Abstract: Strain analyses from experimental series of nano-beam electron diffraction (NBED) patterns in scanning transmission electron microscopy are performed for different specimen tilts. Simulations of NBED series are presented for which strain analysis gives results that are in accordance with experiment. This consequently allows to study the relation between measured strain and actual underlying strain. A two-tilt method which can be seen as lowest-order electron beam precession is suggested and experimentally implemented. Strain determination from NBED series with increasing beam convergence is performed in combination with the experimental realization of a probe-forming aperture with a cross inside. It is shown that using standard evaluation techniques, the influence of beam convergence on spatial resolution is lower than the influence of sharp rings around the diffraction disc which occur at interfaces and which are caused by the tails of the intensity distribution of the electron probe. (C) 2018 Elsevier B.V. All rights reserved.

Abstract: In this study, the healing of N-vacancy boron carbonitride nanosheet (NV-BC2NNS) and nanotube (NV-BC2NNT) by NO molecule is studied by means of density functional theory calculations. Two different N-vacancies are considered in each of these structures in which the vacancy site is surrounded by either three B-atoms (NB) or by two B- and one C-atom (NBC). By means of the healed BC2NNS and BC2NNT as a support, the removal of two toxic gas molecules (NO and CO) are applicable. It should be noted that the obtained energy barriers of both healing and oxidizing processes are significantly lower than those of graphene, carbon nanotubes or boron nitride nanostructures. Also, at the end of the oxidation process, the pure BC2NNS or BC2NNT is obtained without any additional defects. Therefore, by using this method, we can considerably purify the defective BC2NNS/BC2NNT. Moreover, according to the thermochemistry calculations we can further confirm that the healing process of the NV-BC2NNS and NV-BC2NNT by NO are feasible at room temperature. So, we can claim that this study could be very helpful in both purifying the defective BC2NNS/BC2NNT while in the same effort removing toxic NO and CO gases.

Abstract: The permeation of water between neighboring graphene oxide (GO) flakes, i.e., 2D nanochannels, are investigated using a simple model for the GO membrane. We simulate the hydrophilic behavior of nanocapillaries and study the effect of surface charge on the dynamical properties of water flow and the influence of Na+ and Cl- ions on water permeation. Our approach is based on extensive equilibrium molecular dynamics simulations to obtain a better understanding of water permeation through charged nanochannels in the presence of ions. We found significant change in the slippage dynamics of confined water such as a profound increase in viscosity/slip length with increasing charges over the surface. The slip length decreases one order of magnitude (i.e., 1/30) with increasing density of surface charge, while it increases by a factor of 2 with ion concentration. We found that commensurability induced by nanoconfinement plays an important role on the intrinsic dynamical properties of water.

Abstract: Edge functionalization of graphene nanoribbons with nitrogen atoms for various adatom configurations at armchair and zigzag edges are investigated. We provide comprehensive information on the electronic and magnetic properties and investigate the stability of the various systems. Two types of rippling of the nanoribbons, namely edge and bulk rippling depending on the sign of edge stress induced at the edge, are found. They are found to play the decisive role for the stability of the structures. We also propose a type of edge decoration in which every third nitrogen adatom at the zigzag edges is replaced by an oxygen atom. In this way, the electron count is compatible with a full aromatic structure, leading to additional stability and a disappearance of magnetism that is usually associated with zigzag nanoribbons.

Abstract: By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly.
According to our simulations, the β-roll and β-sheet aggregates must be approximately equally
stable.

Abstract: The precipitation mechanism of the Q phase in Al-Mg-Si-Cu alloys has long been the subject of ambiguity and debate since its metastable phase (Q 0) has the same crystal structure and similar lattice parameters as its equilibrium counterparts. In the present work, the evolution of the Q 0 (Q) phase during aging is studied by combination of quantitative atomic-resolution scanning transmission electron microscopy and atom probe tomography. It was found that the transformation from the Q 0 to the Q phase involves changes of the occupancy of Al atoms in atomic columns of the Q 0 (Q) phase. The Al atoms incorporated in the Cu, Si and Mg columns are gradually released into the Al matrix, while mixing between Cu and Si atoms occurs in the Si columns. This transformation process is mainly attributed to the low lattice misfit of the equilibrium Q phase. Besides, the formation of various compositions of the Q phase is due to the different occupancy in the atomic columns of the Q phase. The occupancy changes in the columns of the Q phase are kinetically controlled and are strongly influenced by the alloy composition and aging temperature.

