore structure from the nanometer scale to tens of microns, provides a unique perspective not found in more standard petrophysical approaches. Although large-scale regional studies using this approach are not yet available, over 30 years of work have led to a number of important conclusions. Among the results obtained are data suggesting that multi-scale pores structures, even of less fissile shales, are highly asymmetric. However, this is both scale and maturity dependent. Pore surfaces commonly exhibit highly rough surface fractals, which often smooth with diagenetic alteration and weathering. Mass fractal behavior of larger-scale interpore structures has also been observed. In many cases, pore structures are bimodal, reflecting interlayer spacing in clays at the smaller scales and larger spacing between clay packets or between clay folia and detrital grains at larger scales. Non-clay porosity may also be observed, including significant nanoporosity associated with organic matter (OM). Data obtained as a function of thermal maturity suggest that while the overall porosity does decrease with increasing maturity, the change is not linear with R o (percent vitrinite reflectance), but occurs primarily in the early stages of maturation. Pore size or volume distributions obtained from scattering experiments often differ considerably from those obtained from nitrogen or carbon dioxide absorption or mercury intrusion porosimetry, which may reflect the overall accessibility of various pore sizes to external fluids. Despite these results, however, a significant amount of work and a number of basic questions remain to be answered that can be addressed either uniquely by scattering methods or in a complementary fashion using these and other approaches.

Anovitz, Lawrence {Larry} M.↗

MAGNETIC FIELD STRUCTURES TRIGGERING SOLAR FLARES AND CORONAL MASS EJECTIONS

Solar flares and coronal mass ejections, the most catastrophic eruptions in our solar system, have been known to affect terrestrial environments and infrastructure. However, because their triggering mechanism is still not sufficiently understood, our capacity to predict the occurrence of solar eruptions and to forecast space weather is substantially hindered. Even though various models have been proposed to determine the onset of solar eruptions, the types of magnetic structures capable of triggering these eruptions are still unclear. In this study, we solved this problem by systematically surveying the nonlinear dynamics caused by a wide variety of magnetic structures in terms of three-dimensional magnetohydrodynamic simulations. As a result, we determined that two different types of small magnetic structures favor the onset of solar eruptions. These structures, which should appear near the magnetic polarity inversion line (PIL), include magnetic fluxes reversed to the potential component or the nonpotential component of major field on the PIL. In addition, we analyzed two large flares, the X-class flare on 2006 December 13 and the M-class flare on 2011 February 13, using imaging data provided by the Hinode satellite, and we demonstrated that they conform to the simulation predictions. These results suggest that forecasting of solar eruptions is possible with sophisticated observation of a solar magnetic field, although the lead time must be limited by the timescale of changes in the small magnetic structures.

79 ASTRONOMY AND ASTROPHYSICS↗

Structural Basis for Selective Small Molecule Kinase Inhibition of Activated c-Met

The receptor tyrosine kinase c-Met is implicated in oncogenesis and is the target for several small molecule and biologic agents in clinical trials for the treatment of cancer. Binding of the hepatocyte growth factor to the cell surface receptor of c-Met induces activation via autophosphorylation of the kinase domain. Here we describe the structural basis of c-Met activation upon autophosphorylation and the selective small molecule inhibiton of autophosphorylated c-Met. MK-2461 is a potent c-Met inhibitor that is selective for the phosphorylated state of the enzyme. Compound 1 is an MK-2461 analog with a 20-fold enthalpy-driven preference for the autophosphorylated over unphosphorylated c-Met kinase domain. The crystal structure of the unbound kinase domain phosphorylated at Tyr-1234 and Tyr-1235 shows that activation loop phosphorylation leads to the ejection and disorder of the activation loop and rearrangement of helix {alpha}C and the G loop to generate a viable active site. Helix {alpha}C adopts a orientation different from that seen in activation loop mutants. The crystal structure of the complex formed by the autophosphorylated c-Met kinase domain and compound 1 reveals a significant induced fit conformational change of the G loop and ordering of the activation loop, explaining the selectivity of compound 1 for the autophosphorylated state. The results highlight the role of structural plasticity within the kinase domain in imparting the specificity of ligand binding and provide the framework for structure-guided design of activated c-Met inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket

