Solid-state optical absorption from optimally tuned time-dependent range-separated hybrid density functional theory

We present a framework for obtaining reliable solid-state charge and optical excitations and spectra from optimally tuned range-separated hybrid density functional theory. The approach, which is fully couched within the formal framework of generalized Kohn-Sham theory, allows for the accurate prediction of exciton binding energies. We demonstrate our approach through first principles calculations of one- and two-particle excitations in pentacene, a molecular semiconducting crystal, where our work is in excellent agreement with experiments and prior computations. We further show that with one adjustable parameter, set to produce the known band gap, this method accurately predicts band structures and optical spectra of silicon and lithium fluoride, prototypical covalent and ionic solids. Our findings indicate that for a broad range of extended bulk systems, this method may provide a computationally inexpensive alternative to many-body perturbation theory, opening the door to studies of materials of increasing size and complexity.

Morphological and functional characterisation of the burrow systems of six earthworm species (Lumbricidae)

Earthworm burrow systems are generally described based on postulated behaviours associated with the three ecological types. In this study, we used X-ray tomography to obtain 3D information on the burrowing behaviour of six very common anecic (Aporrectodea nocturna and Lumbricus terrestris) and endogeic (Aporrectodea rosea, Allolobophora chlorotica, Aporrectodea caliginosa, Aporrectodea icterica) earthworm species, introduced into repacked soil cores for 6 weeks. A simple water infiltration test, the Beerkan method, was also used to assess some functional properties of these burrow systems. Endogeic worms make larger burrow systems, which are more highly branched, less continuous and of smaller diameter, than those of anecic worms. Among the anecic species, L. terrestris burrow systems are shorter (9.2 vs 21.2 m) with a higher number (14.5 vs 23.5) of less branched burrows (12.2 vs 20.2 branches m(-1)), which are also wider (7.78 vs 5.16 mm) than those of A. nocturna. In comparison, the burrow systems made by endogeic species appeared similar to each other. However, A. rosea burrows were short and narrow, whereas A. icterica had a longer burrow system (15.7 m), more intense bioturbation intensity (refilled macropores or soil lateral compaction around them) and thus a greater number of burrows. Regarding water infiltration, anecic burrow systems were far more efficient due to open burrows linking the top and bottom of the cores. For endogeic species, we observed a linear relationship between burrow length and the water infiltration rate (R (2) = 0.49, p < 0.01). Overall, the three main characteristics significantly influencing water infiltration were burrow length, burrow number and bioturbation volume. This last characteristic highlighted the effect of burrow refilling by casts.

Electronic and Magnetic Properties of Yttrium-doped Silicon Carbide Nanotubes: Density Functional Theory Investigations

The electronic structure of yttrium-doped Silicon Carbide Nanotubes has been theoretically investigated using first principles density functional theory (DFT). Yttrium atom is bonded strongly on the surface of the nanotube with a binding energy of 2.37 eV and prefers to stay on the hollow site at a distance of around 2.25 angstrom from the tube. The semi-conducting nanotube with chirality (4, 4) becomes half mettalic with a magnetic moment of 1.0 mu(B) due to influence of Y atom on the surface. There is strong hybridization between d orbital of Y with p orbital of Si and C causing a charge transfer from d orbital of the Y atom to the tube. The Fermi level is shifted towards higher energy with finite Density of States for only upspin channel making the system half metallic and magnetic which may have application in spintronic devices.

Functional roles of N-terminal and C-terminal domains in the overall activity of a novel single-stranded DNA binding protein of Deinococcus radiodurans

Single-stranded DNA binding protein (Ssb) of Deinococcus radiodurans comprises N- and C-terminal oligonucleotide/oligosaccharide binding (OB) folds connected by a beta hairpin connector. To assign functional roles to the individual OB folds, we generated three Ssb variants: Ssb(N) (N-terminal without connector), Ssb(NC) (N-terminal with connector) and Ssb(C) (C-terminal), each harboring one OB fold. Both Ssb(N) and Ssb(NC) displayed weak single-stranded DNA (ssDNA) binding activity, compared to the full-length Ssb (Ssb(FL)). The level of ssDNA binding activity displayed by SsbC was intermediate between Ssb(FL) and Ssb(N). Ssb(C) and Ssb(FL) predominantly existed as homo-dimers while Ssb(NC)/Ssb(N) formed different oligomeric forms. In vitro, Ssb(NC) or Ssb(N) formed a binary complex with Ssb(C) that displayed enhanced ssDNA binding activity. Unlike Ssb(FL), Ssb variants were able to differentially modulate topoisomerase-I activity, but failed to stimulate Deinococcal RecA-promoted DNA strand exchange. The results suggest that the C-terminal OB fold is primarily responsible for ssDNA binding. The N-terminal OB fold binds weakly to ssDNA but is involved in multimerization. (C) 2015 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies. This is an open access article under the CC BY-NC-ND license.

Functional expression and purification of Anabaena PCC 7120 XisA protein

Anabaena PCC 7120 xisA gene product mediates the site-specific excision of 11,278 bp nifD element in heterocysts formed under nitrogen starvation conditions. Although XisA protein possesses both site-specific recombinase and endonuclease activities, till date neither xisA transcript nor XisA protein has been detected. Gene encoding XisA protein was isolated from plasmid pMX25 and overexpressed in Escherichia coli BL21 DE3 yielding 7.7 mg enzyme per L of growth culture in soluble fraction. His-tagged XisA was purified using Ni-NTA affinity chromatography with 95% recovery. The purified XisA showed a single band on SDS-PAGE with molecular mass of 52 kDa. Identity of XisA was confirmed by MALDI-TOF analysis and functionality of enzyme was confirmed using restriction digestion. A PCR based method was developed to monitor excision by XisA, which displayed near 100% activity in E. coli within 1 h at 37 degrees C on LB under static condition. (C) 2015 Elsevier Inc. All rights reserved.