Abstract: We report on a combined chemical vapor deposition (CVD)/radio frequency (RF) sputtering synthetic strategy for the controlled surface modification of ZnO nanostructures by Ti-containing species. Specifically, the proposed approach consists in the CVD of grown-on-tip ZnO nanopyramids, followed by titanium RF sputtering under mild conditions. The results obtained by a thorough characterization demonstrate the successful ZnO surface functionalization with dispersed Ti-containing species in low amounts. This phenomenon, in turn, yields a remarkable enhancement of photoactivated superhydrophilic behavior, self-cleaning ability, and photocatalytic performances in comparison to bare ZnO. The reasons accounting for such an improvement are unravelled by a multitechnique analysis, elucidating the interplay between material chemico-physical properties and the corresponding functional behavior. Overall, the proposed strategy stands as an amenable tool for the mastering of semiconductor-based functional nanoarchitectures through ad hoc engineering of the system surface.

Abstract: In the quantum mechanical simulation of exploratory semiconductor devices, continuum methods based on a k.p/envelope function model have the potential to significantly reduce the computational burden compared to prevalent atomistic methods. However, full-zone k.p/envelope function simulation approaches are scarce and existing implementations are not self-consistent with the calculation of the electrostatic potential due to the lack of a stable procedure and a proper normalization of the multi-band envelope functions. Here, we therefore present a self-consistent procedure based on a full-zone spectral k.p/envelope function band structure model. First, we develop a proper normalization for the multi-band envelope functions in the presence of transmitting boundary conditions. This enables the calculation of the free carrier densities. Next, we construct a procedure to obtain self-consistency of the carrier densities with the electrostatic potential. This procedure is stabilized with an adaptive scheme that relies on the solution of Poisson's equation in the Gummel form, combined with successive underrelaxation. Finally, we apply our procedure to homostructure In0.53Ga0.47As tunnel field-effect transistors (TFETs) and staggered heterostructure GaAs0.5Sb0.5/In0.53Ga0.47As TFETs and show the importance of self-consistency on the device predictions for scaled dimensions. Published by AIP Publishing.

Abstract: The thermodynamic aspects of various 2D materials are explored using Density Functional Theory (DFT). Various metal chalcogenides (MX2, M = metal, chalcogen X = S, Se, Te) are investigated with respect to their interaction and stability under different ambient conditions met in the integration process of a transistor device. Their interaction with high- dielectrics is also addressed, in order to assess their possible integration in Complementary Metal Oxide Semiconductor (CMOS) field effect transistors. 2D materials show promise for high performance nanoelectronic devices, but the presence of defects (vacancies, grain boundaries,...) can significantly impact their electronic properties. To assess the impact of defects, their enthalpies of formation and their signature levels in the density of states have been studied. We find, consistently with literature reports, that chalcogen vacancies are the most likely source of defects. It is shown that while pristine 2D materials are in general stable whenever set in contact with different ambient atmospheres, the presence of defective sites affects the electronic properties of the 2D materials to varying degrees. We observe that all the 2D materials studied in the present work show strong reactivity towards radical oxygen plasma treatments while reactivity towards other common gas phase chemical such as O-2 and H2O and groups present at the high- surface varies significantly between species. While energy band-gaps, effective masses and contact resistivities are key criteria in selection of 2D materials for scaled CMOS and tunneling based devices, the phase and ambient stabilities might also play a very important role in the development of reliable nanoelectronic applications.