Though the hepatitis B virus (HBV) core protein is an important participant in many aspects of the viral life cycle, its best-characterized activity is self-assembly into 240-monomer capsids. Small molecules that target core protein (core protein allosteric modulators [CpAMs]) represent a promising antiviral strategy. To better understand the structural basis of the CpAM mechanism, we determined the crystal structure of the HBV capsid in complex with HAP18. HAP18 accelerates assembly, increases protein-protein association more than 100-fold, and induces assembly of nonicosahedral macrostructures. In a preformed capsid, HAP18 is found at quasiequivalent subunit-subunit interfaces. In a detailed comparison to the two other extant CpAM structures, we find that the HAP18-capsid structure presents a paradox. Whereas the two other structures expanded the capsid diameter by up to 10 Å, HAP18 caused only minor changes in quaternary structure and actually decreased the capsid diameter by ~3 Å. These results indicate that CpAMs do not have a single allosteric effect on capsid structure. We suggest that HBV capsids present an ensemble of states that can be trapped by CpAMs, indicating a more complex basis for antiviral drug design. Hepatitis B virus core protein has multiple roles in the viral life cycle—assembly, compartment for reverse transcription, intracellular trafficking, and nuclear functions—making it an attractive antiviral target. Core protein allosteric modulators (CpAMs) are an experimental class of antivirals that bind core protein. The most recognized CpAM activity is that they accelerate core protein assembly and strengthen interactions between subunits. In this study, we observe that the CpAM-binding pocket has multiple conformations. We compare structures of capsids cocrystallized with different CpAMs and find that they also affect quaternary structure in different ways. Furthermore, these results suggest that the capsid “breathes” and is trapped in different states by the drug and crystallization. Understanding that the capsid is a moving target will aid drug design and improve our understanding of HBV interaction with its environment.

59 BASIC BIOLOGICAL SCIENCES↗

Locating Small Leaks in Large Structures

Test tool for detecting minute leads in bimetal joints, welds, or other locations employs fine-control valve and hypodermic needle. Test item is connected in conventional manner to helium mass spectrometer tuned to read extremely small amounts of helium gas. Uniqueness of method is ability to detect tiny leaks, through surfaces, not discoverable by gross coverage of test structures by helium gas.

Lawler, W. F.↗

Plasmaspheric Plume Turbulence: Signature of an Electrostatic Corotation Convection Shear-Layer Instability

As demonstrated by IMAGE-EUV observations, plasmaspheric drainage plumes are a common feature emanating from the plasmasphere during periods of enhanced convection. Concurrent IMAGE-EUV and LANL-MPA observations reveal that plasmaspheric plumes are not a uniform density structure that extends out to geosynchronous orbit and beyond. Instead, in–situ observations reveal a large spatial-scale structure populated by small-scale density structures suggestive of the presence of a turbulent process. Here, we investigate the occurrence and nature of plasmaspheric drainage plumes as observed by concurrent EUV-MPA observations, as well as explore the possibility that the in–situ observed small-scale density structures are the signature of an instability produced by the sheared velocity found within the plasmaspheric layers separating the corotation of the main plasmasphere from the convection-driven flow generating the plume. Particle-in-cell simulations indicate that the generation of shear-flow driven instabilities is possible under plasmaspheric plasma conditions. The initial results of these simulations indicate that the plasmaspheric instabilities generated are electrostatic in nature, consist with in–situ plume observations.

Mark L Adrian↗

Training Data Optimized and Conditioned to Learn Characteristic Patterns of Vibrating Blisks and Fan Blades

At the NASA Glenn Research Center, we have been training artificial neural networks to interpret the characteristic patterns (see the leftmost image) generated from electronic holograms of vibrating structures. These patterns not only visualize the vibration properties of structures, but small changes in the patterns can indicate structural changes, cracking, or damage. Neural networks detect these small changes well. Our objective has been to adapt the neural-network, electronic-holography combination for inspecting components in Glenn's Spin Rig.

Decker, Arthur J.↗

Generalized representative structures for atomistic systems

A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.

atomic cluster expansion↗

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.

