bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal information encoding in dynamic memristive devices
Authors: Ma Wen , Chen Lin , Du Chao , Lu Wei D.
Published: November 2015

We show temporal and frequency information can be effectively encoded in memristive devices with inherent short-term dynamics. Ag/Ag2S/Pd based memristive devices with low programming voltage (∼100 mV) were fabricated and tested. At weak programming conditions, the devices exhibit inherent decay due to spontaneous diffusion of the Ag atoms. When the devices were subjected to pulse train inputs emulating different spiking patterns, the switching probability distribution function diverges from the standard Poisson distribution and evolves according to the input pattern. The experimentally observed switching probability distributions and the associated cumulative probability functions can be well-explained using a model accounting for the short-term decay effects. Such devices offer an intriguing opportunity to directly encode neural signals for neural information storage and analysis.
Graphene nanoribbons production from flat carbon nanotubes
Authors: Melo W. S. , Guerini S. , Diniz E. M.
Published: November 2015

Graphene nanoribbons are of great interest for pure and applied sciences due to their unique properties which depend on the nanoribbon edges, as, for example, energy gap and antiferromagnetic coupling. Nevertheless, the synthesis of nanoribbons with well-defined edges remains a challenge. To collaborate with this subject, here we propose a new route for the production of graphene nanoribbons from flat carbon nanotubes filled with a one-dimensional chain of Fe atoms by first principles calculations based on density functional theory. Our results show that Fe-filled flat carbon nanotubes are energetically more stable than non flattened geometries. Also we find that by hydrogenation or oxygenation of the most curved region of the Fe-filled flat armchair carbon nanotube, it occurred a spontaneous production of zigzag graphene nanoribbons which have metallic or semiconducting behavior depending on the edge and size of the graphene nanoribbon. Such findings can be used to create a new method of synthesis of regular-edge carbon nanoribbons.
Acoustic scattering of a cylindrical quasi-Gaussian beam with arbitrary incidence focused on a rigid elliptical cylinder
Authors: Mitri F. G.
Published: November 2015

Using the partial-wave series expansion method in cylindrical coordinates, a formal analytical solution for the acoustical scattering of a 2D cylindrical quasi-Gaussian beam with an arbitrary angle of incidence θi, focused on a rigid elliptical cylinder in a non-viscous fluid, is developed. The cylindrical focused beam expression is an exact solution of the Helmholtz equation. The scattering coefficients for the elliptical cylinder are determined by forcing the expression of the total (incident + scattered) field to satisfy the Neumann boundary condition for a rigid immovable surface, and performing the product of matrices involving an inversion procedure. Computations for the matrices elements require a single numerical integration procedure for each partial-wave mode. Numerical results are performed with particular emphasis on the focusing properties of the incident beam and its angle of incidence with respect to the major axis a of the ellipse as well as the aspect ratio a/b where b is the minor axis (assuming a > b). The method is validated and verified against previous results obtained via the T-matrix for plane waves. The present analysis is the first to consider an acoustical beam on an elliptic cylinder of variable cross-section as opposed to plane waves of infinite extent. Other 2D non-spherical and Chebyshev surfaces are mentioned that may be examined throughout this analytical formalism assuming a small deformation parameter ε.
Doubly excited 3Pe resonance states of two-electron positive ions in Debye plasmas
Authors: Hu Xiao-Qing , Wang Yang , Jiang Zishi , Jiang Pinghui , Kar Sabyasachi
Published: November 2015

We investigate the doubly excited 3Pe resonance states of two-electron positive ions Li+, Be2+, B3+, and C4+ by employing correlated exponential wave functions. In the framework of the stabilization method, we calculate two series (3pnp and 3dnd) of 3Pe resonances below the N = 3 threshold. The 3Pe resonance parameters (resonance energies and widths) are reported for the first time as a function of the screening parameter. For free-atomic cases, comparisons are made with the reported results and few resonance states are reported for the first time.
A comprehensive study of the impact of dislocation loops on leakage currents in Si shallow junction devices
Authors: Nyamhere C. , Scheinemann A. , Schenk A. , Scheit A. , Olivie F. , Cristiano F.
Published: November 2015

In this work, the electrical properties of dislocation loops and their role in the generation of leakage currents in p-n or Schottky junctions were investigated both experimentally and through simulations. Deep Level Transient Spectroscopy (DLTS) reveals that the implantation of silicon with 2 × 1015 Ge cm−2 and annealing between 1000 °C and 1100 °C introduced two broad electron levels EC − 0.38 eV and EC − 0.29 eV in n-type samples and a single broad hole trap EV + 0.25 eV in the p-type samples. These trap levels are related to the extended defects (dislocation loops) formed during annealing. Dislocation loops are responsible for the significant increase of leakage currents which are attributed to the same energy levels. The comparison between structural defect parameters and electrical defect concentrations indicates that atoms located on the loop perimeter are the likely sources of the measured DLTS signals. The combined use of defect models and recently developed DLTS simulation allows reducing the number of assumptions and fitting parameters needed for the simulation of leakage currents, therefore improving their predictability. It is found that simulations based on the coupled-defect-levels model reproduce well the measured leakage current values and their field dependence behaviour, indicating that leakage currents can be successfully simulated on the exclusive basis of the experimentally observed energy levels.
Sensitivity of domain walls of bismuth-substituted iron garnets to a magneto-electric interactions caused by external complex field influence
Authors: Koronovskyy V. E. , Vakyla Y. A.
Published: November 2015

