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At least 487 records · Page 27

Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression

The structure of the new class of controller proteins (exemplified by C.Csp231I) in complex with its 21 bp DNA-recognition sequence is presented, and the molecular basis of sequence recognition in this class of proteins is discussed. An unusual extended spacer between the dimer binding sites suggests a novel interaction between the two C-protein dimers. In a wide variety of bacterial restriction–modification systems, a regulatory ‘controller’ protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural analysis and design of multivariable control systems: An algebraic approach

The application of algebraic system theory to the design of controllers for multivariable (MV) systems is explored analytically using an approach based on state-space representations and matrix-fraction descriptions. Chapters are devoted to characteristic lambda matrices and canonical descriptions of MIMO systems; spectral analysis, divisors, and spectral factors of nonsingular lambda matrices; feedback control of MV systems; and structural decomposition theories and their application to MV control systems.

Tsay, Yih Tsong↗

Synthesis of Zn–Fe layered double hydroxides via an oxidation process and structural analysis of products

The synthesis of Zn–Fe(III) layered double hydroxides was attempted, employing different pathways using either Fe(II) or Fe(III) species together with Zn as the initial reagents. The product derived from the synthesis employing Fe(II) was found to transition to a Zn–Fe(III) layered double hydroxides phase following oxidation process. In contrast, the product obtained with Fe(III) did not contain a layered double hydroxides phase, but rather consisted of simonkolleite and hydrous ferric oxide. It was determined that the valency of the Fe reagent used in the initial synthesis affected the generation of the layered double hydroxides phase. Fe(II) species have ionic radii and electronegativities similar to those of Zn, and therefore are more likely to form trioctahedral hydroxide layers with Zn species. - Graphical abstract: The synthesis of Zn–Fe(III) layered double hydroxides was attempted, employing different pathways using either Fe(II) or Fe(III) species together with Zn as the initial reagents. - Highlights: • Iron valency affected the generation of Zn–Fe layered double hydroxides. • Zn–Fe layered double hydroxides were successfully synthesized using Fe(II). • Fe(II) species were likely to form trioctahedral hydroxide layers with Zn species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

36 MATERIALS SCIENCE↗

Simplified method for nonlinear structural analysis

A simplified inelastic analysis computer program was developed for predicting the stress-strain history of a thermomechanically cycled structure from an elastic solution. The program uses an iterative and incremental procedure to estimate the plastic strains from the material stress-strain properties and a simulated plasticity hardening model. The simplified method was exercised on a number of problems involving uniaxial and multiaxial loading, isothermal and nonisothermal conditions, and different materials and plasticity models. Good agreement was found between these analytical results and nonlinear finite element solutions for these problems. The simplified analysis program used less than 1 percent of the CPU time required for a nonlinear finite element analysis.

Kaufman, A.↗

Structural analysis of WO 3 -TeO 2 glasses by neutron, high energy X-ray diffraction, reverse Monte Carlo simulations and XANES

The structure of WO 3 -TeO 2 glasses containing 15, 20 and 25 mol% WO 3 are studied by neutron diffraction (ND), high energy X-ray diffraction (XRD) and X-ray Absorption Near Edge spectroscopy (XANES). The short-range structural properties of glasses i.e. Te-O and W-O speciation, coordination number distributions, bond-lengths, and the O-Te-O, O-W-O and O-O-O bond angle distributions in the glass network are determined by the Reverse Monte Carlo (RMC) simulations of the ND and XRD data. RMC technique successfully determined all partial pair correlation functions and the coordination number distributions revealed that glass network consists predominantly of TeO 4 and WO 4 units with small amounts of triangular, penta and hexa co-ordinated units. The average W-O and Te-O bond lengths are in the ranges: 1.69-1.75 +/- 0.01 angstrom and 1.99-2.00 +/- 0.01 angstrom respectively. Both W-O and Te-O correlation peaks are asymmetrical, that indicate a distribution of their bond lengths in the respective structural units. The O-Te-O bond angle distribution has a peak at 107 +/- 2 degrees. Similarly the O-W-O bond angle distribution has a peak at 108 +/- 5 degrees. On increasing the WO3 concentration from 15 to 25 mol%, the average Te-O coordination number decreases from 3.80 to 3.61 +/- 0.02 due to the structural transformation: TeO 4 → TeO 3 , similarly the W-O coordination also decreases and is in the range: 3.79-3.67 +/- 0.02. XANES studies found that the oxidation state of Te and W ions in the glasses are 4 + and 6 + respectively.

