First-principles supercell calculations for simulating a shallow donor state in Si

We present first-principles simulations of As-doped Si carried out using several cubic supercells of up to 10 648 atoms. The 1s As donor level in each supercell splits into three states, which have A₁, T₂, and E symmetries, respectively. The 1s(A₁) wavefunction is well converged in the largest cell, and its spread is close to those of the effective-mass theories. However, the calculated binding energies are smaller than experimental values. This discrepancy would be due to the self-interaction error within the approximated exchange-correlation density functional used in this calculation. Therefore, we also show perturbative calculations based on an impurity potential without the self-interaction error to estimate the binding energies of the 1s(A₁) donor state. The estimated binding energy in the largest supercell agrees well with the experimental value.     

An arrayed-window microfluidic device for observation of mixed nanoparticles with an X-ray free-electron laser

Optical Review - A microfluidic device was developed for coherent diffraction imaging using an X-ray free-electron laser (XFEL-CDI). Liquid samples, which are separately packed in reservoirs of the...     

Isospin properties of () reactions for the formation of deeply-bound antikaonic nuclei

The formation of deeply-bound antikaonic nuclear states in nuclear (K⁻,N) reactions is investigated theoretically within a distorted-wave impulse approximation (DWIA), considering the isospin properties of the Fermi-averaged elementary amplitudes. We calculate the formation cross sections of the deeply-bound states by the (K⁻,N) reactions on the nuclear targets, ¹²C and ²⁸Si, at incident K⁻ lab momentum p_K⁻=1.0 GeV/c and θ_lab=0°, introducing a complex effective nucleon number N_eff for unstable bound states in the DWIA. The results show that the deeply-bound states can be populated dominantly by the (K⁻,n) reaction via the total isoscalar ΔT=0 transition owing to the isospin nature of the amplitudes, and that the cross sections described by ReN_eff and ArgN_eff enable to deduce the structure of the nuclear states; the calculated inclusive nucleon spectra for a deep -nucleus potential do not show distinct peak structure in the bound region. The few-body and states formed in (K⁻,N) reactions on s-shell nuclear targets, ³He, ³H and ⁴He, are also discussed.     

Structure,energy and solute segregation behaviour of [110] symmetric tilt grain boundaries in yttria-stabilized cubic zirconia

Yttria-stabilized cubic zirconia bicrystals with [110] symmetric tilt grain boundaries are systematically fabricated by the diffusion bonding method. It is revealed that the grain-boundary atomistic structures, excess energies and solute segregation behaviours are strongly dependent on the macroscopic geometries of the boundaries. High-resolution transmission electron microscopy combined with lattice statics calculations suggests that the grain-boundary structures are characterized by the accumulation of coordination-deficient cation sites at their cores, whose densities have a clear correlation with excess energies and amounts of solute segregation. The orientation dependence of grain-boundary properties in cubic zirconia can thus be linked and understood via local grain-boundary atomistic structures with the characteristic miscoordinated cation sites.     

Electrochemical intercalation of lithium into graphitized carbons

The change of the carbon structure with electrochemical intercalation of lithium has been investigated by X-ray diffraction (XRD) method. Graphitized carbons showed the first and the second stage structures clearly during the intercalation process. However, the layer spacing corresponding to the 1st stage structure of graphitized carbon was smaller than that of graphite. This is because the first stage structure of graphitized carbon is the mixed structure of lithiated graphite crystallites and lithiated turbostratic disordered layers. The lithium is mainly intercalated into turbostratic disordered layers above 0.1 V versus Li/Li⁺, and intercalated into graphite crystallites rather than turbostratic disordered layers below 0.1 V versus Li/Li⁺.     

Aromatic constituents from the heartwood of Santalum album L

A phytochemical investigation of the polar constituents in the heartwood of Indian Santalum album L. resulted in the isolation of three new neolignans (1-3) and a new aromatic ester (4), along with 14 known components. The structures of the new compounds (1-4) were established using spectroscopic methods.     

Theoretical investigation on electron transport through an organic molecule: effect of the contact structure

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced. Our first-principles calculations on the transport properties of a single benzene dithiolate molecule sandwiched between Au(111) surfaces show that the transmission of the bridge site contact, which is the most stable adsorption configuration in equilibrium, displays different features from those of other configurations, and that the inclusion of the surface layers of Au electrodes into the extended molecule shifts and broadens the transmission peaks due to a stronger and more realistic S-Au bonding. We discuss the geometry dependence of the transport properties by analyzing the density of states of the molecular orbitals.     

Highly saddle shaped (porphyrinato)iron(III) iodide with a pure intermediate spin state

Combined analyses using NMR, EPR and M?ssbauer spectroscopy as well as SQUID magnetometry have revealed that highly saddle shaped Fe(OETPP)I adopts an essentially pure intermediate spin state in spite of the coordination of an iodide ligand.     

Gingipains, the major cysteine proteinases and virulence factors of Porphyromonas gingivalis: structure, function and assembly of multidomain protein complexes

Gingipains, extracellular cysteine proteinases of Porphyromonas gingivalis, constitute the major virulence factor of this periodontopathogenic bacterium. They are the product of three genes, two coding for an Arg-specific (RgpA and RgpB) and one for a Lys-specific proteinase (Kgp). Proteinase domains of RgpA and RgpB are virtually identical; however, the gene encoding the former enzyme is missing a large segment coding for hemaglutinin / adhesin (HA) domains. The latter domains are present also in Kgp. The tertiary structure of RgpB revealed that the proteinase domain of gingipains has a protein fold referred to as the caspase-hemoglobinase fold. On this basis, they are also evolutionary related to other highly specific proteinases including clostripain, caspases, legumains and separase (clan CD of cysteine peptidases). Gingipains are produced as large preproproteins and are subject to elaborate, not yet fully understood, secretion, glycosylation, activation, and maturation processes. How they traverse the outer membrane is unknown, although it can be hypothesized that they use an autotransporter pathway. Apparently during transport through the periplasm the LPS-like glycan moiety is added at the conserved C-terminal portion of progingipains. At the cell surface pro-gingipains fold into partially active, single-chain zymogens and undergo autocatalytic, intermolecular processing. Two sequential cleavages within the profragment domain enhance zymogen activity and in the case of RgpA and Kgp are followed by excision of the individual HA domains. These domains are further truncated at the C-terminus by concerted action of Kgp and carboxypeptidase and form a non-covalent multidomain, multifunctional complex anchored into the outer membrane by the glycated, C-terminal HA domain. This hypothetical scenario is a reasonable explanation for the occurrence of many forms of gingipains.