Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[6916, 17171]
Open Access
Abstract: Glycogen and starch are the major carbon and energy reserve polysaccharides in nature, providing living organisms with a survival advantage. The evolution of the enzymatic machinery responsible for the biosynthesis and degradation of such polysaccharides, led the development of mechanisms to control the assembly and disassembly rate, to store and recover glucose according to cell energy demands. The tetrameric enzyme ADP-glucose pyrophosphorylase (AGPase) catalyzes and regulates the initial step in the biosynthesis of both α-polyglucans. AGPase displays cooperativity and allosteric regulation by sensing metabolites from the cell energy flux. The understanding of the allosteric signal transduction mechanisms in AGPase arises as a long-standing challenge. In this work, we disclose the cryoEM structures of the paradigmatic homotetrameric AGPase from Escherichia coli (EcAGPase), in complex with either positive or negative physiological allosteric regulators, fructose-1,6-bisphosphate (FBP) and AMP respectively, both at 3.0 Å resolution. Strikingly, the structures reveal that FBP binds deeply into the allosteric cleft and overlaps the AMP site. As a consequence, FBP promotes a concerted conformational switch of a regulatory loop, RL2, from a “locked” to a “free” state, modulating ATP binding and activating the enzyme. This notion is strongly supported by our complementary biophysical and bioinformatics evidence, and a careful analysis of vast enzyme kinetics data on single-point mutants of EcAGPase. The cryoEM structures uncover the residue interaction networks (RIN) between the allosteric and the catalytic components of the enzyme, providing unique details on how the signaling information is transmitted across the tetramer, from which cooperativity emerges. Altogether, the conformational states visualized by cryoEM reveal the regulatory mechanism of EcAGPase, laying the foundations to understand the allosteric control of bacterial glycogen biosynthesis at the molecular level of detail.
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Nov 2020
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I09-Surface and Interface Structural Analysis
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Diamond Proposal Number(s):
[15899, 18191]
Abstract: The structure of coadsorption phases formed on Ag(111) by TCNQ (7,7,8,8-tetracyanoquinodimethane) with Cs are compared with previously reported coadsorption phases formed with K, following investigation by scanning tunnelling microscopy (STM), low energy electron diffraction, soft X-ray photoelectrons spectroscopy and normal incidence X-ray standing waves (NIXSW). For each alkali we identify two ordered phases, one with an alkali: TCNQ stoichiometry of 1:1 and the other 2:1. STM images show the molecular organisation is the same for Cs and K, although only the K2TCNQ phase is commensurate with the substrate. A previously-published detailed structure determination of the K2TCNQ phase, complemented by density function theory calculations that identify bonding strengths, showed that the binding within the layer is much stronger than that of the layer to the substrate. Insensitivity to commensuration is thus to be expected. The situation for KTCNQ and CsTCNQ is less clear; these ordered incommensurate overlayers clearly have strong intralayer bonding, but the relative strength of the average overlayer-substrate bonding is unknown. NIXSW data show that the alkalis in these phases occupy adsorption sites far more distant from the substrate than the TCNQ molecules when compared to the near coplanar alkali-TCNQ geometry of K2TCNQ and Cs2TCNQ. Ultraviolet photoelectron spectra show increasing bonding shifts of TCNQ orbital states with alkali coverage.
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Nov 2020
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B18-Core EXAFS
I18-Microfocus Spectroscopy
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Eitaro
Kurihara
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Masato
Takehara
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Mizuki
Suetake
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Ryohei
Ikehara
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Tatsuki
Komiya
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Kazuya
Morooka
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Ryu
Takami
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Shinya
Yamasaki
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Toshihiko
Ohnuki
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Kenji
Horie
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Mami
Takehara
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Gareth T. W.
Law
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William
Bower
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J. Frederick W.
Mosselmans
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Peter
Warnicke
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Bernd
Grambow
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Rodney C.
