Abstract: In this paper, the effect of BC3, C3N and C3N4BC(3) and MoS2/C(3)N4 heterostructures are direct semiconductors with band gaps of 0.4 and 1.74 eV, respectively, while MoS2/C3N is a metal. Furthermore, the influence of strain and electric field on the electronic structure of these van der Waals heterostructures is investigated. The MoS2/BC3 heterostructure, for strains larger than -4%, transforms it into a metal where the metallic character is maintained for strains larger than -6%. The band gap decreases with increasing strain to 0.35 eV (at +2%), while for strain (>+6%) a direct-indirect band gap transition is predicted to occur. For the MoS2/C3N heterostructure, the metallic character persists for all strains considered. On applying an electric field, the electronic properties of MoS2/C3N4 are modified and its band gap decreases as the electric field increases. Interestingly, the band gap reaches 30 meV at +0.8 V/angstrom, and with increase above +0.8 V/angstrom, a semiconductor-to-metal transition occurs. Furthermore, we investigated effects of semi- and full-hydrogenation of MoS2/C3N and we found that it leads to a metallic and semiconducting character, respectively.

Abstract: We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of atomic orbitals (N similar to 10(10)). KITE's core is written in C++, with a versatile Python-based interface, and is fully optimized for shared memory multi-node CPU architectures, thus scalable, efficient and fast. At the core of KITE is a seamless spectral expansion of lattice Green's functions, which enables large-scale calculations of generic target functions with uniform convergence and fine control over energy resolution. Several functionalities are demonstrated, ranging from simulations of local density of states and photo-emission spectroscopy of disordered materials to large-scale computations of optical conductivity tensors and real-space wave-packet propagation in the presence of magneto-static fields and spin-orbit coupling. On-the-fly calculations of real-space Green's functions are carried out with an efficient domain decomposition technique, allowing KITE to achieve nearly ideal linear scaling in its multi-threading performance. Crystalline defects and disorder, including vacancies, adsorbates and charged impurity centres, can be easily set up with KITE's intuitive interface, paving the way to user-friendly large-scale quantum simulations of equilibrium and non-equilibrium properties of molecules, disordered crystals and heterostructures subject to a variety of perturbations and external conditions.

Abstract: The properties of correlated oxides can be manipulated by forming short-period superlattices since the layer thicknesses are comparable with the typical length scales of the involved correlations and interface effects. Herein, we studied the metal-insulator transitions (MITs) in tetragonal NdNiO3/SrTiO3 superlattices by controlling the NdNiO3 layer thickness, n in the unit cell, spanning the length scale of the interfacial octahedral coupling. Scanning transmission electron microscopy reveals a crossover from a modulated octahedral superstructure at n = 8 to a uniform nontilt pattern at n = 4, accompanied by a drastically weakened insulating ground state. Upon further reducing n the predominant dimensionality effect continuously raises the MIT temperature, while leaving the antiferromagnetic transition temperature unaltered down to n = 2. Remarkably, the MIT can be enhanced by imposing a sufficiently large strain even with strongly suppressed octahedral rotations. Our results demonstrate the relevance for the control of oxide functionalities at reduced dimensions.

Abstract: We present the GW band structure of ZnO in its wurtzite (WZ), zincblende (ZB) and rocksalt (RS) phases at the Γ point, calculated within the GW approximation. We have used a Zn20+ pseudopotential which is essential for the adequate treatment of the exchange interaction in the self-energy. The accuracy of the pseudopotential used is also discussed. The effect of the pd hybridization on the GW corrections to the band gap is correlated by comparing the ZB and RS phase.

Abstract: We sampled the Darwin mud volcano (MV) for meiofaunal community and trophic structure in relation to pore-water geochemistry along a 10 m transect from a seep site on the rim of the crater towards the MV slope. Pore-water profiles indicated considerable variation in upward methane (CH4) flow among sediment cores taken along the transect, with highest flux in the seep sediment core, gradually decreasing along the transect, to no CH4 flux in the core taken at a 5 m distance. Low sulphate concentrations and high levels of total alkalinity and sulphide (H2S) suggested that anaerobic oxidation of methane (AOM) occurred close to the sediment surface in the seep sediment core. High H2S levels had a genus- and species-specific impact on meiofaunal densities. Nematode genus composition varied gradually between sediment cores, with the genus Sabatieria dominating almost all sediment cores. However, genus diversity increased with increasing distance from the seep site. These limited data suggest that the community structure of seep meiofauna is highly dependent on local (a)biotic habitat characteristics, and a typical seep meiofaunal community cannot be delineated. Stable isotope values suggested the nematode diet up to 10 m from the seep site included thiotrophic carbon. The thicker hemipelagic sediment layer (photosynthetic carbon), the increased trophic diversity, and the heavier nematode δ13C farther from the seep site suggest a decrease in thiotrophy and an increase in photosynthetic carbon in the nematode diet.

Abstract: In this paper, an overview is given of different modeling approaches used for describing gas discharge plasmas, as well as plasma-surface interactions. A fluid model is illustrated for describing the detailed plasma chemistry in capacitively coupled rf discharges. The strengths and limitations of Monte Carlo simulations and of a particle-in-cell-Monte Carlo collisions model are explained for a magnetron discharge, whereas the capabilities of a hybrid Monte Carlo-fluid approach are illustrated for a direct current glow discharge used for spectrochemical analysis of materials. Finally, some examples of molecular dynamics simulations, for the purpose of plasma-deposition, are given.

