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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Stochastic generation of explicit pore structures by thresholding Gaussian random fields

We provide a description and computational investigation of an efficient method to stochastically generate realistic pore structures. Smolarkiewicz and Winter introduced this specific method in pores resolving simulation of Darcy flows (Smolarkiewicz and Winter, 2010 [1]) without giving a complete formal description or analysis of the method, or indicating how to control the parameterization of the ensemble. We address both issues in this paper. The method consists of two steps. First, a realization of a correlated Gaussian field, or topography, is produced by convolving a prescribed kernel with an initial field of independent, identically distributed random variables. The intrinsic length scales of the kernel determine the correlation structure of the topography. Next, a sample pore space is generated by applying a level threshold to the Gaussian field realization: points are assigned to the void phase or the solid phase depending on whether the topography over them is above or below the threshold. Hence, the topology and geometry of the pore space depend on the form of the kernel and the level threshold. Manipulating these two user prescribed quantities allows good control of pore space observables, in particular the Minkowski functionals. Extensions of the method to generate media with multiple pore structures and preferential flow directions are also discussed. To demonstrate its usefulness, the method is used to generate a pore space with physical and hydrological properties similar to a sample of Berea sandstone. -- Graphical abstract: -- Highlights: •An efficient method to stochastically generate realistic pore structures is provided. •Samples are generated by applying a level threshold to a Gaussian field realization. •Two user prescribed quantities determine the topology and geometry of the pore space. •Multiple pore structures and preferential flow directions can be produced. •A pore space based on Berea sandstone is generated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

Factors governing Yb magnetism in Yb{sub 0.95}PtIn{sub 2} and other MgCuAl{sub 2}-type structures

The ternary compound 'YbPtIn{sub 2}' has been synthesized and its crystal structure determined using single crystal X-ray diffraction techniques. The compound crystallizes in the MgCuAl{sub 2} structure, a ternary structure type often formed when rare earth metals, Group 10 transition metals, and indium are present in a 1:1:2 ratio. The unit cell is C-centered orthorhombic, space group Cmcm (no. 63) with lattice parameters of a=4.3410(1) A, b=10.3230(2) A, and c=7.8510(2) A. Evidence is found for a substantial non-stoichiometry on the Yb site, in contrast to the Pt and In sites which behave as expected, and it is believed that the stoichiometry of this compound is more properly described as Yb{sub 0.95}PtIn{sub 2}. Magnetic and resistivity measurements reveal that 'YbPtIn{sub 2}' is a weakly interacting, non-magnetic metal exclusively containing Yb{sup 2+}, and with a resistivity ({rho}) varying from 34 {mu}{Omega} cm at room temperature to a residual resistivity {rho}{sub 0} of 23 {mu}{Omega} cm at 1.8 K. Density functional theory calculations suggest that the observed diamagnetic Yb behavior is expected for this compound, but that certain substitutions on the Pt or In site could help stabilize magnetic Yb{sup 3+} and potentially induce heavy fermion behavior. - Graphical abstract: The crystal structure, magnetic behavior, and temperature-dependent resistivity of the new ternary compound Yb{sub 0.95}PtIn{sub 2.} Highlights: Black-Right-Pointing-Pointer Flux growth method used to produce Yb{sub 0.95}PtIn{sub 2} single crystals. Black-Right-Pointing-Pointer Found rare example of non-stoichiometry in a MgCuAl{sub 2}-type structure. Black-Right-Pointing-Pointer The resistivity and diamagnetic response of Yb{sub 0.95}PtIn{sub 2} were modeled. Black-Right-Pointing-Pointer DFT correctly predicts presence of Yb{sup 2+} in Yb{sub 0.95}PtIn{sub 2}. Black-Right-Pointing-Pointer COHP results suggest other MgCuAl{sub 2}-type indides that may contain paramagnetic Yb{sup 3+}.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Synthesis, crystal growth, structural and magnetic characterization of NH{sub 4}MCl{sub 2}(HCOO), M=(Fe, Co, Ni)