36 MATERIALS SCIENCE↗

Multi-scale structural analysis of proteins by deep semantic segmentation

Abstract Motivation Recent advances in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidate structures that can lead to native folds or designable structures remains a challenge, since few existing metrics capture high-level structural features such as architectures, folds and conformity to conserved structural motifs. Convolutional Neural Networks (CNNs) have been successfully used in semantic segmentation—a subfield of image classification in which a class label is predicted for every pixel. Here, we apply semantic segmentation to protein structures as a novel strategy for fold identification and structure quality assessment. Results We train a CNN that assigns each residue in a multi-domain protein to one of 38 architecture classes designated by the CATH database. Our model achieves a high per-residue accuracy of 90.8% on the test set (95.0% average per-class accuracy; 87.8% average per-structure accuracy). We demonstrate that individual class probabilities can be used as a metric that indicates the degree to which a randomly generated structure assumes a specific fold, as well as a metric that highlights non-conformative regions of a protein belonging to a known class. These capabilities yield a powerful tool for guiding structural sampling for both structural prediction and design. Availability and implementation The trained classifier network, parser network, and entropy calculation scripts are available for download at https://git.io/fp6bd, with detailed usage instructions provided at the download page. A step-by-step tutorial for setup is provided at https://goo.gl/e8GB2S. All Rosetta commands, RosettaRemodel blueprints, and predictions for all datasets used in the study are available in the Supplementary Information. Supplementary information Supplementary data are available at Bioinformatics online.

Eguchi, Raphael R.↗

Evaluation of inelastic constitutive models for nonlinear structural analysis

The influence of inelastic material models on computed stress-strain states, and therefore predicted lives, was studied for thermomechanically loaded structures. Nonlinear structural analyses were performed on a fatigue specimen which had been subjected to thermal cycling in fluidized beds and on a mechanically load cycled benchmark notch specimen. Four incremental plasticity creep models (isotropic, kinematic, combined isotropic kinematic, combined plus transient creep) were exercised using the MARC program. Of the plasticity models, kinematic hardening gave results most consistent with experimental observations. Life predictions using the computed strain histories at the critical location with a strainrange partitioning approach considerably overpredicted the crack initiation life of the thermal fatigue specimen.

Kaufman, A.↗

Evaluation of Inelastic Constitutive Models for Nonlinear Structural Analysis

The influence of inelastic material models on computed stress-strain states, and therefore predicted lives, was studied for thermomechanically loaded structures. Nonlinear structural analyses were performed on a fatigue specimen which was subjected to thermal cycling in fluidized beds and on a mechanically load cycled benchmark notch specimen. Four incremental plasticity creep models (isotropic, kinematic, combined isotropic-kinematic, combined plus transient creep) were exercised. Of the plasticity models, kinematic hardening gave results most consistent with experimental observations. Life predictions using the computed strain histories at the critical location with a Strainrange Partitioning approach considerably overpredicted the crack initiation life of the thermal fatigue specimen.

Kaufman, A.↗

Element-by-element Solution Procedures for Nonlinear Structural Analysis

Element-by-element approximate factorization procedures are proposed for solving the large finite element equation systems which arise in nonlinear structural mechanics. Architectural and data base advantages of the present algorithms over traditional direct elimination schemes are noted. Results of calculations suggest considerable potential for the methods described.

Hughes, T. J. R.↗

Structural Analysis of ZnO Nanoparticles Reinforced P(3HB-co-15 mol% 3HHx) Bioplastic Composite

Bioplastics are gaining interest due to their biodegradable and biocompatible nature which can be used as a replacement for petroleum based plastics. Poly (3-hydroxybutyrate-co-15 mol% 3-hydroxyhexanoate) [P(3HB-co-15 mol% 3HHx)]/ZnO nanoparticles (NPs) blended bioplastic films were fabricated by solution casting method using chloroform as solvent. The structural characteristics such as peak intensity analysis, crystallite size, dislocation density, and texture coefficient of ZnO NPs mixed P(3HB-co-15 mol% 3HHx) samples were studied using X-Ray Diffraction (XRD) and Fourier Transform Infra-Red (FTIR) analyses. It is clear from the XRD analyses that the crystallinity of P(3HB-co-15 mol% 3HHx) was decreased considerably as ZnO NPs concentration increased. The crystallite size of P(3HB-co-15 mol% 3HHx) was decreased with an increase in ZnO NPs concentration and observed within 150 nm and the dislocation density was decreased with respect to the orientation of P(3HB-co-15 mol% 3HHx) crystals. Simultaneously, the structural properties of ZnO NPs in P(3HB-co-15 mol% 3HHx) matrix were affected noticeably with respect to the ZnO NPs and copolymer concentrations. The characteristic peak positions from FTIR spectra of P(3HB-co-15 mol% 3HHx) copolymer shifted towards higher frequency and evidenced the existence of structural defects. Overall, it was found from both XRD and FTIR analyses that the presence of ZnO NPs affected the crystallinity of P(3HB-co-15 mol% 3HHx) copolymer due to the formation of intermolecular bonds, which restricted the preferential orientation of P(3HB-co-15 mol% 3HHx) molecules which was observed from the texture coefficient analyses. Based on these observations, ZnO NPs at low concentrations can be used with P(3HB-co-15 mol% 3HHx) copolymer effectively and the resulting composite may be used for packaging application.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Structural analysis and ferroelectric properties of Fe doped BaTiO{sub 3}