We revealed the “smearing” effect of domain walls' local areas under conditions with the joint impact of AC and DC electric fields in inhomogeneous magnetic structures of bismuth-substituted iron garnet films. Magneto-optical measurements and the direct visual observations in transmitted light were used for the investigation. The revealed effect depends essentially on the curvature of the domain walls and occurred visually only when an external magnetic field of certain orientation was applied to the sample.
Broadband architecture for galvanically accessible superconducting microwave resonators
Authors: Bosman Sal J. , Singh Vibhor , Bruno Alessandro , Steele Gary A.
Published: November 2015

In many hybrid quantum systems, a superconducting circuit is required, which combines DC-control with a coplanar waveguide (CPW) microwave resonator. The strategy thus far for applying a DC voltage or current bias to microwave resonators has been to apply the bias through a symmetry point in such a way that it appears as an open circuit for certain frequencies. Here, we introduce a microwave coupler for superconducting CPW cavities in the form of a large shunt capacitance to ground. Such a coupler acts as a broadband mirror for microwaves while providing galvanic connection to the center conductor of the resonator. We demonstrate this approach with a two-port λ/4-transmission resonator with linewidths in the MHz regime (Q∼103) that shows no spurious resonances and apply a voltage bias up to 80 V without affecting the quality factor of the resonator. This resonator coupling architecture, which is simple to engineer, fabricate, and analyse, could have many potential applications in experiments involving superconducting hybrid circuits.
Nanoscale calibration of n-type ZnO staircase structures by scanning capacitance microscopy
Authors: Wang L. , Laurent J. , Chauveau J. M. , Sallet V. , Jomard F. , Brémond G.
Published: November 2015

Cross-sectional scanning capacitance microscopy (SCM) was performed on n-type ZnO multi-layer structures homoepitaxially grown by molecular beam epitaxy method. Highly contrasted SCM signals were obtained between the ZnO layers with different Ga densities. Through comparison with dopant depth profiles from secondary ion mass spectroscopy measurement, it is demonstrated that SCM is able to distinguish carrier concentrations at all levels of the samples (from 2 × 1017 cm−3 to 3 × 1020 cm−3). The good agreement of the results from the two techniques indicates that SCM can be a useful tool for two dimensional carrier profiling at nanoscale for ZnO nanostructure development. As an example, residual carrier concentration inside the non-intentionally doped buffer layer was estimated to be around 2 × 1016 cm−3 through calibration analysis.
Exciton dynamics in a site-controlled quantum dot coupled to a photonic crystal cavity
Authors: Jarlov C. , Lyasota A. , Ferrier L. , Gallo P. , Dwir B. , Rudra A. , Kapon E.
Published: November 2015

Exciton and cavity mode (CM) dynamics in site-controlled pyramidal quantum dots (QDs), integrated with linear photonic crystal membrane cavities, are investigated for a range of temperatures and photo-excitation power levels. The absence of spurious multi-excitonic effects, normally observed in similar structures based on self-assembled QDs, permits the observation of effects intrinsic to two-level systems embedded in a solid state matrix and interacting with optical cavity modes. The coupled exciton and CM dynamics follow the same trend, indicating that the CM is fed only by the exciton transition. The Purcell reduction of the QD and CM decay times is reproduced well by a theoretical model that includes exciton linewidth broadening and temperature dependent non-radiative processes, from which we extract a Purcell factor of 17 ± 5. For excitation powers above QD saturation, we show the influence of quantum wire barrier states at short delay time, and demonstrate the absence of multiexcitonic background emission.
Dielectric barrier discharge-based plasma actuator operation in artificial atmospheres for validation of modeling and simulation
Authors: Mangina R. S. , Enloe C. L. , Font G. I.
Published: November 2015

We present an experimental case study of time-resolved force production by an aerodynamic plasma actuator immersed in various mixtures of electropositive (N2) and electronegative gases (O2 and SF6) at atmospheric pressure using a fixed AC high-voltage input of 16 kV peak amplitude at 200 Hz frequency. We have observed distinct changes in the discharge structures during both negative- and positive-going voltage half-cycles, with corresponding variations in the actuator's force production: a ratio of 4:1 in the impulse produced by the negative-going half-cycle of the discharge among the various gas mixtures we explored, 2:1 in the impulse produced by the positive-going half-cycle, and cases in which the negative-going half-cycle dominates force production (by a ratio of 1.5:1), where the half-cycles produce identical force levels, and where the positive-going half cycle dominates (by a ratio of 1:5). We also present time-resolved experimental evidence for the first time that shows electrons do play a significant role in the momentum coupling to surrounding neutrals during the negative going voltage half-cycle of the N2 discharge. We show that there is sufficient macroscopic variation in the plasma that the predictions of numerical models at the microscopic level can be validated even though the plasma itself cannot be measured directly on those spatial and temporal scales.
Optimal electron, phonon, and magnetic characteristics for low energy thermally induced magnetization switching
Authors: Atxitia U. , Ostler T. A. , Chantrell R. W. , Chubykalo-Fesenko O.
Published: November 2015