Ewing
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Satoshi
Utsunomiya
Diamond Proposal Number(s):
[21211]
Abstract: Traces of Pu have been detected in material released from the Fukushima Daiichi Nuclear Power Plant (FDNPP) in March of 2011; however, to date the physical and chemical form of the Pu have remained unknown. Here we report the discovery of particulate Pu associated with cesium-rich microparticles (CsMPs) that formed in and were released from the reactors during the FDNPP meltdowns. The Cs-pollucite-based CsMP contained discrete U(IV)O2 nanoparticles, <~10 nm, one of which is enriched in Pu adjacent to fragments of Zr-cladding. The isotope ratios, 235U/238U, 240Pu/239Pu, and 242Pu/239Pu, of the CsMPs were determined to be ~0.0193, ~0.347, and ~0.065, respectively, which are consistent with the calculated isotopic ratios of irradiated-fuel fragments. Thus, considering the regional distribution of CsMPs, the long-distance dispersion of Pu from FNDPP is attributed to the transport by CsMPs that have incorporated nanoscale fuel fragments prior to their dispersion up to 230 km away from the Fukushima Daiichi reactor site.
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Nov 2020
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I15-1-X-ray Pair Distribution Function (XPDF)
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Abstract: The central theme of this thesis is the application of radial and pair distribution function analysis to materials characterisation problems for nanotechnology. These concepts are introduced in Chapter 1, and the associated methods are described in Chapter 2. Chapter 3 details the first of the results which discusses the design and development of a software tool called ImageDataExtractor. This auto-extracts microscopy images and then analyses them to afford quantitative information regarding particles in a sample, such as shape, size and distribution. It realises an opportunity for data-mining the ubiquity of readily available images in the literature. Chapter 4 presents results of the development and execution of a novel experimental technique, called glancing-angle pair distribution function (gaPDF) analysis, applied to the structure of the working electrode in dye-sensitised solar cells (DSSCs). This structure was successfully observed, validating this novel method. The investigation also suggested preferred binding modes of the carboxylic acid anchoring groups present in this interfacial structure. Chapters 5 and 6 demonstrate the application of PDF analysis to synchrotron-based powder diffraction data of two material case studies: the rare earth phosphate glass (REPG) (Gd2O3)0.230(P2O5)0.770, and four Ru based photo-isomers. The closest R…R rare earth separation, which governs optical properties of REPGs, was determined to be 4.2(1) Å, aided by various statistical techniques. Analysis on four Ru-based photo-isomers confirmed: the existence of local structure in such compounds, their ability to be photo-isomerised in powder form, the theoretical models constructed using computational techniques, and the lack of heterogeneity in photo-isomerisation throughout a given light-induced sample. Chapter 7 concludes the work and offers a future outlook.
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Oct 2020
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I07-Surface & interface diffraction
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Cem
Ornek
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Alfred
Larsson
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Gary S.
Harlow
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Fan
Zhang
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Robin
Kroll
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Francesco
Carla
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Hadeel
Hussain
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Ulf
Kivisäkk
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Dirk L.
Engelberg
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Edvin
Lundgren
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Jinshan
Pan
Diamond Proposal Number(s):
[23388]
Open Access
Abstract: Grazing-incidence x-ray diffraction was employed to measure, operando, during electrochemical hydrogen charging, the lattice strain development of the near-surface in super duplex stainless steel under applied tensile load. Hydrogen absorption led to the formation of tensile strains in both the austenite (γ) and ferrite (δ) phases perpendicular to the loading axis, whereas compressive strains were formed in the ferrite phase parallel to the loading direction, despite the acting tensile load. The earliest stages of degradation are discussed in light of understanding hydrogen embrittlement.