An ambient-pressure solution route and an improved solvothermal synthetic method have been developed to produce polycrystalline powders and large single crystals of NH{sub 4}MCl{sub 2}(HCOO) (M=Fe, Co, Ni). The magnetic structure of the 1D linear chain compound NH{sub 4}FeCl{sub 2}(HCOO) has been determined by low-temperature neutron powder diffraction, revealing ferromagnetic intra-chain interactions and antiferromagnetic inter-chain interactions. The newly-reported Co and Ni analogs are isostructural with NH{sub 4}FeCl{sub 2}(HCOO), but there are significant differences in the magnetic properties of each compound; the Ni analog behaves similarly to the Fe compound but with stronger magnetic coupling, exhibiting antiferromagnetic ordering (T{sub N}=8.5 K) and a broad metamagnetic transition between 2 and 5 T, while the Co analog does not order magnetically above 2 K, despite strong antiferromagnetic nearest-neighbor interactions. - Graphical abstract: Large single crystals of NH{sub 4}MCl{sub 2}(HCOO) (M=Fe, Co, Ni), which adopt a 1D zig-zag chain structure, can be grown via a solvothermal method. Neutron diffraction experiments revealed that the magnetic structure of the iron compound exhibits ferromagnetic intra-chain coupling and antiferromagnetic inter-chain coupling. - Highlights: • Large crystals of NH{sub 4}MCl{sub 2}(HCOO) (M=Fe, Co, Ni) have been grown solvothermally. • The magnetic structure of M=Fe was solved by low-temperature neutron diffraction. • NH{sub 4}FeCl{sub 2}(HCOO) exhibits FM intra-chain and AFM inter-chain interactions. • NH{sub 4}CoCl{sub 2}(HCOO) exhibits no 3D magnetic ordering above 2 K. • NH{sub 4}NiCl{sub 2}(HCOO) exhibits AFM ordering (T{sub N}=8.5 K) and FM intra-chain interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A phase width for CaGaSn. Crystal structure of mixed intermetallic Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} and SmGa{sub x}Sn{sub 3−x}, stability, geometry and electronic structure

X-ray single-crystal structure has been established for new compositions in intermetallic systems of tin and gallium. Crystals were successfully obtained in alloys prepared from elements. The structure of SmGaSn{sub 2} (cubic Pm3̄m, a=4.5778(8) Å, Z=1, R1=0.012) is described with atomic disorder at all Sn/Ga positions and the structure of Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} (hexagonal, P6{sub 3}/mmc, a=4.2233(9), c=17.601(7) Å, Z=1, R1=0.062) raises an interesting question about existence of a composition domain for CaGaSn. Finally, Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} should be considered as a particular composition of Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}, a compound assumed to exist in the range x ~ 0−1. Partial atomic ordering characterizes the Sn/Ga puckered layers of hexagons whose geometries are analyzed and discussed comparatively with analogous arrangements in AlB{sub 2} related hexagonal compounds. The study is supported by rigid band model and DFT calculations performed for different experimental and hypothetic arrangements. - Graphical abstract: A phase width for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} belonging to the hexagonal YPtAs structure-type. - Highlights: • Single crystals of mixed tin gallium ternary intermetallics were obtained. • Partial ordering at metal sites and phase width are evidenced for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}. • Layer deviation to flatness is studied comparatively with related structures. • Geometry and stability analyses based on DFT calculations are provided.

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

Pore- and micro-structural characterization of a novel structural binder based on iron carbonation

The pore- and micro-structural features of a novel binding material based on the carbonation of waste metallic iron powder are reported in this paper. The binder contains metallic iron powder as the major ingredient, followed by additives containing silica and alumina to facilitate favorable reaction product formation. Compressive strengths sufficient for a majority of concrete applications are attained. The material pore structure is investigated primarily through mercury intrusion porosimetry whereas electron microscopy is used for microstructural characterization. Reduction in the overall porosity and the average pore size with an increase in carbonation duration from 1 day to 4 days is noticed. The pore structure features are used in predictive models for gas and moisture transport (water vapor diffusivity and moisture permeability) through the porous medium which dictates its long-term durability when used in structural applications. Comparisons of the pore structure with those of a Portland cement paste are also provided. The morphology of the reaction products in the iron-based binder, and the distribution of constituent elements in the microstructure are also reported. - Highlights: • Carbonation of iron produces a dense microstructure. • Pore volume in iron carbonate lower, critical size higher than those in OPC pastes • Reaction product contains iron, carbon, silicon, aluminum and calcium. • Power-law for porosity-moisture permeability relationship was established.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Electronic structure, morphology and emission polarization of enhanced symmetry InAs quantum-dot-like structures grown on InP substrates by molecular beam epitaxy

