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All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

CLASH: COMPLETE LENSING ANALYSIS OF THE LARGEST COSMIC LENS MACS J0717.5+3745 AND SURROUNDING STRUCTURES

The galaxy cluster MACS J0717.5+3745 (z = 0.55) is the largest known cosmic lens, with complex internal structures seen in deep X-ray, Sunyaev-Zel'dovich effect, and dynamical observations. We perform a combined weak- and strong-lensing analysis with wide-field BVR{sub c} i'z' Subaru/Suprime-Cam observations and 16-band Hubble Space Telescope observations taken as part of the Cluster Lensing And Supernova survey with Hubble. We find consistent weak distortion and magnification measurements of background galaxies and combine these signals to construct an optimally estimated radial mass profile of the cluster and its surrounding large-scale structure out to 5 Mpc h {sup –1}. We find consistency between strong-lensing and weak-lensing in the region where these independent data overlap, <500 kpc h {sup –1}. The two-dimensional weak-lensing map reveals a clear filamentary structure traced by distinct mass halos. We model the lensing shear field with nine halos, including the main cluster, corresponding to mass peaks detected above 2.5σ{sub κ}. The total mass of the cluster as determined by the different methods is M{sub vir} ≈ (2.8 ± 0.4) × 10{sup 15} M{sub ☉}. Although this is the most massive cluster known at z > 0.5, in terms of extreme value statistics, we conclude that the mass of MACS J0717.5+3745 by itself is not in serious tension with ΛCDM, representing only a ∼2σ departure above the maximum simulated halo mass at this redshift.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Kohn anomaly and elastic softening in body-centered cubic molybdenum at high pressure

Transition metals in body-centered cubic (bcc) structures under compression can display several novel physical properties because of their complex electronic structures and electron-phonon interactions. Here, we used inelastic x-ray scattering experiments in a diamond-anvil cell up to ∼45 GPa and density-functional theory calculations up to 210 GPa to investigate the phonon dispersions, and electronic and elastic properties of single-crystal molybdenum (Mo). Our results show a pressure-induced Kohn anomaly at 𝑞∼0.5 along the [ξ00] direction in the longitudinal acoustic mode at ∼45 GPa; this anomaly is triggered by the pressure-enhanced Fermi-surface nesting effect. Theoretical calculations show that electron redistributions in the 𝑠-to-𝑑 orbitals of bcc-Mo contribute to the shear modulus anomaly at ∼50 GPa. In contrast, the Young's modulus anomaly in bcc-Mo at ∼210 GPa results from a Lifshitz-type electronic topological transition. In conclusion, our results shed light on the complex electronic behaviors that are associated with macroscopic elastic properties in typical bcc 𝑑-block transition metals under compression.

3-dimensional systems↗
DOE OSTI2022

Structures of the TMC-1 complex illuminate mechanosensory transduction

The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid–protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cross-species analysis of FcγRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque

Introduction Antibodies play a critical role in immunity in part by mediating clearance of pathogens and infected cells by antibody-dependent cellular phagocytosis (ADCP) through engagement of Fc gamma receptors (FcγRs) on innate immune cells. Among these, FcγRIIa (CD32a) is a key activating receptor expressed on macrophages, dendritic cells, and other antigen-presenting cells. Its affinity for IgG and ability to mediate ADCP is influenced by allelic polymorphisms. In humans, a single amino acid polymorphism at position 131, where histidine (H) is substituted with arginine (R), leads to decreased IgG1 and IgG2 subclass binding affinity and, consequently, lower efficiency of phagocytic responses. Rhesus macaques ( Macaca mulatta ), which are widely used as nonhuman primate models, exhibit a similar polymorphism at position 131 of FcγRIIa, but with arginine replaced by proline (P). Here, we investigated structure-function relationships associated with the FcγRIIa polymorphism at position 131 in both species, specifically with respect to IgG1 and IgG2. Methods We determined the structures of complexes formed by each variant with IgG1 Fc and those formed by the higher affinity variant with IgG2 Fc for both species by x-ray crystallography and linked these structures to affinity and activity using SPR and an ADCP assay. We also determined the structure of human inhibitory FcγRIIb (CD32b) in complex with IgG1 Fc by x-ray crystallography. Results Through analysis of these structures, our studies reveal that FcγRIIa engagement is minimally influenced by Fc glycan composition, distinguishing it from FcγRIIIa whose affinity is strongly influenced by glycan-composition. Comparative structures of human and macaque FcγRIIa variants demonstrate species- and allele-specific differences in Fc binding, but our functional assays showed only minimal allele-specific effects in humans. In contrast, allele-specific effects in macaques were highly significant; the macaque P 131 variant showing uniformly reduced IgG affinity. Conclusion These insights highlight fundamental interspecies and allelic distinctions that are critical for interpreting FcγRIIa-mediated effector functions in macaque models and for optimizing translational antibody and vaccine design.