Using large-scale computer simulations, we thoroughly study the minimum energy required to thermally induced magnetization switching (TIMS) after the application of a femtosecond heat pulse in transition metal-rare earth ferrimagnetic alloys. We find that for an energy efficient TIMS, a low ferrimagnetic net magnetization with a strong temperature dependence is the relevant factor for the magnetic system. For the lattice and electron systems, the key physics for efficient TIMS is a large electron-phonon relaxation time. Importantly, we show that as the cooling time of the heated electrons is increased, the minimum power required to produce TIMS can be reduced by an order of magnitude. Our results show the way to low power TIMS by appropriate engineering of magnetic heterostructures.
Correlated rattling-ion origins of dielectric properties in reentrant dipole glasses BaTiO3-BiScO3
Authors: Krayzman Victor , Levin Igor , Woicik Joseph C. , Bridges Frank
Published: November 2015

The local structure of the pseudo-cubic solid solution 0.6BaTiO3-0.4BiScO3, which exhibits reentrant dipole-glass behavior, has been determined using the Reverse Monte Carlo method to simultaneously fit (1) neutron and X-ray total scattering data (including the corresponding real-space pair-distribution functions), (2) Bi and Sc extended X-ray absorption fine structure, and (3) patterns of diffuse scattering in electron diffraction. These structural refinements revealed the multi-site probability density distributions for both Bi (14-sites) and Ti (8 sites), whereas Ba and Sc featured normal unimodal distributions. Bi atoms are displaced along both the 〈111〉 and 〈100〉 directions, while Ti atoms are shifted along 〈111〉. Correlated dynamic hopping of Bi and Ti over their corresponding split sites combined with chemical disorder is proposed as the origin of the strong frequency dispersion observed in dielectric measurements. The existence of split sites also explains the reentrant dipole-glass behavior reported for this system.
Spontaneous orientation-tuning driven by the strain variation in self-assembled ZnO-SrRuO3 heteroepitaxy
Authors: Zhu Yuanmin , Chang Wei Sea , Yu Rong , Liu Ruirui , Wei Tzu-Chiao , He Jr-Hau , Chu Ying-Hao , Zhan Qian
Published: November 2015

Heteroepitaxial ZnO and SrRuO3 were grown on SrTiO3 (111) substrates and formed a self-assembled wurtzite-perovskite nanostructure. Spontaneous orientation-tuning of the SrRuO3 pillars was observed, with the growth direction changing from [111]SRO to [011]SRO as the film thickness increased, which is attributed to a misfit strain transition from the biaxial strain imposed by the SrTiO3 substrate to the vertical strain provided by the ZnO matrix. The [011]-SrRuO3 and [0001]-ZnO combination presents a favorable matching in the nanocomposite films, resulting in higher charge carrier mobility. This vertically integrated configuration and regulation on the crystallographic orientations are expected to be employed in designing multi-functional nanocomposite systems for applications in electronic devices.
Control multiple electrocaloric effect peak in Pb(Mg1/3Nb2/3)O3-PbTiO3 by phase composition and crystal orientation
Authors: Bai Yang , Wei De , Qiao Li-Jie
Published: November 2015

This paper demonstrates the effect of phase composition and crystal orientation on the electrocaloric effect (ECE) in Pb(Mg1/3Nb2/3)O3-PbTiO3 ceramics and single crystals. The ECE features are closely related to phase diagram. Each ECE peak refers to a transition between rhombohedra, tetragonal, and cubic phases. The samples near morphotropic phase boundary have two ECE peaks corresponding to rhombohedra-tetragonal and tetragonal-cubic transitions, the latter induces large ECE of ΔT = 0.60 K (@20 kV/cm) in ceramics and ΔT = 0.69 K (@10 kV/cm) in 〈001〉 single crystal. Different orientations of single crystal change both ECE value and position, where 〈001〉-orientation works for tetragonal-cubic ECE peak and 〈111〉-orientation for rhombohedra-tetragonal peak.
Generating femtosecond X-ray pulses using an emittance-spoiling foil in free-electron lasers
Authors: Ding Y. , Behrens C. , Coffee R. , Decker F.-J. , Emma P. , Field C. , Helml W. , Huang Z. , Krejcik P. , Krzywinski J. , Loos H. , Lutman A. , Marinelli A. , Maxwell T. J. , Turner J.
Published: November 2015

Generation of femtosecond to sub-femtosecond pulses is attracting much attention in X-ray free-electron laser user community. One method is to use a slotted, emittance-spoiling foil which was proposed before (P. Emma et al., Phys. Rev. Lett. 92, 074801 (2004)) and has been widely used at the Linac Coherent Light Source. Direct experimental characterization of the slotted-foil performance was previously unfeasible due to a lack of appropriate diagnostics. With a recently installed X-band radio-frequency transverse deflector, we are able to characterize the electron bunch spoiling effect and X-ray pulse when using the slotted foil. We show that few-femtosecond X-ray pulses are generated with flexible control of the single-pulse duration or double-pulse separation with comparison to the theoretical model.
Electrodynamics and quantum capacity: The case of Bi2Se3 topological insulator
Authors: Craco L.
Published: November 2015