The optical and structural properties of a new kind of InAs/InGaAlAs/InP quantum dot (QD)-like objects grown by molecular beam epitaxy have been investigated. These nanostructures were found to have significantly more symmetrical shapes compared to the commonly obtained dash-like geometries typical of this material system. The enhanced symmetry has been achieved due to the use of an As{sub 2} source and the consequent shorter migration length of the indium atoms. Structural studies based on a combination of scanning transmission electron microscopy (STEM) and atom probe tomography (APT) provided detailed information on both the structure and composition distribution within an individual nanostructure. However, it was not possible to determine the lateral aspect ratio from STEM or APT. To verify the in-plane geometry, electronic structure calculations, including the energy levels and transition oscillator strength for the QDs have been performed using an eight-band k·p model and realistic system parameters. The results of calculations were compared to measured polarization-resolved photoluminescence data. On the basis of measured degree of linear polarization of the surface emission, the in-plane shape of the QDs has been assessed proving a substantial increase in lateral symmetry. This results in quantum-dot rather than quantum-dash like properties, consistent with expectations based on the growth conditions and the structural data.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Rationalizing the role of structural motif and underlying electronic structure in the finite temperature behavior of atomic clusters

Melting in finite size systems is an interesting but complex phenomenon. Many factors affect melting and owing to their interdependencies it is a challenging task to rationalize their roles in the phase transition. In this work, we demonstrate how structural motif of the ground state influences melting transition in small clusters. Here, we report a case with clusters of aluminum and gallium having same number of atoms, valence electrons, and similar structural motif of the ground state but drastically different melting temperatures. We have employed Born-Oppenheimer molecular dynamics to simulate the solid-like to liquid-like transition in these clusters. Our simulations have reproduced the experimental trends fairly well. Further, the detailed analysis of isomers has brought out the role of the ground state structure and underlying electronic structure in the finite temperature behavior of these clusters. For both clusters, isomers accessible before cluster melts have striking similarities and does have strong influence of the structural motif of the ground state. Further, the shape of the heat capacity curve is similar in both the cases but the transition is more spread over for Al{sub 36} which is consistent with the observed isomerization pattern. Our simulations also suggest a way to characterize transition region on the basis of accessibility of the ground state at a specific temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A first principles study of structural stability, electronic structure and mechanical properties of ABeH{sub 3} (A = Li, Na)

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of ABeH{sub 3} (A = Li, Na) for three different crystal structures, namely orthorhombic (Pnma), monoclinic (P2{sub 1}/c) and triclinic (P-1) phase. Among the considered structures monoclinic (P2{sub 1}/c) phase is found to be the most stable one for all the three hydrides at ambient condition. The electronic structure reveals that these materials are wide band gap semiconductors. The calculated elastic constants indicate that these materials are mechanically stable at ambient condition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Molecular structure determination: Equilibrium structure of pyrimidine (m-C 4 H 4 N 2 ) from rotational spectroscopy (reSE) and high-level ab initio calculation (re) agree within the uncertainty of experimental measurement

The pure rotational spectrum of pyrimidine (m-C 4 H 4 N 2 ), the meta-substituted dinitrogen analog of benzene, has been studied in the millimeter-wave region from 235 GHz to 360 GHz. The rotational spectrum of the ground vibrational state has been assigned and fit to yield accurate rotational and distortion constants. Over 1700 distinct transitions were identified for the normal isotopologue in its ground vibrational state and least-squares fit to a partial sextic S-reduced Hamiltonian. Transitions for all four singly substituted 13 C and 15 N isotopologues were observed at natural abundance and were likewise fit. Deuterium-enriched samples of pyrimidine were synthesized, giving access to all eleven possible deuterium-substituted isotopologues, ten of which were previously unreported. Experimental values of rotational constants and computed values of vibration–rotation interaction constants and electron-mass corrections were used to determine semi-experimental equilibrium structures (r e SE ) of pyrimidine. The r e SE structure obtained using coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] corrections shows exceptional agreement with the re structure computed at the CCSD(T)/cc-pCV5Z level (≤0.0002 Å in bond distance and ≤0.03° in bond angle). Of the various computational methods examined, CCSD(T)/cc-pCV5Z is the only method for which the computed value of each geometric parameter lies within the statistical experimental uncertainty (2σ) of the corresponding semi-experimental coordinate. The exceptionally high accuracy and precision of the structure determination is a consequence of the large number of isotopologues measured, the precision and extent of the experimental frequency measurements, and the sophisticated theoretical treatment of the effects of vibration–rotation coupling and electron mass. Taken together, these demanding experimental and computational studies establish the capabilities of modern structural analysis for a prototypical monocyclic aromatic compound.