Tolbert, William D.↗
DOE OSTI2013

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} are studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

High-throughput simulations for insight into grain boundary structure-property relationships and other complex microstructural phenomena

High-throughput simulations can be a powerful tool in the discovery of new materials and behaviors. As part of a special issue on Rising Stars in Computational Materials Science, this paper uses the work of the author to show how high-throughput simulations have had an impact in grain boundary structure-property relationships and other complex microstructural phenomena. The work demonstrates how new tools designed to analyze large datasets produced by high-throughput simulations are enabling comprehensive grain boundary structure-property relationships to be obtained. High-throughput simulations are also used to demonstrate the impact descriptive and inferential statistics has had in extracting key aspects of deformation in metallic glasses. Finally, several different examples are used to show a balanced approach between simulations designed to survey and simulations designed for detailed analysis. Together, the two approaches provide a comprehensive picture of the variety of behaviors that exist, while ensuring that the physics underlying the behaviors are thoroughly understood.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Unexpected Hydricity of a Bis-Carbene Iridium Complex Provides Insight into Electronic Structure Impacts on Hydride Donor Ability

The hydricity (ΔG° H– ), or hydride donor ability, of a transition metal complex is a thermodynamic parameter which can aid in the design and interpretation of various catalytic reactions that involve hydride transfer as a key step. In an attempt to generate a strong hydride donor, the bis-carbene ligand 3,3′-methylenebis(1-methyl-imidazol-2-ylidene) (“bis-mim”) was installed in an iridium hydride complex, [Cp*Ir(bis-mim)H] + . Experimental and computational studies show that [Cp*Ir(bis-mim)H] + is actually a relatively weak hydride donor, however. To understand why the complex is an unexpectedly weak hydride donor, experimental and computational studies probing the steric and electronic effects on hydricity were conducted. Steric factors had a minimal impact on thermodynamic hydricity but dampened kinetic hydricity. In conclusion, the poor thermodynamic hydride donor ability can be attributed to an electronic structure that results in relatively long Cp*−Ir bonds, an unusually high Ir–H BDFE and pK a values that have an outsized influence on thermochemical cycles for hydricity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Extracting h-Backbone as a Core Structure in Weighted Networks

Determining the core structure of complex network systems allows us to simplify them. Using h -bridge and h -strength measurements in a weighted network, we extract the h -backbone core structure. We find that focusing on the h -backbone in a network allows greater simplification because it has fewer edges and thus fewer adjacent nodes. We examine three practical applications: the co-citation network in an information system, the open flight network in a social system, and coauthorship in network science publications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C