Layered Bi-chalcogenide topological insulators are among the most available energy conversion (thermoelectric) and storage (battery) materials. Motivated by this applied aspect of fundamental importance and the good agreement between theory and key experiments probing spectroscopy and dc transport, we undertake a detailed study of electrodynamic responses of bulk Bi2Se3 topological insulator. In particular, we confirm that the interplay between spin-orbit and electron correlations underpins its bulk metallicity. We show the implications of our proposal for the multi-channel nature of galvanostatic, voltage-capacity profiles intrinsic to LixBi2Se3 battery material. Supported by a microscopic description of quantum capacity, we predict that layered Bi-based topological insulators are promising candidates for future high-voltage solid-state batteries.
THz photomixers based on nitrogen-ion-implanted GaAs
Authors: Peytavit E. , Billet M. , Desmet Y. , Ducournau G. , Yarekha D. , Lampin J-F.
Published: November 2015

Ultrafast photoconductors using GaAs implanted by low energy N+ ions (<55 keV) are fabricated and characterized up to 320 GHz by means of a photomixing experiment. Around 90 μW of output power was obtained at 290 GHz with a 2-μm-diameter photoconductor based on a 160-nm-thick GaAs layer implanted with a main dose of 1.1 × 1012 cm−2 and a subsequent annealing at 600 °C. These performances are similar to those obtained with LT-GaAs photoconductors having same electrodes geometry. Besides, it is shown that the frequency dependence of the output power is not correlated to the carrier lifetime as measured by time-resolved photoreflectance.
Photoconductivity in Dirac materials
Authors: Shao J. M. , Yang G. W.
Published: November 2015

Two-dimensional (2D) Dirac materials including graphene and the surface of a three-dimensional (3D) topological insulator, and 3D Dirac materials including 3D Dirac semimetal and Weyl semimetal have attracted great attention due to their linear Dirac nodes and exotic properties. Here, we use the Fermi’s golden rule and Boltzmann equation within the relaxation time approximation to study and compare the photoconductivity of Dirac materials under different far- or mid-infrared irradiation. Theoretical results show that the photoconductivity exhibits the anisotropic property under the polarized irradiation, but the anisotropic strength is different between 2D and 3D Dirac materials. The photoconductivity depends strongly on the relaxation time for different scattering mechanism, just like the dark conductivity.
Manipulation of multiple 360o domain wall structures and its current-driven motion in a magnetic nanostripe
Authors: Dong Wenjun , Su Yuanchang , Lei Haiyang , Hu Jingguo
Published: November 2015

Dynamics of multiple transverse walls (TWs) in a magnetic nanostripe is studied by micromagnetic simulations. It shows that, when TWs are arranged in a stripe with same orientation, they will attract each other and finally annihilate. However, when adjacent TWs are arranged with opposite orientation, a metastable complex wall can be formed, e.g., two TWs lead to 360o wall. For three or more TWs, the formed complex wall includes a number of 360o substructures, which is called multiple 360o structure (M360S) here. The M360S itself may be used to store multiple logical data since each 360o substructure can act as logical ”0” or ”1”. On the other hand, the M360S may behave like single TW under an applied current, namely, the M360S can be driven steadily by current like that of single TW. A parity effect of the number of 360o substructures on the critical current for the annihilation is found. Namely, when the number is odd or even, the critical current increase or decrease with the increasing of the number, respectively. The parity effect is relevant to the out-of-plane magnetic moment of the M360S.
The DYRK-family kinase Pom1 phosphorylates the F-BAR protein Cdc15 to prevent division at cell poles
Authors: Ullal Pranav , McDonald Nathan A. , Chen Jun-Song , Lo Presti Libera , Roberts-Galbraith Rachel H. , Gould Kathleen L. , Martin Sophie G.
Published: November 2015

Division site positioning is critical for both symmetric and asymmetric cell divisions. In many organisms, positive and negative signals cooperate to position the contractile actin ring for cytokinesis. In rod-shaped fission yeast Schizosaccharomyces pombe cells, division at midcell is achieved through positive Mid1/anillin-dependent signaling emanating from the central nucleus and negative signals from the dual-specificity tyrosine phosphorylation-regulated kinase family kinase Pom1 at the cell poles. In this study, we show that Pom1 directly phosphorylates the F-BAR protein Cdc15, a central component of the cytokinetic ring. Pom1-dependent phosphorylation blocks Cdc15 binding to paxillin Pxl1 and C2 domain protein Fic1 and enhances Cdc15 dynamics. This promotes ring sliding from cell poles, which prevents septum assembly at the ends of cells with a displaced nucleus or lacking Mid1. Pom1 also slows down ring constriction. These results indicate that a strong negative signal from the Pom1 kinase at cell poles converts Cdc15 to its closed state, destabilizes the actomyosin ring, and thus promotes medial septation.
Diversity of Xanthomonas campestris Isolates from Symptomatic Crucifers in New York State
Authors: Lange H. W. , Tancos M. A. , Carlson M. O. , Smart C. D.
Published: November 2015

