Structure and disorder in ice VII on the approach to hydrogen-bond symmetrization
Abstract not provided
Guthrie, M.↗
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Direct Observation of Quark-Hadron Duality in the Free Neutron {ital F}{sub 2} Structure Function
Using the recently published data from the BONuS(Barely Off-shell Nucleon Structure) experiment at Jefferson Lab, which utilized a spectator tagging technique to extract the inclusive electron-free neutron scattering cross section, we obtain the first direct observation of quark-hadron duality in the neutron F-2 structure function. The data are used to reconstruct the lowest few (N = 2, 4, and 6) moments of F-2 in the three prominent nucleon resonance regions, as well as the moments integrated over the entire resonance region. Comparison with moments computed from global parametrizations of parton distribution functions suggest that quark-hadron duality holds locally for the neutron in the second and third resonance regions down to Q(2) approximate to 1 GeV2, with violations possibly up to 20% observed in the first resonance region.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Structure of Ne 20 states in resonance O 16 + α elastic scattering
Background: The nuclear structure of the cluster bands in 20 Ne presents a challenge for different theoretical approaches. It is especially difficult to explain the broad 0 + , 2 + states at 9 MeV excitation energy. Simultaneously, it is important to obtain more reliable experimental data for these levels in order to quantitatively assess the theoretical framework. Purpose: To obtain new data on 20 Ne α- cluster structure. Method: Thick target inverse kinematics technique was used to study the 16 O+α resonance elastic scattering and the data were analyzed using an R matrix approach. The 20 Ne spectrum, the cluster and nucleon spectroscopic factors were calculated using cluster-nucleon configuration interaction model (CNCIM). Results: We determined the parameters of the broad resonances in 20 Ne: 0 + level at 8.77 ± 0.150 MeV with a width of 750 $^{+500}_{-220}$ keV; 2 + level at 8.75 ± 0.100 MeV with the width of 695 ± 120 keV; the width of 9.48 MeV level of 65 ± 20 keV and showed that 9.19 MeV, 2 + level (if exists) should have width ≤ 10 keV. The detailed comparison of the theoretical CNCIM predictions with the experimental data on cluster states was made. Conclusions: Our experimental results by the TTIK method generally confirm the adopted data on α-cluster levels in 20 Ne. The CNCIM gives a good description of the 20 Ne positive parity states up to an excitation energy of ~7 MeV, predicting reasonably well the excitation energy of the states and their cluster and single particle properties. At higher excitations, the qualitative disagreement with the experimentally observed structure is evident, especially for broad resonances.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Neural network approach for characterizing structural transformations by X-ray absorption fine structure
The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Site-Specific Structure at Multiple Length Scales in Kagome Quantum Spin Liquid Candidates
Realizing a quantum spin liquid (QSL) ground state in a real material is a leading issue in condensed matter physics research. In this pursuit, it is crucial to fully characterize the structure and influence of defects, as these can significantly affect the fragile QSL physics. In this work, we perform a variety of cutting-edge synchrotron x-ray scattering and spectroscopy techniques, and we advance new methodologies for site-specific diffraction and L-edge Zn absorption spectroscopy. The experimental results along with our first-principles calculations address outstanding questions about the local and long-range structures of the two leading kagome QSL candidates, Zn-substituted barlowite Cu 3 Zn x Cu 1-x (OH) 6 FBr and herbertsmithite Cu 3 Zn(OH) 6 Cl 2 . On all length scales probed, there is no evidence that Zn substitutes onto the kagome layers, thereby preserving the QSL physics of the kagome lattice. Our calculations show that antisite disorder is not energetically favorable and is even less favorable in Zn-barlowite compared to herbertsmithite. Site-specific x-ray diffraction measurements of Zn-barlowite reveal that Cu 2+ and Zn 2+ selectively occupy distinct interlayer sites, in contrast to herbertsmithite. Using the first measured Zn L-edge inelastic x-ray absorption spectra combined with calculations, we discover a systematic correlation between the loss of inversion symmetry from pseudo-octahedral (herbertsmithite) to trigonal prismatic coordination (Zn-barlowite) with the emergence of a new peak. Overall, our measurements suggest that Zn-barlowite has structural advantages over herbertsmithite that make its magnetic properties closer to an ideal QSL candidate: its kagome layers are highly resistant to nonmagnetic defects while the interlayers can accommodate a higher amount of Zn substitution.