Abstract: With the aim of an improved understanding of the metal-complexation properties of alicyclic β-amino acid stereoisomers, and their peptides, the complex equilibria and modes of coordination with copper(II) of l-phenylalanine (F) derivatives of cis/trans-2-aminocyclohexanecarboxylic acid (c/tACHC), i.e. the dipeptides F-c/tACHC and c/tACHC-F, were investigated by a combination of CW and pulsed EPR methods. For the interpretation of the experimental data, DFT quantum-chemical calculations were carried out. Simulation of a pH-dependent series of room-temperature CW-EPR spectra revealed the presence of EPR-active complexes ([Cu(aqua)]2+, [CuL]+, [CuLH1], [CuLH2]−, and [CuL2H1]−), and an EPR-inactive species ([Cu2L2H3]−) in aqueous solutions for all studied cases. [CuLH]2+ was included in the equilibrium model for the c/tACHC-Fcopper(II) systems, and [CuL2], together with two coordination isomers of [CuL2H1]−, were also identified in the F-tACHCcopper(II) system. Comparison of the complexation properties of the diastereomeric ligand pair F-(1S,2R)-ACHC and F-(1R,2S)-ACHC did not reveal significant differences. Considerably lower formation constants were obtained for the trans than for the cis isomers for both the F-c/tACHC and the c/tACHC-F pairs in the case of [CuLH1] involving tridentate coordination by the amino, the deprotonated peptide, and the carboxylate groups. A detailed structural analysis by pulsed EPR methods and DFT calculations indicated that there was no significant destabilization for the complexes of the trans isomers. The lower stability of their complexes was explained by the limitation that only the conformer with donor groups in equatorialequatorial ring positions can bind to copper(II), whereas both equatorial-axial conformers of the cis isomers are capable of binding. From a consideration of the proton couplings obtained with X-band 1H HYSCORE, 2H exchange experiments, and DFT, the thermodynamically most stable cyclohexane ring conformer was assigned for all four [CuLH1] complexes. For the F-cACHC case, the conformer did not match the most stable conformer of the free ligand.

Abstract: Dark-held electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain-reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quantify the influence of various experimental parameters like strain magnitude, specimen thickness, excitation error and surface relaxation. (C) 2013 Elsevier B.V. All rights reserved.

Abstract: The buckling of graphene nano-ribbons containing a grain boundary is studied using atomistic simulations where free and supported boundary conditions are invoked. We consider the buckling transition of two kinds of grain boundaries with special symmetry. When graphene contains a large angle grain boundary with theta = 21.8 degrees, the buckling strains are larger than those of perfect graphene when the ribbons with free (supported) boundary condition are subjected to compressive tension parallel (perpendicular) to the grain boundary. This is opposite for the results of theta = 32.2 degrees. The shape of the deformations of the buckled graphene nanoribbons depends on the boundary conditions, the presence of the particular used grain boundaries, and the direction of applied in-plane compressive tension. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3692573]

Abstract: We study the energy and temperature relaxation of electrons in graphene on a piezoelectric substrate. Scattering from the combined potential of extrinsic piezoelectric surface acoustical (PA) phonons of the substrate and intrinsic deformation acoustical phonons of graphene is considered for a (non) degenerate gas of Dirac fermions. It is shown that in the regime of low energies or temperatures the PA phonons dominate the relaxation and change qualitatively its character. This prediction is relevant for quantum metrology and electronic applications using graphene devices and suggests an experimental setup for probing electron-phonon coupling in graphene.

Abstract: Objective: We aim to investigate if anatomical and functional properties of the upper airway using computerized 3D models derived from computed tomography (CT) scans better predict obstructive sleep apnea (OSA) severity than standard clinical markers. Methods: Consecutive children with suspected OSA underwent polysomnography, clinical assessment of upper airway patency, and a CT scan while awake. A three-dimensional (3D) reconstruction of the pharyngeal airway was built from these images, and computational fluid dynamics modeling of low inspiratory flow was performed using open-source software. Results: Thirty-three children were included (23 boys; mean age, was 6.0 +/- 3.2 y). OSA was diagnosed in 23 patients. Children with OSA had a significantly lower volume of the overlap region between tonsils and the adenoids (median volume, 1408 mm compared to 2173 mm; p = 0.04), a lower mean cross-sectional area at this location (median volume, 69.3 mm(2) compared to 114.3 mm(2); p = 0.04), and a lower minimal cross-sectional area (median volume, 17.9 mm(2) compared to 25.9 mm(2); p = 0.05). Various significant correlations were found between several imaging parameters and the severity of OSA, most pronounced for upper airway conductance (r = -0.46) (p < 0.01) for correlation between upper airway conductance and the apnea-hypopnea index. No differences or significant correlations were observed with clinical parameters of upper airway patency. Preliminary data after treatment showed that none of the patients with residual OSA had their smallest cross-sectional area located in segment 3, and this frequency was significantly lower than in their peers whose sleep study normalized (64%; p = 0.05). Conclusion: Functional imaging parameters are highly correlated with OSA severity and are a more powerful correlate than clinical scores of upper airway patency. Preliminary data also showed that we could identify differences in the upper airway of those subjects who did not benefit from a local upper airway treatment. (c) 2013 Elsevier B.V. All rights reserved.

Abstract: Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations.

Abstract: The magneto- and Hall resistance of a locally gated cross shaped graphene Hall bar is calculated. The edge of the top gate is placed diagonally across the center of the Hall cross. Four-probe resistance is calculated using the Landauer-Büttiker formalism, while the transmission coefficients are obtained using the non-equilibrium Green's function approach. The interplay between transport due to edge channels and snake states is investigated. When two edge channels are occupied, we predict oscillations in the Hall and the bend resistance as function of the magnetic field, which are a consequence of quantum interference between the occupied snake states.