To assess the diversity of Xanthomonas campestris spp. infecting crucifers in New York, 154 isolates were collected over 10 years across the state. The goal was to determine if isolates of the pathogen were overwintering in New York and serving as primary inoculum in subsequent years, or if novel isolates were entering the state each year. Pure cultures of isolates were characterized using multilocus sequence analysis (MLSA), a greenhouse pathogenicity assay, repetitive element-polymerase chain reaction (Rep-PCR) using the BOX-A1R primer, and enzyme-linked immunosorbent assay. The MLSA scheme proved to be more efficient than Rep-PCR for a large sample population and for comparison with global isolates. X. campestris isolated from crucifers in New York comprised of X. campestris pv. campestris and X. campestris pv. raphani, with X. campestris pv. raphani being predominately isolated from transplants. Evidence for unique haplotypes persisting on the same farm for several years due to improper seedbed rotations was documented in addition to novel haplotypes being spread throughout states through infected transplants and seed. Rep-PCR confirmed the high diversity of X. campestris and was used to generate 15 unique fingerprint patterns from isolates collected in the first 5 years. A worldwide comparison of isolates suggests that the X. campestris pv. campestris population appears to be very homogenous with dominant haplotypes persisting for extended periods and being globally disseminated.
Virulence and Simple Sequence Repeat Marker Segregation in a Puccinia striiformis f. sp. tritici Population Produced by Selfing a Chinese Isolate on Berberis shensiana
Authors: Tian Yuan , Zhan Gangming , Chen Xianming , Tungruentragoon Angkana , Lu Xia , Zhao Jie , Huang Lili , Kang Zhensheng
Published: November 2015

Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust, frequently produces new races overcoming resistance in wheat cultivars. A recently identified race, V26 with virulence to Yr26 and many other stripe rust resistance genes, has a high potential to cause epidemics in China. In this study, teliospores from a single-urediniospore isolate of V26 (Pinglan 17-7) produced on the wheat line 92R137 (Yr26) were used to produce a sexual population through selfing by infecting Berberis shensiana plants under controlled conditions. One hundred and eighteen progeny isolates and the parental isolate were phenotyped for virulence/avirulence on 24 Yr gene lines of wheat. These progeny isolates were all avirulent to Yr5, Yr8, Yr15, and YrTr1 and virulent to Yr1, Yr2, Yr7, Yr9, Yr10, Yr17, Yr24, Yr25, Yr26, YrA, YrExp2, and YrV23, indicating that the parental isolate is homozygous avirulent or homozygous virulent at these loci. The progeny population segregated for avirulence to Yr6, Yr43, and YrSP at one locus (3 avirulent:1 virulent ratio); for virulence to Yr27 and Yr28 at one locus (3 virulent:1 avirulent); and for Yr4, Yr32, and Yr44 at two loci (15 virulent:1 avirulent). Among the eight segregating avirulence/virulence loci, association was found between virulence to Yr4 and Yr32, as well as between virulence to Yr6 and Yr43 based on χ2 tests. From 82 genotypically different progeny isolates, 24 pathotypes and 82 multilocus genotypes were identified. The results show that a highly diverse population can be produced from a single isolate by selfing on a barberry plant and sexually produced population can be used to genetically characterize virulence of the stripe rust pathogen.
Simultaneous high-resolution scanning Bragg contrast and ptychographic imaging of a single solar cell nanowire
Authors: Wallentin Jesper , Wilke Robin N. , Osterhoff Markus , Salditt Tim
Published: November 2015

Simultaneous scanning Bragg contrast and small-angle ptychographic imaging of a single solar cell nanowire are demonstrated, using a nanofocused hard X-ray beam and two detectors. The 2.5 µm-long nanowire consists of a single-crystal InP core of 190 nm diameter, coated with amorphous SiO2and polycrystalline indium tin oxide. The nanowire was selected and aligned in real space using the small-angle scattering of the 140 × 210 nm X-ray beam. The orientation of the nanowire, as observed in small-angle scattering, was used to find the correct rotation for the Bragg condition. After alignment in real space and rotation, high-resolution (50 nm step) raster scans were performed to simultaneously measure the distribution of small-angle scattering and Bragg diffraction in the nanowire. Ptychographic reconstruction of the coherent small-angle scattering was used to achieve sub-beam spatial resolution. The small-angle scattering images, which are sensitive to the shape and the electron density of all parts of the nanowire, showed a homogeneous profile along the nanowire axis except at the thicker head region. In contrast, the scanning Bragg diffraction microscopy, which probes only the single-crystal InP core, revealed bending and crystalline inhomogeneity. Both systematic and non-systematic real-space movement of the nanowire were observed as it was rotated, which would have been difficult to reveal only from the Bragg scattering. These results demonstrate the advantages of simultaneously collecting and analyzing the small-angle scattering in Bragg diffraction experiments.
Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program
Authors: Lübben Jens , Bourhis Luc J. , Dittrich Birger
Published: November 2015

Invariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation–libration–screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four example structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program calledAPD-Toolkithas been coded to overcome technical limitations of the established programTHMA. The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.
A multi-functional dual-energy laboratory Mo-Cr-SAXS system
Authors: Koppoju Suresh
Published: November 2015