36 MATERIALS SCIENCE↗
Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution
The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. Two near-atomic resolution structures of PBGD from B. megaterium are reported that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor, including one that possesses a tetrahedral C atom in the terminal pyrrole ring. The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes
Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB) 3 ] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10 6 Å 3 . While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λ max = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.
Peng, Pan-Pan↗
Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome
Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.
Woitowich, Nicole C.↗
Structure of Plasmodium falciparum orotate phosphoribosyltransferase with autologous inhibitory protein-protein interactions
Abstract not provided
Kumar, Shiva↗
High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design
Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPε), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPε D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPε D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure-based drug design, and a microarray-based assay for high-throughput screening to identify small-molecule inhibitors of the PTPε D1 domain is also described.
Lountos, George T.↗
Influence of calcium content on the atomic structure and phase formation of alkali-activated cement binder
Abstract not provided
Si, Ruizhe↗
Functional and structural characterization of AntR, an Sb(III) responsive transcriptional repressor
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Viswanathan, Thiruselvam↗
Pressure-induced superconductivity and structural transitions in Ba(Fe[subscript 0.9]Ru[subscript 0.1])[subscript 2]As[subscript 2]
Abstract not provided
Uhoya, Walter O.↗
Studies of Nucleon Resonance Structure in Exclusive Meson Electroproduction
The studies of N* structure represent a key direction in the N* Program with CLAS detector. After 12 GeV Upgrade, the dedicated experiment on the studies of N* structure at largest photon virtualities ever achieved Q^2<12 GeV^2 is scheduled for the first year of running with the CLAS12 detector. The current status and plans for theory support of the N* structure studies in exclusive meson electroproduction are presented. They include the recent advances in the reaction theory for extraction of N* electrocouplings from the data and the approaches for high level theoretical interpretation of these fundamental quantities, allowing us to access dynamics of non-perturbative strong interaction which is responsible for the resonance formation and explore how it emerges from QCD.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Multifunctional structural lithium-ion battery for electric vehicles
An innovative concept for a multifunctional structural battery using lithium-ion battery materials as load bearing elements in a sandwich panel construction has been demonstrated. The structural battery prototype has exhibited an initial capacity of 17.85 Ah, an energy density of 248 Wh L −1 , a specific energy of 102 Wh kg −1 , and a capacity retention of 85.8% after 190 charge–discharge cycles at ~ C/3 rate and eight mechanical loading cycles (upto 1060 N). The mechanical stiffness in three-point bend tests follows expectations based on sandwich beam theory, proving that the battery materials are sharing in the load-carrying function of the sandwich panel. While areas for improvement of the fabrication and performance of the prototype still exist, the results of the current investigation demonstrate the promising potential of the proposed structural battery concept for the efficient use of space and mass in an electric vehicle.
Zhang, Yancheng↗
Nanometer-scale structure differences in the myofilament lattice spacing of two cockroach leg muscles correspond to their different functions
ABSTRACT Muscle is highly organized across multiple length scales. Consequently, small changes in the arrangement of myofilaments can influence macroscopic mechanical function. Two leg muscles of a cockroach have identical innervation, mass, twitch responses, length–tension curves and force–velocity relationships. However, during running, one muscle is dissipative (a ‘brake’), while the other dissipates and produces significant positive mechanical work (bifunctional). Using time-resolved X-ray diffraction in intact, contracting muscle, we simultaneously measured the myofilament lattice spacing, packing structure and macroscopic force production of these muscles to test whether structural differences in the myofilament lattice might correspond to the muscles' different mechanical functions. While the packing patterns are the same, one muscle has 1 nm smaller lattice spacing at rest. Under isometric stimulation, the difference in lattice spacing disappeared, consistent with the two muscles' identical steady-state behavior. During periodic contractions, one muscle undergoes a 1 nm greater change in lattice spacing, which correlates with force. This is the first identified structural feature in the myofilament lattice of these two muscles that shares their whole-muscle dynamic differences and quasi-static similarities.
Tune, Travis Carver↗
Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates
A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.
59 BASIC BIOLOGICAL SCIENCES↗