Biochemistry & Molecular Biology↗

SMALL-SCALE PRESSURE-BALANCED STRUCTURES DRIVEN BY MIRROR-MODE WAVES IN THE SOLAR WIND

Recently, small-scale pressure-balanced structures (PBSs) have been studied with regard to their dependence on the direction of the local mean magnetic field B{sub 0} . The present work continues these studies by investigating the compressive wave mode forming small PBSs, here for B{sub 0} quasi-perpendicular to the x-axis of Geocentric Solar Ecliptic coordinates (GSE-x). All the data used were measured by WIND in the quiet solar wind. From the distribution of PBSs on the plane determined by the temporal scale and angle θ{sub xB} between the GSE-x and B{sub 0} , we notice that at θ{sub xB} = 115° the PBSs appear at temporal scales ranging from 700 s to 60 s. In the corresponding temporal segment, the correlations between the plasma thermal pressure P{sub th} and the magnetic pressure P{sub B}, as well as that between the proton density N{sub p} and the magnetic field strength B, are investigated. In addition, we use the proton velocity distribution functions to calculate the proton temperatures T and T{sub ∥}. Minimum Variance Analysis is applied to find the magnetic field minimum variance vector B{sub N} . We also study the time variation of the cross-helicity σ{sub c} and the compressibility C{sub p} and compare these with values from numerical predictions for the mirror mode. In this way, we finally identify a short segment that has T > T{sub ∥}, proton β ≅ 1, both pairs of P{sub th}-P{sub B} and N{sub p}-B showing anti-correlation, and σ{sub c} ≈ 0 with C{sub p} > 0. Although the examination of σ{sub c} and C{sub p} is not conclusive, it provides helpful additional information for the wave mode identification. Additionally, B{sub N} is found to be highly oblique to B{sub 0} . Thus, this work suggests that a candidate mechanism for forming small-scale PBSs in the quiet solar wind is due to mirror-mode waves.

79 ASTRONOMY AND ASTROPHYSICS↗

Probing small-scale power spectra with pulsar timing arrays

Models of Dark Matter (DM) can leave unique imprints on the Universe’s small scale structure by boosting density perturbations on small scales. We study the capability of Pulsar Timing Arrays to search for, and constrain, subhalos from such models. The models of DM we consider are ordinary adiabatic perturbations in ΛCDM, QCD axion miniclusters, models with early matter domination, and vector DM produced during inflation. We show that ΛCDM, largely due to tidal stripping effects in the Milky Way, is out of reach for PTAs. Axion miniclusters may be within reach, although this depends crucially on whether the axion relic density is dominated by the misalignment or string contribution. Models where there is matter domination with a reheat temperature below 1 GeV may be observed with future PTAs. Lastly, vector DM produced during inflation can be detected if it is lighter than 10 16 GeV. We also make publicly available a Python Monte Carlo tool for generating the PTA time delay signal from any model of DM substructure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Load Deflection of Dow Corning SE 1700 Face Centered Tetragonal Direct Ink Write Materials: Effect of Thickness and Filament Spacing

Dow Corning SE 1700 (reinforced polydimethylsiloxane) porous structures were made by direct ink writing (DIW) in a face centered tetragonal (FCT) configuration. The filament diameter was 250 μm. Structures consisting of 4, 8, or 12 layers were fabricated with center-to-center filament spacing (“road width” (RW)) of 475, 500, 525, 550, or 575 μm. Three compressive load-unload cycles to 2000 kPa were performed on four separate areas of each sample; three samples of each thickness and filament spacing were tested. At a given strain during the third loading phase, stress varied inversely with porosity. At 10% strain, the stress was nearly independent of the number of layers (i.e., thickness). At higher strains (20- 40%), the stress was highest for the 4-layer structure; the 8- and 12-layer structures were nearly equivalent suggesting that the load deflection is independent of number of layers above 8 layers. Intra-and inter-sample variability of the load deflection response was higher for thinner and less porous structures.