A laboratory small-angle X-ray scattering (SAXS) system with a dual energy (Mo and Cr) source has been designed and established with the aim of studying the heterogeneity in high-Zmetallic structural materials such as steels (Fe alloy) and other materials. With the combination of Mo and Cr energies, various camera lengths (maximum of 2400 mm), and an area detector, three decades ofqrange has been achieved, from 0.024 to 14 nm−1. In real space, the probing periodic distance is a maximum of 261 nm. SAXS profiles of 9Cr-ODS steel powders with good statistics with a measurement time of 6 h show the aptness and viability of this system for the investigation of high-`Z' (high-absorption) metallic structural materials. In addition to having Mo and Cr sources, a flexible sample mounting stage permits measurements on a wide range of materials from soft to hard and liquid to solid, both in transmission and in grazing-incidence geometry.
Modeling solution X-ray scattering of biomacromolecules using an explicit solvent model and the fast Fourier transform
Authors: Tong Dudu , Yang Jianbin , Lu Lanyuan
Published: November 2015

A novel computational method based on atomic form factors and the fast Fourier transform (FFT) is developed to compute small- and near-wide-angle X-ray scattering profiles of biomacromolecules from explicit solvent modeling. The method is validated by comparing the results with those from non-FFT approaches and experiments, and good agreement with experimental data is observed for both small and near-wide angles. In terms of computational efficiency, the FFT-based method is advantageous for protein solution systems of more than 3000 atoms. Furthermore, the computational cost remains nearly constant for a wide range of system sizes. The FFT-based approach can potentially handle much larger molecular systems compared with popular existing methods.
Structure and spectroscopy of CuH preparedviaborohydride reduction
Authors: Bennett Elliot L. , Wilson Thomas , Murphy Patrick J. , Refson Keith , Hannon Alex C. , Imberti Silvia , Callear Samantha K. , Chass Gregory A. , Parker Stewart F.
Published: November 2015

Copper(I) hydride (cuprous hydride, CuH) was the first binary metal hydride to be discovered (in 1844) and is singular in that it is synthesized in solution, at ambient temperature. There are several synthetic paths to CuH, one of which involves reduction of an aqueous solution of CuSO4·5H2O by borohydride ions. The product from this procedure has not been extensively characterized. Using a combination of diffraction methods (X-ray and neutron) and inelastic neutron scattering spectroscopy, we show that the CuH from the borohydride route has the same bulk structure as CuH produced by other routes. Our work shows that the product consists of a core of CuH with a shell of water and that this may be largely replaced by ethanol. This offers the possibility of modifying the properties of CuH produced by aqueous routes.
Crystal engineering on superpolyhedral building blocks in metal–organic frameworks applied in gas adsorption
Authors: Chen Ying-Pin , Liu Tian-Fu , Fordham Stephen , Zhou Hong-Cai
Published: November 2015

Two metal–organic frameworks [PCN-426(Ni) and PCN-427(Cu)] have been designed and synthesized to investigate the structure predictability using a SBB (supermolecular building blocks) approach. Tetratopic ligands featuring 120° angular carboxylate moieties were coordinated with a [Ni3(μ3-O)] cluster and a [Cu2O2] unit, respectively. As topologically predicted, 4-connected networks with square coordination adopted the nbo net for the Ni-MOF and ssb net for the Cu-MOF. PCN-426(Ni) was augmented with 12-connected octahedral SBBs, while PCN-427(Cu) was constructed with tetragonal open channels. After a CO2 supercritical drying procedure, the PCN-426(Ni) possessed a Brunauer–Emmett–Teller (BET) surface area as high as 3935 m2 g−1 and impressively high N2 uptake of 1500 cm3 g−1. This work demonstrates the generalization of the SBB strategy, finding an alternative to inconvenient synthetic processes to achieve the desired structural features.
Polymorph engineering of CuMO2 (M = Al, Ga, Sc, Y) semiconductors for solar energy applications: from delafossite to wurtzite
Authors: Scanlon David O. , Walsh Aron
Published: November 2015

The cuprous oxide based ternary delafossite semiconductors have been well studied in the context of p-type transparent conducting oxides. CuAlO2, CuGaO2 and CuInO2 represent a homologous series where the electronic properties can be tuned over a large range. The optical transparency of these materials has been associated with dipole forbidden transitions, which are related to the linear O—Cu—O coordination motif. The recent demonstration that these materials can be synthesized in tetrahedral structures (wurtzite analogues of the chalcopyrite lattice) opens up a new vista of applications. We investigate the underlying structure–property relationships (for Group 3 and 13 metals), from the perspective of first-principles materials modelling, towards developing earth-abundant photoactive metal oxides. All materials studied possess indirect fundamental band gaps ranging from 1 to 2 eV, which are smaller than their delafossite counterparts, although in all cases the difference between direct and indirect band gaps is less than 0.03 eV.
Structure Determination of LASSBio-1289: A New Antihypertensive Lead-Compound
Authors: Sato Juliana , Costa Fanny , Fraga Carlos , Barreiro Eliezer , Ferreira Fabio
Published: November 2015