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Oct 2020
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[21686]
Abstract: Li1+xAlxGe2-x(PO4)3 (LAGP) thin films have been grown on sapphire substrates by RF magnetron sputtering and post annealing. The effects of varying sputtering parameters such as power and pressure were studied, and the deposited films were characterized to investigate how the ionic conductivity values depend on the microstructure. The composition of as-sputtered films was found to be more strongly influenced by power than the pressure. The films deposited at lower powers, which results in lower deposition rates, have compositions similar to that of the target. Heating the substrates during deposition is found to minimise the formation of pinhole defects in films subsequently annealed at higher temperatures. Post annealing leads to a gradual transformation from the as-sputtered amorphous phase to crystalline LAGP thin films. At high annealing temperatures (above 700 °C) both porosity and the GeO2 impurity phase appear in the films and result in lower ionic conductivities. We have optimised the processing conditions to achieve ionic conductivities in excess of 10−4 Scm−1 and activation energies as low as 0.31 eV in films only 1 μm thick, suggesting that LAGP could offer attractive properties as a thin film battery electrolyte material.
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Oct 2020
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[17716]
Abstract: Six industrial clinker samples, produced using petroleum coke as kiln fuel, were analysed using high resolution synchrotron XRPD data, one sample (HM) presenting predominantly M1 C3S polymorph. Refinement of data collected on this sample was used to revise the M1 structural model, improving the Rwp and RB of the original model (from Rwp = 9.25 and RB = 5.517 in the original model to Rwp = 8.07 and RB = 2.965). The revised model was validated through bond length and Bond Valence Sum (BVS) distribution. Using the BVS method, two preferential substitutional calcium sites were identified for Mg2+ and two silicon sites for Al3+, while two interstitial sites were identified for S6+ and Fe3+. Using the revised model for refinement of the six industrial clinker samples showed improvement in the Rwp and GoF indices. The amount of M1 and M3 polymorph present was found to be significantly different using the revised M1 C3S model.
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Oct 2020
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[19662]
Abstract: Chemical short range order and topology of GexGaxTe100-2x glasses was investigated by neutron- and x-ray diffraction as well as Ge and Ga K-edge extended x-ray absorption fine structure (EXAFS) measurements. Large scale structural models were obtained by fitting experimental datasets simultaneously with the reverse Monte Carlo simulation technique. Models, relying only on experimental data and basic physical information without constraining the average coordination numbers, give 3.9–4.1 for the number of the atoms in the first coordination sphere of Ge atoms, while the average number of first neighbors of Ga atoms scatters around 3.8. The average coordination number of Te atoms is significantly higher than 2 for x = 12.5 and 14.3. It is found that the vast majority of MTe4 (M = Ge or Ga) tetrahedra have at least one corner sharing MTe4 neighbor.
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Sep 2020
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M.
Dendebera
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Y.
Chornodolskyy
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R.
Gamernyk
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O.
Antonyak
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I.
Pashuk
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S.
Myagkota
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I.
Gnilitskyi
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V.
Pankratov
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V.
Vistovskyy
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V.
Mykhaylyk
,
M.
Grinberg
,
A.
Voloshinovskii
Abstract: The work reports the results of spectroscopic and luminescence-kinetic studies of CsPbBr3 single crystal over 14–300 K temperature range. It is shown that at low temperatures the luminescence spectrum contains three narrow bands at 534, 537, and 541.5 nm exhibiting a fast decay and a broad emission band at ca. 560 nm with long decay. The evolution of the luminescence bands and their temporal characteristics with temperature are discussed from the viewpoint of possible emission mechanisms. The origin of the luminescence bands is discussed in relation with the observed features of their temporal characteristics. The mechanism of luminescence quenching for different emission band is suggested.
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Sep 2020
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I12-JEEP: Joint Engineering, Environmental and Processing
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Diamond Proposal Number(s):
[11204]
Abstract: The fracture resistance of load-bearing trabecular bone is adversely affected by diseases such as osteoporosis. However, there are few published measurements of trabecular bone fracture toughness due to the difficulty of conducting reliable tests in small specimens of this highly porous material. A new approach is demonstrated that uses digital volume correlation of X-ray computed tomographs to measure 3D displacement fields in which the crack shape and size can be objectively identified using a phase congruency analysis. The criteria for crack propagation, i.e. fracture toughness, can then be derived by finite element simulation, with knowledge of the elastic properties.
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Sep 2020
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