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The goal of the proposed research is to establish a computational and experimental platform that will allow reliable and efficient power and structural performance evaluation of FOWT. A secondary goal of the research is to establish an educational FOWT setup to promote renewable energy research among undergraduate and high-school students.
NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, 'closed' conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.
Highlights: • Crystal structures of activating mutants of P. aeruginosa YfiB were determined. • F48S and W55L activating mutants of YfiB crystallize as dimers. • The L43P mutant of YfiB is monomeric and forms a stable complex with YfiR. • The YfiB activating region undergoes a dramatic rearrangement upon YfiR binding. • Extensive interactions are formed between the YfiB activating region and YfiR. Bacterial cyclic-di-GMP (c-di-GMP) is an important messenger molecule that influences diverse cellular processes including motility, virulence and cytotoxicity systems, polysaccharide synthesis and biofilm formation. The YfiBNR tripartite signalling system in P. aeruginosa modulates the cellular c-di-GMP levels in response to signals received from the periplasm. In this study, we analyse the structures of activating mutants of the outer membrane protein YfiB that give rise to increased surface attachment and biofilm formation. The F48S and W55L mutants of YfiB(27–168) crystallize in the same dimeric arrangement as our previously reported YfiB structures that preclude complex formation with YfiR. The L43P mutant of YfiB(27–168) is monomeric and forms a stable complex with YfiR. The YfiB(L43P)-YfiR crystal structure reveals a dramatic rearrangement of the N-terminal fragment, which is implicated in increased YfiB activation and membrane attachment, upon YfiR binding. Comparison with our previous complex structure between YfiB(59–168) and YfiR reveals extensive interactions between the N-terminal fragment of YfiB (residues 35–55) and YfiR.
This report presents thermo-structural (Williamson 2012) constitutive relationships and models pertaining to Transformational Challenge Reactor (TCR) core components using BISON. The material correlations for TCR core candidate materials include 316L stainless steel, uranium dioxide, and Chemical Vapor Infiltrated (CVI) silicon carbide were compiled. Preliminary, sensitivity analyses were performed on a simple cylindrical geometry by parametrically varying material properties. The sensitivity analyses elucidate the impact of material properties on the induced stresses in the TCR core structures. The results of the sensitivity studies for the SiC concept showed that the swelling is expected to be the largest source of uncertainty, followed by the elastic modulus. In the SS316L and UO 2 concept, the thermal conductivity of the can was the dominate effect, and a temperature dependent correlation or tabulated data would be advisable. The geometry and modeling method simulations showed that the inclusion of the heat generation is the SiC can does alter the stress and temperature magnitudes. However, the stress concentrations and profiles remain consistent.
The plant cell wall is composed of many complex polysaccharides. The composition and structure of the polysaccharides affect various cell properties including cell shape, cell function and cell adhesion. Many techniques to characterize polysaccharide structure are complicated, requiring expensive equipment and specialized operators e.g. NMR, MALDI-MS. PACE (Polysaccharide Analysis using Carbohydrate gel Electrophoresis) uses a simple, rapid technique to analyze polysaccharide quantity and structure (Goubet et al. 2002). Whilst the method here describes xylan analysis, it can be applied (by use of the appropriate glycosyl hydrolase) to any cell wall polysaccharide.
Sandia National Laboratories has interest in mounting enclosures to gather scientific data aboard NASA scientific balloons. This report documents the structural integrity of three separate payloads considered ‘piggybacks.’ To date, there are no design criteria for piggybacks, therefore each piggyback shall follow the same design requirements set by NASA per the Gondola Structural Design Requirements. This analysis report shall describe how each payload meets the design requirements laid out in the Gondola Design Requirements.