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

Crystal structure of the m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon 4-1BB receptor binding

The interaction between the receptor 4-1BB and its ligand 4-1BBL provides co-stimulatory signals for T-cell activation and proliferation. However, differences in the mouse and human molecules might result in differential engagement of this pathway. Here, we report the crystal structure of mouse 4-1BBL and of the mouse 4-1BB/4-1BBL complex, which together provided insights into the molecular mechanism by which m4-1BBL and its cognate receptor recognize each other. Unlike all human or mouse tumor necrosis factor ligands that form noncovalent and mostly trimeric assemblies, the m4-1BBL structure formed a disulfide-linked dimeric assembly. The structure disclosed that certain differences in the amino acid composition along the intramolecular interface, together with two specific residues (Cys-246 and Ser-256) present exclusively in m4-1BBL, are responsible for this unique dimerization. Unexpectedly, upon m4-1BB binding, m4-1BBL undergoes structural changes within each protomer; moreover, the individual m4-1BBL protomers rotate relative to each other, yielding a dimerization interface with more inter-subunit interactions. We also observed that in the m4-1BB/4-1BBL complex, each receptor monomer binds exclusively to a single ligand subunit with contributions of cysteine-rich domain 1 (CRD1), CRD2, and CRD3. Furthermore, structure-guided mutagenesis of the binding interface revealed that novel binding interactions with the GH loop, rather than the DE loop, are energetically critical and define the m4-1BB receptor selectivity for m4-1BBL. As a result, a comparison with the human 4-1BB/4-1BBL complex highlighted several differences between the ligand- and receptor-binding interfaces, providing an explanation for the absence of inter-species cross-reactivity between human and mouse 4-1BB and 4-1BBL molecules.

4-1BB↗
DOE OSTI2016

The effects of post-growth annealing on the structural and magnetic properties of BaFe 2 As 2

Here, we investigate the effects of post-growth annealing on the structural and magnetic properties of BaFe 2 As 2 . Magnetic susceptibility measurements, which exhibit a signal corresponding to the magnetic phase transition, and high-resolution x-ray diffraction measurements, which directly probe the structural order parameter, show that annealing causes the ordering temperatures of both the phase transitions to increase, sharpen and converge. In the as grown sample, our measurements show two distinct transitions corresponding to structural and magnetic ordering, which are separated in temperature by approximately 1 K. After 46 days (d) of annealing at 700 °C, the two become concurrent in temperature. These measurements demonstrate that the structural phase transition is second-order like when the magnetic and structural phase transitions are separated in temperature, and first-order like when the two phase transition temperatures coincide. This observation indicates that annealing causes the system to cross a hitherto undiscovered tricritical point. In addition, x-ray diffraction measurements show that the c-axis lattice parameter increases with annealing up to 30 d, but remains constant for longer annealing times. Comparisons of BaFe 2 As 2 to SrFe 2 As 2 are made when possible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6

Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80s loop, the primary site for known protein-recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances, which reflects a slow conformational transition centered in the 80s loop. The primary known physiological function of FKBP12.6 involves its role in regulating the RyR2 isoform of ryanodine receptor Ca{sup 2+} channels in cardiac muscle, pancreatic β islets and the central nervous system. With only a single previously reported X-ray structure of FKBP12.6, bound to the immunosuppressant rapamycin, structural inferences for this protein have been drawn from the more extensive studies of the homologous FKBP12. X-ray structures at 1.70 and 1.90 Å resolution from P2{sub 1} and P3{sub 1}21 crystal forms are reported for an unligated cysteine-free variant of FKBP12.6 which exhibit a notable diversity of conformations. In one monomer from the P3{sub 1}21 crystal form, the aromatic ring of Phe59 at the base of the active site is rotated perpendicular to its typical orientation, generating a steric conflict for the immunosuppressant-binding mode. The peptide unit linking Gly89 and Val90 at the tip of the protein-recognition ‘80s loop’ is flipped in the P2{sub 1} crystal form. Unlike the >30 reported FKBP12 structures, the backbone conformation of this loop closely follows that of the first FKBP domain of FKBP51. The NMR resonances for 21 backbone amides of FKBP12.6 are doubled, corresponding to a slow conformational transition centered near the tip of the 80s loop, as recently reported for 31 amides of FKBP12. The comparative absence of doubling for residues along the opposite face of the active-site pocket in FKBP12.6 may in part reflect attenuated structural coupling owing to increased conformational plasticity around the Phe59 ring.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