Hypertension is considered a multi-factorial disease being an important worldwide public-health challenge due to its high frequency and concomitant risks of cardiovascular and other diseases. It has been identified as the leading risk factor for mortality, and is ranked as the third cause of disability-adjusted life-years[1]. The LASSBio-1289 compound was designed from the lead compound LASSBio-294 through the use of medicinal chemistry strategy of bioisosteric replacement of aromatic rings[2]. Many factors are involved in the task of describing the relationship between chemical structure and pharmacological activity of a prototype of a new drug. Among these factors the study of atomic-level structure can be included. The aim of this work is to carry out the structural characterization of LASSBio-1289, in solid-state. Since many NAH derivatives, as LASSBio-1289, do not form single crystals for proper structure determination, this task was overcome by using X-ray powder diffraction data and an ab initio simulated annealing procedure. This study can contribute to better understand the full pharmacodynamic profiles and physicochemical properties of this class of compounds. The LASSBio-1289 compound was synthesized following the procedure described in literature[3]. The sample was sofly hand-grinded in an agate mortar in order to get a fine powder suitable for X-ray powder diffraction analysis. The final refined values for the unit-cell parameters after the Rietveld fit were: a = 14.5119(3) Å, b = 12.1375(2) Å, c = 7.5498(1) Å, β = 91.113(1) Å, Z = 4, Z' = 1 and ρcalc = 1.44039(5) g.m-3. The goodness-of-fit indicator and R-factors were: χ2 = 1.290, RBragg = 1.749%, Rwp = 4.903%, Rexp = 3.802% and Rp = 3.661%. The crystal structure of LASSBio-1289 compound consists of four formula units per unit cell (Z = 4), accommodating one molecule in the asymmetric unit (Z' = 1). The sample was indexed as monoclinic space group (P21/c).
The crystal structure of human Aldehyde Oxidase in native and inhibited forms
Authors: Coelho Catarina , Hartmann Tobias , Foti Alessandro , Santos-Silva Teresa , Leimkühler Silke , Romao Maria Joao
Published: November 2015

Aldehyde oxidases (AOX; E.C. 1.2.3.1) are molybdo-flavoenzymes with broad substrate specificity, oxidizing aldehydes and N-heterocycles. AOX belongs to the xanthine oxidase (XO) family of Mo-containing enzymes. The true physiological function of AOX is still unknown, although it is recognized to play a role in the metabolism of compounds with medicinal and toxicological relevance [1]. AOX importance has increased in recent years since it is substituting Cyt-P450 as the central drug-metabolizing system in humans. We have solved the 3D structure of mouse AOX3 to 2.9 Å resolution [2] that was the first structure of an aldehyde oxidase, providing important evidences on substrate and inhibitor specificities between AOX and XO. The complement of AOX proteins in mammals varies from one in humans (hAOX1) to four in rodents (mAOX1, mAOX3, mAOX4 and mAOX3L1) as a result of evolutionary genetic events. Due to this unusual complement of AOX genes in different animal species, conclusions regarding protein metabolism in humans cannot be taken exclusively from the mouse model. Using the human aldehyde oxidase (hAOX1) purified after heterologous expression in Escherichia coli we were able to crystallize it and solve its 3D structure to 2.7 Å resolution (submitted). In addition to the native protein we also solved the structure of an inhibited form of the enzyme to 2.6Å resolution. Analysis of the protein active site and comparison with the structure of the mouse isoform (mAOX3) allowed us to identity, for the first time, the unique features that characterize hAOX1 as an important drug-metabolizing enzyme. In spite of the similarities of both enzymes, they show marked and relevant differences at the Mo active site, substrate tunnel as well as at the FAD site. The ensemble of these structures provides important insights into the role of aldehyde oxidases, contributing to elucidate the clinical metabolism implications of hAOX1 in humans which has particular relevance for novel drug design studies.
Structural basis for hydroxymethylcytosine recognition by the SRA domain of UHRF2
Authors: Yang Na , Zhou Ting , Xiong Jun , Wang Mingzhu , Wong Jiemin , Zhu Bing , Xu Rui-Ming
Published: November 2015

Methylated cytosine of CpG dinucleotides in vertebrates may be oxidized by Tet proteins, a process that can lead to DNA demethylation. The predominant oxidation product, 5-hydroxymethylcytosine (5hmC), has been implicated in embryogenesis, cell differentiation and human diseases. Recently, the SRA domain of UHRF2 (UHRF2-SRA) has been reported to specifically recognize 5hmC, but how UHRF2 recognizes this modification is unclear. Here we report the structure of UHRF2-SRA in complex with a 5hmC-containing DNA. The structure reveals that the conformation of a phenylalanine allows the formation of an optimal 5hmC-binding pocket, and a hydrogen bond between the hydroxyl group of 5hmC and UHRF2-SRA is critical for their preferential binding. Further structural and biochemical analyses unveiled the role of SRA domains as a versatile reader of modified DNA, and the knowledge should facilitate further understanding of the biological function of UHRF2, and the comprehension of DNA hydroxymethylation in general.
The structure of an ABC toxin particle determined by X-ray crystallography and single particle EM.
Authors: Busby Jason , Panjikar Santosh , Landsberg Michael , Hurst Mark , Lott Shaun
Published: November 2015