This paper reports the first structure refinement of natural wangdaodeite, LiNbO3-type FeTiO3 from the Ries impact structure. Wangdaodeite occurs together with recrystallized ilmenite clasts in shock melt veins which have experienced peak shock pressures of between 17 and 22 GPa. Comparison of natural and synthetic wangdaodeite points toward a correlation between the distortion of ferrate- and titanate-polyhedra and the c/a ratio of the unit cell. The Raman spectrum of wangdaodeite is calculated based on the refined structure. Comparison to the reported spectrum of the type-material shows that the Raman peak at 738–740 cm−1 is indicative for this phase, whereas other features in type-wangdaodeite are tentatively assigned to disordered ilmenite.
Four tests characterizing the structural response of the Chopped-Dummy In-Pile tube (CDIPT) experiment design were measured in the Hydro-Mechanical Fuel Test Facility (HMFTF). Four different test configurations were tried. These configurations tested the pressure drop and flow impact of various plate configurations and flow control orifices to be used later at different reactor power levels. Accelerometers were placed on the test vehicle and flow simulation housing. A total of five accelerometers were used with one on the top and bottom of the flow simulator and vehicle, and one on the outside of the flow simulator. Data were collected at a series of flow rates for 5 seconds each at an acquisition rate of 2 kHz for a Nyquist frequency of 1 kHz. The data were then analyzed using a Fast Fourier Transform (FFT) algorithm. The results show very coherent vibrations of the CDIPT experiment on the order of 50 Hz in frequency and 0.01 m/s{sup 2} in magnitude. The coherent vibrations, although small in magnitude pose a potential design problem if the frequencies coincide with the natural frequency of the fueled plates or test vehicle. The accelerometer data was integrated and combined to create a 3D trace of the experiment during the test. The merits of this data as well as further anomalies and artifacts are also discussed as well as their relation to the instrumentation and experiment design. (authors)
The 23S rRNA methylating enzyme Cfr, found in pathogens including Staphylococcus aureus, Clostridium difficile, Escherichia coli, and Klebsiella pneumoniae, confers resistance to phenicols, lincosamides, oxazolidinones (including linezolid), pleuromutilins, and streptogramins A (the PhLOPS A phenotype). Cfr catalyzes methylation of the C8 position of the A2503 base in 23S rRNA, the recognition site of the above antibiotic classes. Along with the RlmN housekeeping enzyme, Cfr can also promote methylation of the C2 position of the same base. The molecular and structural basis of Cfr’s dual substrate specificity is not known, which hinders our ability to design Cfr-targeting inhibitors necessary to curb PhLOPS A resistance. Here, we present the first crystal structure of Cfr and a detailed analysis of its possible interactions with rRNA. Using structure-guided mutagenesis, mass spectrometry analysis of in cellulo 23S rRNA methylated species, and in cellulo resistance studies, we identify the key amino acids essential for Cfr methylation and multidrug resistance activity. In particular, we found that Cfr’s Q329 residue is important for C8- specific methylation. These data provide a framework for further studies of the biochemistry, structure, and inhibition of this important resistance determinant.
Single phase of nanocrystalline Ba{sub x}Sr{sub 1-x}Fe{sub 12}O{sub 19} (x = 1.0; 0.6; and 0.4) was successfully synthesized by mechanical milling method and thermal process. Stoichiometric quantities of analytical-grade SrCO{sub 3}, BaCO{sub 3}, and Fe{sub 2}O{sub 3}, were mixed and milled using a high-energy milling. The mixture of all precursors was sintered at a temperature of 1000 °C for 10 hours. The refinement of x-ray diffraction trace for all samples confirmed a single phase material with a hexagonal structure. The increase of the amount of strontium content in the barium atoms in the Ba{sub x}Sr{sub 1-x}Fe{sub 12}O{sub 19} system can decrease the lattice parameter which have been successfully substituted into the barium atoms. The calculation result of cationic distribution showed that the Ba{sub x}Sr{sub 1-x}Fe{sub 12}O{sub 19} (x = 0.6) and (x = 0.4) samples have nominal composition of Ba{sub 0,61}Sr{sub 0,39}Fe{sub 12}O{sub 19} and Ba{sub 0,37}Sr{sub 0,63}Fe{sub 12}O{sub 19}, respectively. Results of the mean of crystallite size evaluation for respective powder materials showed that the Ba{sub x}Sr{sub 1-x}Fe{sub 12}O{sub 19} (x = 1.0; 0.6; and 0.4) samples have the crystallite size of 22 nm, 25 nm and 34 nm, respectively. We concluded that the cationic distribution of barium atoms was successfully substituted by strontium atoms approaching the nominal stoichiometric composition.