The polycrystalline samples of Fe doped BaTiO{sub 3} (BTO) with compositional formula BaTi{sub 1-x}Fe{sub x}O{sub 3} (x = 0, 0.03, 0.04 and 0.05) were prepared by solid-state reaction route. The influence of the Fe content on the structural, vibrational and electric properties of BaTiO{sub 3} was investigated using X-ray powder diffraction (XRD), Raman spectroscopy and Polarization techniques. XRD analysis indicates the formation of single-phase tetragonal structure for all the prepared samples. Tetragonal cubic structure with space group P4mm of all samples is further approved by Rietveld refinement. Room temperature Raman spectra of pure BaTiO{sub 3} show four active modes of vibration whose intensity decreases with increasing Fe doping. Small shift in Raman modes and increment in the line width has been observed with the doping ions. The hysteresis loop is very well performed with regular sharp characteristic of ferroelectric materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A structural analysis of small vapor-deposited 'multiply twinned' gold particles

High resolution selected zone dark field, Bragg reflection imaging and weak beam dark field techniques of transmission electron microscopy were used to determine the structure of small gold particles vapor deposited on NaCl substrates. Attention was focused on the analysis of those particles in the 50-150 A range that have pentagonal or hexagonal bright field profiles. These particles have been previously described as multiply twinned crystallites composed of face-centered cubic tetrahedra. The experimental evidence of the present studies can be interpreted on the assumption that the particle structure is a regular icosahedron or decahedron for the hexagonal or the pentagonal particles respectively. The icosahedron is a multiply twinned rhombohedral crystal and the decahedron is a multiply twinned body-centered orthorhombic crystal, each of which constitutes a slight distortion from the face-centered cubic structure.

Yang, C. Y.↗

Integrating Magnetotellurics, Soil Gas Geochemistry and Structural Analysis to Identify Hidden, High Enthalpy, Extensional Geothermal Systems

Our research group comprising personnel from University of Utah/EGI (UU/EGI), University of Nevada at Reno (UNR) and Lawrence Berkeley National Laboratory (LBNL) has been applying magnetotellurics (MT), diagnostic structural affiliations, and soil gas flux and geochemistry to assist in identifying hidden, high-enthalpy geothermal systems in extensional regimes of the U.S. Great Basin. We are specifically looking for upwelling low-resistivity and geologic structures that can carry fluids from magmatic or high-grade metamorphic conditions in the deep crust upward to exploitable depths, and to verify the nature of the deep sources through soil gas geochemical compositions. The project was motivated by prior MT transect coverage of western and central Nevada centered upon the Dixie Valley geothermal system where such favorable indicators were first recognized. The high-angle structures are taken to be fluidized fault zones connecting deep magmatic/metamorphic activity with the geothermal system but the concept requires verification by testing at other systems. The project was set up with a two-phased organization. Phase I was carried out at the McGinness Hills system, central Nevada, where Ormat’s flagship power facility is located and a considerable amount of pre-existing data was available. Transect MT data also showed a strong low-resistivity upwelling originating from interpreted deep crustal magmatic underplating. Controlling structures on production as indicated by Ormat data and new mapping by UNR were favorable to dilatency being an accommodation zone between major normal faults of opposing dip. A 3D MT survey and inversion confirmed the existence of the steep low-resistivity zone dipping ESE toward the deep crust and placed N-S bounds upon the feature. Ormat personnel cooperated with PI Wannamaker in the field in providing fluid samples from the production intervals for He isotope composition. Elevated 3He was verified through analysis at LBNL confirming that there was a magmatic connection into the producing system. High CO2 soil gas flux including possibly metamorphic 13C and 14C component was measured over the area of dilatent structures. Hence, the triad of indicators posed above was confirmed in Phase I. Subsequently, Phase II of the project proceeded in the greenfield Kumiva-Blackrock Desert district of northwestern Nevada to see if a new system could be identified. Transect MT data also showed a strong low-resistivity upwelling originating from interpreted deep crustal magmatic underplating. However, given that there was no exploitable geothermal system recognized at the outset in the region, the collection of new geoscientific data was required. An areal MT survey of 131 sites over the Kumiva-Blackrock Desert district was completed, and a 3D inversion produced using the in-house, DOE-supported finite element inversion algorithm. Particular MT low resistivity upwellings that received followup study occurred under the west flank of the Seven Troughs Range, under the playa immediately west of the Blue Wing Mountains, and under northern Granite Springs Valley. Structural assessment of the project area by Co-I J. Faulds at UNR provided numerous favorable Quaternary fault settings, which were correlated to the MT upwelling structures. Extensive profiling for CO2 soil gas flux over favorable geophysical and geological structure was performed by LBNL personnel. Soil gas flux anomalies generally were not large but did show correlation with MT upwelling structure and favorably dilatent geological structures. Isotope analyses showed presence of possible inorganic/metamorphic 13C but 14C concentrations did not exceed background values. We view the initial concept of a confluence of MT low-resistivity upwelling, favorably dilatent 3D geological structure, and elevated soil gas flux including 13C component to be supported by the further evidence of this project although the indicators in the Phase II study were more diffuse. The northern Granite Springs Valley structure is receiving followup in the UNR Play Fairway Analysis, being in the southern termination of a major normal fault with silicified soil and warm temperature probe results