36 MATERIALS SCIENCE↗

Load Deflection of Dow Corning SE 1700 Simple Cubic Direct Ink Write Materials: Effect of Thickness and Filament Spacing

Dow Corning SE 1700 (reinforced polydimethylsiloxane) porous structures were made by direct ink writing (DIW) in a simple cubic (SC) configuration. The filament diameter was 250 μm. Structures consisting of 4, 8, or 12 layers were fabricated with center-to-center filament spacing (“road width” (RW)) of 475, 500, 525, 550, or 575 μm. Three compressive load-unload cycles to 2000 kPa were performed on four separate areas of each sample; three samples of each thickness and filament spacing were tested. Geometry-dependent buckling of the SC structure was evident. At a given strain during the third loading phase, stress varied inversely with porosity. At strains of 25% and higher, the stress varied inversely with the number of layers (i.e., thickness); however, the relationship between stress and number of layers was more complex at lower strains. Intra-and inter-sample variability of the load deflection response was higher for thinner and less porous structures.

36 MATERIALS SCIENCE↗

Development of a facility for large-scale testing of multistory buildings

Current experimental research pertaining to response of structures subjected to lateral loads such as strong winds or earthquake motions is limited to either tests of single structural components or small scale multistory structures. The feasibility of developing a facility where large scale multistory structures could be loaded to failure is discussed. The test facility would consist of a series of hydraulic actuators mounted on reaction frames currently in use at the Marshall Space Flight Center for structural testing of spacecraft components. The actuators would be controlled from signals computed by an on-line analysis of measured data. This method of loading could be used to simulate inertial forces resisted by a structure behaving in the non linear range of response subjected to motion at the base or to impulses along the height as would occur during a strong earthquake or wind.

Abrams, D. P.↗

Coronal and Prominence Plasmas

Various aspects of solar prominences and the solar corona are discussed. The formation of prominences, prominence diagnostics and structure, prominence dissappearance, large scale coronal structure, coronal diagnostics, small scale coronal structure, and non-equilibrium/coronal heating are among the topics covered.

Poland, Arthur I.↗

Basic research in solar physics

This grant, dating back more than 20 years has supported a variety of investigations of the chromospheres and coronae of the Sun and related cool stars by the Principal Investigator, his postdocs and graduate students, and colleagues at other institutions. This work involved studies of radiative transfer and spectral line formation theory, and the application of these techniques to the analysis of spectra obtained from space and ground-based observatories in the optical, ultraviolet, x-ray and radio portions of the spectrum. Space observations have included the analysis of spectra from OSO-7, Skylab, SMM, and the HRTS rocket experiments. Recent work has concentrated on the interaction of magnetic fields, plasma and radiation in the outer atmospheres of the Sun and other magnetically active stars with different fundamental parameters. Our study of phenomena common to the Sun and stars, the 'solar-stellar connection', can elucidate the fundamental physics, because spatially-resolved observations of the Sun provide us with the 'groundtruth,' while interpretation of stellar data permit us to isolate those parameters critical to stellar activity. Recently, we have studied the differences in physical properties between solar regions of high magnetic flux density and the surrounding plasma. High-resolution CN and CO spectroheliograms have been used to model the thermal inhomogeneities driven by unstable CO cooling, and we have analyzed spatially resolved UV spectra from HRTS to model the thermal structure and energy balance of small-scale structures. The study of nonlinear relations between atmospheric radiative losses and the photospheric magnetic flux density has been continued. We have also proposed a new model for the decay of plages by random walk diffusion of magnetic flux. Our analysis of phenomena common to the Sun and stars included the application of available spectroscopic diagnostics, establishing evidence that the atmospheres of the least active stars are heated at a 'basal' rate that is also found in the centers of solar supergranules, and using the Doppler-imaging technique to measure the position, size, and brightness of stellar active regions. We are computing multi-component models for solar and stellar atmospheres, and models for coronal loops and for the transition-region down flows. The study of solar and stellar flares permits us to assess the role of turbulent energy transport, to pinpoint the mechanism behind Type I radio bursts, to determine whether plasma radiation or cyclotron maser is responsible for microwave flares on M dwarfs, and to extend our knowledge of the basic physics pertinent to cyclotron-maser processes operating on the Sun.

Linsky, Jeffrey L.↗