The MARVEL microreactor consists of five main systems: MRS (MARVEL Reactor Structure), PGS (Power Generation System), FCS (Fuel Core System), RCS (Reactivity Control System), and ICS (Instrument Control System). The RSS (Reflector Control System) is a sub system of the MRS which contains the upper and lower reflector support plates which support and locate the stationary core reflector and provide vertical support for the control drums. They are suspended from the Primary Coolant System by bolted structural straps which utilize a turnbuckle to allow for adjustment and leveling of the support plates. The stainless-steel support plates are each formed from four quarter circle segments which are bolted together around the lower core barrel. Bearing plates of non-galling Nitronic 60 alloy are fitted to the inner diameter of the support plates to prevent adhesive wear between the plates and the core barrel as the barrel expands and contracts due to changes in the temperature of the reactor.
Campylobacter jejuni is a bacterium that uses flagella for motility and causes worldwide acute gastroenteritis in humans. The C. jejuni N-acetyltransferase PseH (cjPseH) is responsible for the third step in flagellin O-linked glycosylation and plays a key role in flagellar formation and motility. cjPseH transfers an acetyl group from an acetyl donor, acetyl coenzyme A (AcCoA), to the amino group of UDP-4-amino-4,6-dideoxy-N-acetyl-β-L-altrosamine to produce UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose. To elucidate the catalytic mechanism of cjPseH, crystal structures of cjPseH alone and in complex with AcCoA were determined at 1.95 Å resolution. cjPseH folds into a single-domain structure of a central β-sheet decorated by four α-helices with two continuously connected grooves. A deep groove (groove-A) accommodates the AcCoA molecule. Interestingly, the acetyl end of AcCoA points toward an open space in a neighboring shallow groove (groove-S), which is occupied by extra electron density that potentially serves as a pseudosubstrate, suggesting that the groove-S may provide a substrate-binding site. Structure-based comparative analysis suggests that cjPseH utilizes a unique catalytic mechanism of acetylation that has not been observed in other glycosylation-associated acetyltransferases. Thus, our studies on cjPseH will provide valuable information for the design of new antibiotics to treat C. jejuni-induced gastroenteritis. - Highlights: • cjPseH adopts a single-domain structure of a central β-sheet decorated by α-helices. • cjPseH features two continuously connected grooves on the protein surface. • Acetyl coenzyme A (AcCoA) binds into a deep groove of cjPseH in an ‘L’ shape. • The acetyl end of AcCoA points to a wide groove, a potential substrate-binding site.
Molybdenum oxides and sulfides on various low-cost high-surface-area supports are excellent catalysts for several industrially relevant reactions. The surface layer structure of these materials is, however, difficult to characterize due to small and disordered MoO x domains. Here, it is shown how X-ray total scattering can be applied to gain insights into the structure through differential pair distribution function (d-PDF) analysis, where the scattering signal from the support material is subtracted to obtain structural information on the supported structure. MoO x catalysts supported on alumina nanoparticles and on zeolites are investigated, and it is shown that the structure of the hydrated molybdenum oxide layer is closely related to that of disordered and polydisperse polyoxometalates. By analysing the PDFs with a large number of automatically generated cluster structures, which are constructed in an iterative manner from known polyoxometalate clusters, information is derived on the structural motifs in supported MoO x .