15 GEOTHERMAL ENERGY↗

Crystal-structure analysis of four mineral samples of anhydrite, CaSO[subscript 4], using synchrotron high-resolution powder X-ray diffraction data

The crystal structures of four samples of anhydrite, CaSO{sub 4}, were obtained by Rietveld refinements using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and space group Amma. As an example, for one sample of anhydrite from Hants County, Nova Scotia, the unit-cell parameters are a = 7.00032(2), b = 6.99234(1), c = 6.24097(1) {angstrom}, and V = 305.487(1) {angstrom}{sup 3} with a > b. The eight-coordinated Ca atom has an average <Ca-O> distance of 2.4667(4) {angstrom}. The tetrahedral SO{sub 4} group has two independent S-O distances of 1.484(1) to O1 and 1.478(1) {angstrom} to O2 and an average <S-O> distance of 1.4810(5) {angstrom}. The three independent O-S-O angles [108.99(8) x 1, 110.38(3) x 4, 106.34(9){sup o} x 1; average <O-S-O> [6] = 109.47(2){sup o}] and S-O distances indicate that the geometry of the SO{sub 4} group is quite distorted in anhydrite. The four anhydrite samples have structural trends where the a, b, and c unit-cell parameters increase linearly with increasing unit-cell volume, V, and their average <Ca-O> and <S-O> distances are nearly constant. The grand mean <Ca-O> = 2.4660(2) {angstrom}, and grand mean <S-O> = 1.4848(3) {angstrom}, the latter is longer than 1.480(1) {angstrom} in celestite, SrSO{sub 4}, as expected.

58 GEOSCIENCES↗

Development of High Energy Resolution Fluorescence Detection Methods for Advanced Microscale X-ray Absorption Fine Structure Analysis of Critical Elements (Final Report)

This project is developing High-Energy Resolution Fluorescence Detection (HERFD) X-ray Absorption Fine-Structure Spectroscopy (XAFS) at the hard X-ray microprobe beamline at GSECARS beamline 13-ID-E, at the Advanced Photon Source at Argonne National Laboratory. This enhancement will improve sensitivity and spectral interpretation limitations of conventional XAFS which uses energy dispersive solid-state detectors (SSD) to measure the total fluorescence yield (TFY-XAFS). By using high-quality Si and Ge crystal analyzers to select X-ray fluorescence (XRF) from specific emission lines, background signals from other elements or X-ray scattering that can paralyze SSDs can be nearly eliminated, improving the sensitivity to the oxidation and chemical state of dilute species even though the solid angle of the analyzers is relatively small. Furthermore, by using analyzers of low-strain Si or Ge, the energy selection can be smaller than the natural widths of the core electron level. We are particularly interested in applying these enhanced sensitivities to Lanthanide series of rare-earth elements, which are typically at concentrations at or below 10 ppm, and where spectral overlaps with the 3rd row transition metals degrade sensitivity.

47 OTHER INSTRUMENTATION↗

Structural analysis of three space crane articulated-truss joint concepts

Three space crane articulated truss joint concepts are studied to evaluate their static structural performance over a range of geometric design parameters. Emphasis is placed on maintaining the four longeron reference truss performance across the joint while allowing large angle articulation. A maximum positive articulation angle and the actuator length ratio required to reach the angle are computed for each concept as the design parameters are varied. Configurations with a maximum articulation angle less than 120 degrees or actuators requiring a length ratio over two are not considered. Tip rotation and lateral deflection of a truss beam with an articulated truss joint at the midspan are used to select a point design for each concept. Deflections for one point design are up to 40 percent higher than for the other two designs. Dynamic performance of the three point design is computed as a function of joint articulation angle. The two lowest frequencies of each point design are relatively insensitive to large variations in joint articulation angle. One point design has a higher maximum tip velocity for the emergency stop than the other designs.

In-space construction↗

Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavoring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a -barrel structure and two -helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the -barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site.

59 BASIC BIOLOGICAL SCIENCES↗