The ABC toxin complexes produced by certain bacteria are of interest owing to their potent insecticidal activity and potential role in human disease. These complexes comprise at least three proteins (A, B and C), which must assemble to be fully toxic. The carboxy-terminal region of the C protein is the main cytotoxic component, and is poorly conserved between different toxin complexes. A general model of action has been proposed, in which the toxin complex binds to the cell surface via the A protein, is endocytosed, and sub-sequently forms a pH-triggered channel, allowing the translocation of C into the cytoplasm, where it can cause cytoskeletal disruption in both insect and mammalian cells. We have determined the three-dimensional structure of the complex formed between the B and C proteins by X-ray crystallography to 2.5Å. These proteins assemble to form an unprecedented, large hollow structure that encapsulates and sequesters the cytotoxic, C-terminal region of the C protein like the shell of an egg. The shell is decorated on one end by a β-propeller domain, which mediates attachment of the B–C heterodimer to the A protein in the native complex. The structure reveals how C auto-proteolyses when folded in complex with B. The C protein is the first example of a structure that contains rearrangement hotspot (RHS) repeats, and illustrates a striking structural architecture that we predict to be conserved across both this widely distributed bacterial protein family and the related eukaryotic tyrosine-aspartate (YD)-repeat-containing protein family, which includes the teneurins. The structure provides the first clues about the function of these protein repeat families, and suggests a generic mechanism for protein encapsulation and delivery. We have been able to model the complete ABC toxin complex for the by docking the B–C complex and both associated chitinase enzymes, Chi1 and Chi2, onto the single-particle electron microscopy structure of the Y. entomophaga A pentamer. The structure of the complete complex presented here reveals how the cytotoxic C proteins of ABC-type toxin complexes are processed and protected, demonstrates the function of the B protein within the complex and provides a framework for further experiments to build a complete mechanistic model of action for this class of toxins. More broadly, it also illuminates the function of the widely distributed RHS- and YD-repeat families of proteins, which had previously been unknown.
Trigonal representation of quantum orbitals, from hydrogen to calcium
Authors: Audet Lise
Published: November 2015

Inspired from the work of Van Meersshe and Feneau-Dupont (1984), the ternary representation of the basic models in crystallography offers interesting perspectives to illustrate quantum orbitals, the classical S, P, D and F orbitals, by using a 3D representation of a trigonal system in place of the orthogonal system . On the other hand, the studies of the molecular orbitals of orthohydrogen (spins in the same sense) induces the hypothesis of a singularity zone between the atoms of hydrogen which could be a neutral zone favourable to the emergence of neutral particles and potentially can reorganize the repartition of electronic orbitals. Therefore, the nuclear spins can be related to the quantum orbitals distribution. Finally, by associating the ternary system in crystallisation with the orientation of nuclear spins and chemical bonds between the elements, we could work out a "trigonal" representation for the first elements of the periodic table, from hydrogen to calcium. The trigonal approach can facilitate the 3D representation of complex orbital systems. It offers a theoretical potential for crystallographic studies and it can support a large program of experimentation about the formation of the isotopes, the ionic character of covalent bonds and the gas state at low temperature for the electronegative elements of the periodic table.
Structural studies on the catalytic mechanism of Diaminopropionate ammonia lyase
Authors: Deka Geeta , Bisht Shveta , Savithri H.S. , Murthy M.R.N
Published: November 2015

Diaminopropionate ammonia lyase (DAPAL) is a non-stereo specific fold-type II pyridoxal 5' phosphate (PLP) dependent enzyme that catalyzes the conversion of both D/L isoforms of the nonstandard amino acid Diaminopropionate (DAP) to pyruvate and ammonia. DAP is important for the synthesis of nonribosomal peptide antibiotics such as viomycin and capreomycin. Earlier structural studies on EcDAPAL bound to a reaction intermediate (aminoacrylate) suggested that the enzyme follows a two base mechanism, where Asp120 and Lys77 function as general bases to abstract proton from D-DAP and L-DAP respectively. A novel disulfide was observed near the active site, although its functional significance was not clear. In the present study, structural and biochemical characterization of active site mutants Asp120 (Asp120Asn/Ser/Thr/Cys) and Lys77 (Lys77His/ Thr/Ala/Val) of EcDAPAL has been carried out. Reduction of catalytic efficiency (Kcat/Km) of D120N EcDAPAL for D-DAP by 140 fold and presence of the uncatalyzed ligand at the active site in the crystal structure suggested that Asp120 indeed abstracts proton from D-DAP. Lys77, which was speculated to be important for proton abstraction from L DAP, however seemed to be crucial for PLP binding only. Presence of non-covalently bound PLP in the L77W mutant and occurence of both the ketoenamine, enolimine forms of internal aldimine in L77R mutant provided an in depth insight into the unique chemistry of internal aldimine formation in PLP dependent enzymes. To investigate the role of the novel disulfide bond near the active site, C265 and C291 were mutated to Serine. Studies on these mutants show that this disulfide bond gives additional stability to the protein and might regulate the entry of substrates to the active site. Thus, these studies provide deeper insights into the reaction mechanism of EcDAPAL, representing the overall reaction mechanism followed by several other fold-type II PLP pendent enzymes.