Many studies have shown the feasibility of in vivo cardiac transplantation of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) in animal experiments. However, nano-structural confirmation of the successful incorporation of the engrafted iPSC-CMs including electron microscopy (EM) has not been accomplished, partly because identification of graft cells in EM has proven to be difficult. Using APEX2, an engineered ascorbate peroxidase imaging tag, we successfully localized and analyzed the fine structure of sarcomeres and the excitation contraction machinery of iPSC-CMs 6 months after their engraftment in infarcted mouse hearts. APEX2 made iPSC-CMs visible in multiple imaging modalities including light microscopy, X-ray microscopic tomography, transmission EM, and scanning EM. EM tomography allowed assessment of the differentiation state of APEX2-positive iPSC-CMs and analysis of the fine structure of the sarcomeres including T-tubules and dyads.
The atomic structure of a bacterial aryl acylamidase (EC 3.5.1.13; AAA) is reported and structural features are investigated to better understand the catalytic profile of this enzyme. Structures of AAA were determined in its native form and in complex with the analgesic acetanilide, p-acetaminophenol, at 1.70 Å and 1.73 Å resolutions, respectively. The overall structural fold of AAA was identified as an α/β fold class, exhibiting an open twisted β-sheet core surrounded by α-helices. The asymmetric unit contains one AAA molecule and the monomeric form is functionally active. The core structure enclosing the signature sequence region, including the canonical Ser-cisSer-Lys catalytic triad, is conserved in all members of the Amidase Signature enzyme family. The structure of AAA in a complex with its ligand reveals a unique organization in the substrate-binding pocket. The binding pocket consists of two loops (loop1 and loop2) in the amidase signature sequence and one helix (α10) in the non-amidase signature sequence. We identified two residues (Tyr{sup 136} and Thr{sup 330}) that interact with the ligand via water molecules, and a hydrogen-bonding network that explains the catalytic affinity over various aryl acyl compounds. The optimum activity of AAA at pH > 10 suggests that the reaction mechanism employs Lys{sup 84} as the catalytic base to polarize the Ser{sup 187} nucleophile in the catalytic triad. - Highlights: • We determined the first structure of a bacterial aryl acylamidase (EC 3.5.1.13). • Structure revealed spatially distinct architecture of the substrate-binding pocket. • Hydrogen-bonding with Tyr{sup 136} and Thr{sup 330} mediates ligand-binding and substrate.
A research team with membership from the University of Utah/Energy & Geoscience Institute, the University of Utah/Dept. of Geology & Geophysics, and the Utah Geological Survey, undertook a play fairway analysis (PFA) for geothermal resources in the Eastern Great Basin (EGB) extensional tectonic regime of western Utah. This is a high-priority region for geothermal exploration because active Basin and Range (B&R) extension with volcanism having a N-S strike is superimposed upon pre-existing E-W belts of plutonic rocks and large-scale structural lineaments. Cumulative heat flow along the N-S strike of the state totals approximately 5 GWt above background stable interior. Three electricity producing power plants currently exist with substantial potential for increase. Succinctly, our PFA approach aims to resolve potential sources of heat and permeability in the region, which are the two principal criteria for establishing a geothermal resource. An initial Phase 1 was carried out using only existing geoscientific data in the area. Criteria selected for focusing heat potential include direct heat flow measurements in boreholes, magnetotelluric (MT) low resistivity anomalies, fluid/gas geochemistry, and proximity to recent volcanic eruptions. Permeability is established through geological structures (fault density, critically stressed areas, seismicity, gravity), and MT low resistivity anomalies. In Phase II of this PFA project, additional geological, geophysical and geochemical data were acquired and analysis carried out primarily over promising composite common risk (CCR) areas initially identified in Phase I in order to focus prospectivity and prepare for drilling recommendations. These prospects are near the Twin Peaks rhyolite field, high heat flow areas north of the producing Cove Fort system, and geophysical structure beneath the Crater Knoll area off the northeast flank of the Mineral