Prussian blue as a single precursor for synthesis of Fe/Fe3C encapsulated N-doped graphitic nanostructures as bi-functional catalysts

We report a unique, single source precursor Prussian blue (iron(III) ferrocyanide (Fe-4(III)Fe-II(CN)(6)](3))) for the synthesis of Fe/Fe3C nanoparticle encapsulated N-doped graphitic layers and bamboo-like graphitic nanotubes. Hollow N-doped graphite (N-HG) nanostructures are obtained when the encapsulated nanostructures are treated with an acid. Both the encapsulated nanostructures and N-HG are shown to be applicable as bi-functional electrocatalysts for oxygen reduction (ORR) and oxygen evolution reactions (OER). The ORR activity is shown to be improved for N-HG and is comparable to commercial Pt/C. On the other hand, encapsulated nanostructures exhibit OER activity with long-term stability comparable to commercial RuO2.

Prussian blue as a single precursor for synthesis of Fe/Fe3C encapsulated N-doped graphitic nanostructures as bi-functional catalysts

We report a unique, single source precursor Prussian blue (iron(III) ferrocyanide (Fe-4(III)Fe-II(CN)(6)](3))) for the synthesis of Fe/Fe3C nanoparticle encapsulated N-doped graphitic layers and bamboo-like graphitic nanotubes. Hollow N-doped graphite (N-HG) nanostructures are obtained when the encapsulated nanostructures are treated with an acid. Both the encapsulated nanostructures and N-HG are shown to be applicable as bi-functional electrocatalysts for oxygen reduction (ORR) and oxygen evolution reactions (OER). The ORR activity is shown to be improved for N-HG and is comparable to commercial Pt/C. On the other hand, encapsulated nanostructures exhibit OER activity with long-term stability comparable to commercial RuO2.

Spin-glass state in nanoparticulate (La0.7Sr0.3MnO3)(1-x) (BaTiO3)(x) solid solutions: Experimental and density-functional studies

We report the transition from robust ferromagnetism to a spin- glass state in nanoparticulate La0.7Sr0.3MnO3 through solid solution with BaTiO3. The field- and temperature-dependent magnetization and the frequency-dependent ac magnetic susceptibility measurements strongly indicate the existence of a spin- glass state in the system, which is further confirmed from memory effect measurements. The breaking of long-range ordering into short-range magnetic domains is further investigated using density-functional calculations. We show that Ti ions remain magnetically inactive due to insufficient electron leakage from La0.7Sr0.3MnO3 to the otherwise unoccupied Ti-d states. This results in the absence of a Mn-Ti-Mn spin exchange interaction and hence the breaking of the long-range ordering. Total-energy calculations suggest that the segregation of nonmagnetic Ti ions leads to the formation of short-range ferromagnetic Mn domains.

Quantum stochastic calculus associated with quadratic quantum noises

We first study a class of fundamental quantum stochastic processes induced by the generators of a six dimensional non-solvable Lie dagger-algebra consisting of all linear combinations of the generalized Gross Laplacian and its adjoint, annihilation operator, creation operator, conservation, and time, and then we study the quantum stochastic integrals associated with the class of fundamental quantum stochastic processes, and the quantum Ito formula is revisited. The existence and uniqueness of solution of a quantum stochastic differential equation is proved. The unitarity conditions of solutions of quantum stochastic differential equations associated with the fundamental processes are examined. The quantum stochastic calculus extends the Hudson-Parthasarathy quantum stochastic calculus. (C) 2016 AIP Publishing LLC.

Error Correcting Functional Source Coding with Decoder Side Information using Row-Latin Rectangles

The functional source coding problem in which the receiver side information (Has-set) and demands (Want-set) include functions of source messages is studied using row-Latin rectangle. The source transmits encoded messages, called the functional source code, in order to satisfy the receiver's demands. We obtain a minimum length using the row-Latin rectangle. Next, we consider the case of transmission errors and provide a necessary and sufficient condition that a functional source code must satisfy so that the receiver can correctly decode the values of the functions in its Want-set.

Density functional theory based study of chlorine doped WS2-metal interface

Investigation of a transition metal dichalcogenide (TMD)-metal interface is essential for the effective functioning of monolayer TMD based field effect transistors. In this work, we employ the Density Functional Theory calculations to analyze the modulation of the electronic structure of monolayer WS2 with chlorine doping and the relative changes in the contact properties when interfaced with gold and palladium. We initially examine the atomic and electronic structures of pure and doped monolayer WS2 supercell and explore the formation of midgap states with band splitting near the conduction band edge. Further, we analyze the contact nature of the pure supercell with Au and Pd. We find that while Au is physiosorbed and forms n-type contact, Pd is chemisorped and forms p-type contact with a higher valence electron density. Next, we study the interface formed between the Cl-doped supercell and metals and observe a reduction in the Schottky barrier height (SBH) in comparison to the pure supercell. This reduction found is higher for Pd in comparison to Au, which is further validated by examining the charge transfer occurring at the interface. Our study confirms that Cl doping is an efficient mechanism to reduce the n-SBH for both Au and Pd, which form different types of contact with WS2. (C) 2016 AIP Publishing LLC.