Cantharidin is a natural toxin and an active constituent in a traditional Chinese medicine used to treat tumors. Cantharidin acts as a semi-selective inhibitor of PPP-family ser/thr protein phosphatases. Despite sharing a common catalytic mechanism and marked structural similarity with PP1C, PP2AC and PP5C, human PP4C was found to be insensitive to the inhibitory activity of cantharidin. To explore the molecular basis for this selectivity, in this work we synthesized and tested novel C5/C6-derivatives designed from quantum-based modeling of the interactions revealed in the co-crystal structures of PP5C in complex with cantharidin. Structure–activity relationship studies and analysis of high-resolution (1.25 Å) PP5C-inhibitor co-crystal structures reveal close contacts between the inhibitor bridgehead oxygen and both a catalytic metal ion and a non-catalytic phenylalanine residue, the latter of which is substituted by tryptophan in PP4C. Quantum chemistry calculations predicted that steric clashes with the bulkier tryptophan side chain in PP4C would force all cantharidin-based inhibitors into an unfavorable binding mode, disrupting the strong coordination of active site metal ions observed in the PP5C co-crystal structures, thereby rendering PP4C insensitive to the inhibitors. This prediction was confirmed by inhibition studies employing native human PP4C. Mutation of PP5C (F446W) and PP1C (F257W), to mimic the PP4C active site, resulted in markedly suppressed sensitivity to cantharidin. These observations provide insight into the structural basis for the natural selectivity of cantharidin and provide an avenue for PP4C deselection. The novel crystal structures also provide insight into interactions that provide increased selectivity of the C5/C6 modifications for PP5C versus other PPP-family phosphatases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

General rotating quantum vortex filaments in the low-temperature Svistunov model of the local induction approximation

In his study of superfluid turbulence in the low-temperature limit, Svistunov [“Superfluid turbulence in the low-temperature limit,” Phys. Rev. B 52, 3647 (1995)] derived a Hamiltonian equation for the self-induced motion of a vortex filament. Under the local induction approximation (LIA), the Svistunov formulation is equivalent to a nonlinear dispersive partial differential equation. In this paper, we consider a family of rotating vortex filament solutions for the LIA reduction of the Svistunov formulation, which we refer to as the 2D LIA (since it permits a potential formulation in terms of two of the three Cartesian coordinates). This class of solutions holds the well-known Hasimoto-type planar vortex filament [H. Hasimoto, “Motion of a vortex filament and its relation to elastica,” J. Phys. Soc. Jpn. 31, 293 (1971)] as one reduction and helical solutions as another. More generally, we obtain solutions which are periodic in the space variable. A systematic analytical study of the behavior of such solutions is carried out. In the case where vortex filaments have small deviations from the axis of rotation, closed analytical forms of the filament solutions are given. A variety of numerical simulations are provided to demonstrate the wide range of rotating filament behaviors possible. Doing so, we are able to determine a number of vortex filament structures not previously studied. We find that the solution structure progresses from planar to helical, and then to more intricate and complex filament structures, possibly indicating the onset of superfluid turbulence.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Micro- and nanodomain imaging in uniaxial ferroelectrics: Joint application of optical, confocal Raman, and piezoelectric force microscopy

The application of the most effective methods of the domain visualization in model uniaxial ferroelectrics of lithium niobate (LN) and lithium tantalate (LT) family, and relaxor strontium-barium niobate (SBN) have been reviewed in this paper. We have demonstrated the synergetic effect of joint usage of optical, confocal Raman, and piezoelectric force microscopies which provide extracting of the unique information about formation of the micro- and nanodomain structures. The methods have been applied for investigation of various types of domain structures with increasing complexity: (1) periodical domain structure in LN and LT, (2) nanodomain structures in LN, LT, and SBN, (3) nanodomain structures in LN with modified surface layer, (4) dendrite domain structure in LN. The self-assembled appearance of quasi-regular nanodomain structures in highly non-equilibrium switching conditions has been considered.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Time dependent mechanical modeling for polymers based on network theory

Despite of a lot of attempts during recent years, complex mechanical behaviour of polymers remains incompletely modelled, making industrial design of structures under complex, cyclic and hard loadings not totally reliable. The non linear and dissipative viscoelastic, viscoplastic behaviour of those materials impose to take into account non linear and combined effects of mechanical and thermal phenomena. In this view, a visco-hyperelastic, viscoplastic model, based on network description of the material has recently been developed and designed in a complete thermodynamic frame in order to take into account those main thermo-mechanical couplings. Also, a way to account for coupled effects of strain-rate and temperature was suggested. First experimental validations conducted in the 1D limit on amorphous rubbery like PMMA in isothermal conditions led to pretty goods results. In this paper a more complete formalism is presented and validated in the case of a semi crystalline polymer, a PA66 and a PET (either amorphous or semi crystalline) are used. Protocol for identification of constitutive parameters is described. It is concluded that this new approach should be the route to accurately model thermo-mechanical behaviour of polymers using a reduced number of parameters of some physical meaning.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