Mountains. Additional data included MT site fill-in, structural mapping and analysis using high-resolution imagery, gravity and on-ground mapping, Nodal 3C passive seismic collection, and passive 3He surveying. Heat source and permeability potential are again expressed in terms of their individual common risk segment (CRS) maps, with a color scheme using green for most favorable (low risk) and red for least favorable (high risk). Diverse data types are united through the technique of probability kriging, which establishes prospectivity thresholds for each data type and then computes probability of exceeding that threshold over the PFA area. Modified CRS and CCRS maps are compared to those of Phase I to highlight tighter prospectivity focus. In doing so, the prospectivity threshold for heat was increased significantly to narrow the targeting. In the final Phase III of this project where a recommended deep thermal gradient hole was sited, additional geophysical, geochemical and geological field collection and analysis was carried out to refine drill hole targeting. This includes prospect-scale MT, gravity, structure, passive seismic deployment (Cove Fort area), and detailed 3He isotope profiling. It was the recommendation of the DOE Technical Monitoring Team (TMT) that one or more holes be sited in the north-ern Cove Fort area where legacy TG gradient holes showed high cumulative heat flow. These were to be of moderate depth, 2000-3000 feet, to reach the geothermal fluid table expected to start in excess of 1000 feet depth. The drilling organization stipulated by the DOE/GTO was that of the USGS Research Drilling Program (RDP) centered in Las Vegas, NV. A detailed well plan, appended to this report, was developed principally by Dr. Ben Barker consulting to University of Utah, Dr. Steve Pye on the DOE TMT, Mr. Steven Crawford of the USGS-RDP, and the project PI Phil Wannamaker. However, temperature and possible H 2 S at the systems lead to cancellation of the drilling last-minute as this appeared outside the experience base of the USGS-RDP. We hope to have the opportunity to revisit the test drilling and expand the Play Fairway Analysis of this region at some point in the future.
Carbonate rocks store more than 50% of world's petroleum. These rocks' structures are highly complex and vary depending on many factors regarding their formation, e.g., lithification and diagenesis. In order to perform an effective extraction of petroleum it is necessary to know petrophysical parameters, such as total porosity, pore size and permeability of the reservoir rocks. Carbonate rocks usually have a range of pore sizes that goes from nanometers to meters or even dozen of meters. The nanopores and micropores might play an important role in the pores connectivity of carbonate rocks. X-ray computed tomography (CT) has been widely used to analyze petrophysical parameters in recent years. This technique has the capability to generate 2D images of the samples' inner structure and also allows the 3D reconstruction of the actual analyzed volume. CT is a powerful technique, but its results depend on the spatial resolution of the generated image. Spatial resolution is a measurement parameter that indicates the smallest object that can be detected. There are great difficulties to generate images with nanoscale resolution (nanotomographic images). In this work three carbonate rocks, one dolomite and two limestones (that will be called limestone A and limestone B) were analyzed by nanotomography. The measurements were performed with the SkyScan2011 nanotomograph, operated at 60 kV and 200 μA to measure the dolomite sample and 40 kV and 200 μA to measure the limestone samples. Each sample was measured with a given spatial resolution (270 nm for the dolomite sample, 360 nm for limestone A and 450 nm for limestone B). The achieved results for total porosity were: 3.09 % for dolomite, 0.65% for limestone A and 3.74% for limestone B. This paper reports the difficulties to acquire nanotomographic images and further analysis about the samples' pore sizes.
A new diphosphine disulphide compound with the formula C{sub 27}H{sub 26}O{sub 2}|P{sub 2}S{sub 2}, was synthesized from the reaction between PPh{sub 2}SCl and 1,3-propanediol and characterized with different spectroscopic methods. Its structure has also been studied by X-ray diffraction. The compound crystallizes in the triclinic space group <##> } P } 1 }¯<!-- ?? --> $ P/bar 1 $ P 1-bar </##>. Pentavalent phosphorus atoms in the molecule are in distorted tetrahedral environments.