THE STELLAR MASS STRUCTURE OF MASSIVE GALAXIES FROM z = 0 TO z = 2.5: SURFACE DENSITY PROFILES AND HALF-MASS RADII

We present stellar mass surface density profiles of a mass-selected sample of 177 galaxies at 0.5 < z < 2.5, obtained using very deep Hubble Space Telescope optical and near-infrared data over the GOODS-South field, including recent CANDELS data. Accurate stellar mass surface density profiles have been measured for the first time for a complete sample of high-redshift galaxies more massive than 10{sup 10.7} M {sub Sun }. The key advantage of this study compared to previous work is that the surface brightness profiles are deconvolved for point-spread function smoothing, allowing accurate measurements of the structure of the galaxies. The surface brightness profiles account for contributions from complex galaxy structures such as rings and faint outer disks. Mass profiles are derived using radial rest-frame ug color profiles and a well-established empirical relation between these colors and the stellar mass-to-light ratio. We derive stellar half-mass radii from the mass profiles, and find that these are on average {approx}25% smaller than rest-frame g-band half-light radii. This average size difference of 25% is the same at all redshifts, and does not correlate with stellar mass, specific star formation rate, effective surface density, Sersic index, or galaxy size. Although on average the difference between half-mass size and half-light size is modest, for approximately 10% of massive galaxies this difference is more than a factor of two. These extreme galaxies are mostly extended, disk-like systems with large central bulges. These results are robust, but could be impacted if the central dust extinction becomes high. ALMA observations can be used to explore this possibility. These results provide added support for galaxy growth scenarios wherein massive galaxies at these epochs grow by accretion onto their outer regions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Enormous electron-electron scattering in the filled-cage cubic compound B a 10 T i 24 B i 39

Cubic intermetallic compound Ba 10 Ti 24 Bi 39 has a Ba 6 Bi 16 polyhedral cage with a Bi guest atom encapsulated inside. The compound can be formulated as Ba 5 Ti 12 Bi$_{19+x}$ when $x$ signifies the extra Bi atoms filling cages. It crystallizes in a complex noncentrosymmetric cubic structure in space group $P-43m$ with cell parameter $a = 12.6787(4)Å$. The guest Bi atoms distribute diffusely in the cages and seem to play a role in stabilizing the crystal structure. The magnetic susceptibility of this compound shows a weak temperature dependence with a positive slope coefficient. The charge transport properties as a function of temperature exhibit two competing components which are in charge of positive and negative magnetoresistances. Electronic band-structure calculations reveal the complex multiband hybridization of Ti/Bi orbitals near the Fermi surface, which may play a role in the enormous electron-electron scattering in this material evidenced by the large Kadowaki-Woods ratio.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Rationalizing Calcium Electrodeposition Behavior by Quantifying Ethereal Solvation Effects on Ca 2+ Coordination in Well-Dissociated Electrolytes

Ca-ion electrochemical systems have been pushed to the forefront of recent multivalent energy storage advances due to their use of earth-abundant redox materials and their high theoretical specific densities in relation to monovalent or even other more widely explored multivalent-charge carriers. However, significant pitfalls in metal plating and stripping arise from electrolyte decomposition and can be related to the coordination environment around Ca 2+ with both the negatively charged anion and the organic–aprotic solvent. Here, we apply multiple spectroscopic techniques in conjunction with density functional theory to evaluate the coordination environment of Ca 2+ across a class of ethereal solvents. Through the combination of X-ray absorption fine structure and time-dependent density functional theory, descriptive measures of the local geometry, coordination, and electronic structure of Ca–ethereal complexes provide distinct structural trends depending on the extent of the Ca 2+ –solvent interaction. Finally, we correlate these findings with electrochemical measurements of calcium tetrakis(hexafluoroisopropoxy)borate (CaBHFIP 2 ) salts dissolved within this class of solvents to provide insight into the preferred structural configuration of Ca 2+ electrolytic solutions for optimized electrochemical plating and stripping.

25 ENERGY STORAGE↗
DOE OSTI2024

StructuredFuzzer: Fuzzing Structured Text-Based Control Logic Applications

Rigorous testing methods are essential for ensuring the security and reliability of industrial controller software. Fuzzing, a technique that automatically discovers software bugs, has also proven effective in finding software vulnerabilities. Unsurprisingly, fuzzing has been applied to a wide range of platforms, including programmable logic controllers (PLCs). However, current approaches, such as coverage-guided evolutionary fuzzing implemented in the popular fuzzer American Fuzzy Lop Plus Plus (AFL++), are often inadequate for finding logical errors and bugs in PLC control logic applications. They primarily target generic programming languages like C/C++, Java, and Python, and do not consider the unique characteristics and behaviors of PLCs, which are often programmed using specialized programming languages like Structured Text (ST). Furthermore, these fuzzers are ill suited to deal with complex input structures encapsulated in ST, as they are not specifically designed to generate appropriate input sequences. This renders the application of traditional fuzzing techniques less efficient on these platforms. To address this issue, this paper presents a fuzzing framework designed explicitly for PLC software to discover logic bugs in applications written in ST specified by the IEC 61131-3 standard. The proposed framework incorporates a custom-tailored PLC runtime and a fuzzer designed for the purpose. We demonstrate its effectiveness by fuzzing a collection of ST programs that were crafted for evaluation purposes. We compare the performance against a popular fuzzer, namely, AFL++. The proposed fuzzing framework demonstrated its capabilities in our experiments, successfully detecting logic bugs in the tested PLC control logic applications written in ST. On average, it was at least 83 times faster than AFL++, and in certain cases, for example, it was more than 23,000 times faster.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Dinuclear Complexes of Uranyl, Neptunyl, and Plutonyl: Structures and Oxidation States Revealed by Experiment and Theory

Dinuclear perchlorate complexes of uranium, neptunium, and plutonium were characterized by reactivity and DFT, with results revealing structures containing pentavalent, hexavalent, and heptavalent actinyls, and actinyl-actinyl interactions (AAIs). Electrospray ionization produced native complexes [(AnO 2 ) 2 (ClO 4 ) 3 ] - for An:An = U:U, Np:Np, Pu:Pu, and Np:Pu, which are intuitively formulated as actinyl(V) perchlorates. However, DFT identified lower-energy structures [(AnO 2 )(AnO 3 )(ClO 4 ) 2 (ClO 3 )] - comprising a perchlorate fragmented to ClO 3 , actinyl(VI) cation An VI O 2 2+ , and neutral AnO 3 . For U:U and Np:Np, and Np in Np:Pu, the coordinated AnO 3 is calculated as actinyl(VI) with an equatorial oxo, [O yl =An VI =O yl ][=O eq ], whereas for Pu:Pu, it is plutonyl(V) oxyl, [O yl =Pu V =O yl ][-O eq • ]. The implied lower stability of Pu VI versus Np VI indicates weaker Pu=O eq versus Np=O eq bonding. Adsorption of O 2 by the U:U complex suggests oxidation of U V to U VI , corroborating the assignment of perchlorate [(An V O 2 ) 2 (ClO 4 ) 3 ] - . DFT predicts the O 2 adducts are [(An VI O 2 )(O 2 )(An VI O 2 )(ClO 4 ) 3 ] - with actinyls oxidized from +V to +VI by bridging peroxide, O 2 2- . In accordance with reactivity, O 2- addition is computed as substantially exothermic for U:U and least favorable for Pu:Pu. Collision-induced dissociation of native complexes eliminated ClO 2 to yield [(AnO 2 )(O) 2 (AnO 2 )(ClO 4 ) 2 ] - , in which fragmented O atoms bridge as oxyl O -• and oxo O 2- to yield uranyl(VI) and plutonyl(VI), or as oxos O 2- to yield neptunyl(VII), [O yl =Np VII =O yl ] 3+ .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