Abstract: Melittin (MEL), a small peptide component of bee venom, has been reported to exhibit anti-cancer effects in vitro and in vivo. However, its clinical applicability is disputed because of its non-specific cytotoxicity and haemolytic activity in high treatment doses. Plasma-treated phosphate buffered saline solution (PT-PBS), a solution rich in reactive oxygen and nitrogen species (RONS) can disrupt the cell membrane integrity and induce cancer cell death through oxidative stress-mediated pathways. Thus, PT-PBS could be used in combination with MEL to facilitate its access into cancer cells and to reduce the required therapeutic dose. The aim of our study is to determine the reduction of the effective dose of MEL required to eliminate cancer cells by its combination with PT-PBS. For this purpose, we have optimised the MEL threshold concentration and tested the combined treatment of MEL and PT-PBS on A375 melanoma and MCF7 breast cancer cells, using in vitro, in ovo and in silico approaches. We investigated the cytotoxic effect of MEL and PT-PBS alone and in combination to reveal their synergistic cytological effects. To support the in vitro and in ovo experiments, we showed by computer simulations that plasma-induced oxidation of the phospholipid bilayer leads to a decrease of the free energy barrier for translocation of MEL in comparison with the non-oxidized bilayer, which also suggests a synergistic effect of MEL with plasma induced oxidation. Overall, our findings suggest that MEL in combination with PT-PBS can be a promising combinational therapy to circumvent the non-specific toxicity of MEL, which may help for clinical applicability in the future.

Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

Abstract: Thin films of C/Mo/W deposited using combined UBM/HIPIMS sputtering show 2-8 nm clusters of material richer in Mo and W than the matrix (found by EDS microanalysis), with structures that resemble graphitic onions with the metal atoms arranged regularly within them. EELS microanalysis showed the clusters to be rich in W and Mo. As the time averaged power used in the pulsed HIPIMS magnetron was increased, the clusters became more defined, larger, and arranged into layers with amorphous matrix between them. Films deposited with average HIPIMS powers of 4 kW and 6 kW also showed a periodic modulation of the cluster density within the finer layers giving secondary, wider stripes in TEM. By analysing the ratio between the finer and coarser layers, it was found that this meta-layering is related to the substrate rotation in the deposition chamber but in a non-straightforward way. Reasons for this are proposed. The detailed structure of the clusters remains unknown and is the subject of further work. Fluctuation electron microscopy results indicated the presence of crystal planes with the graphite interlayer spacing, crystal planes in hexagonal WC perpendicular to the basal plane, and some plane spacings found in Mo2C. Other peaks in the FEM results suggested symmetry-related starting points for future determination of the structure of the clusters.

Abstract: New hybrid materials-photosensitized nanocomposites containing nanocrystal heterostructures with spatial charge separation, show high response for practically important sub-ppm level NO2 detection at room temperature. Nanocomposites ZnO/CdSe, ZnO/(CdS@CdSe), and ZnO/(ZnSe@CdS) were obtained by the immobilization of nanocrystals-colloidal quantum dots (QDs), on the matrix of nanocrystalline ZnO. The formation of crystalline core-shell structure of QDs was confirmed by HAADF-STEM coupled with EELS mapping. Optical properties of photosensitizers have been investigated by optical absorption and luminescence spectroscopy combined with spectral dependences of photoconductivity, which proved different charge localization regimes. Photoelectrical and gas sensor properties of nanocomposites have been studied at room temperature under green light (max = 535 nm) illumination in the presence of 0.12-2 ppm NO2 in air. It has been demonstrated that sensitization with type II heterostructure ZnSe@CdS with staggered gap provides the rapid growth of effective photoresponse with the increase in the NO2 concentration in air and the highest sensor sensitivity toward NO2. We believe that the use of core-shell QDs with spatial charge separation opens new possibilities in the development of light-activated gas sensors working without thermal heating.

Abstract: Reaction of the n = 1 Ruddlesden-Popper oxide LaSr3CoRuO8 with CaH2 yields the oxyhydride phase LaSr3CoRuO4H4 via topochemical anion-exchange. Close inspection of X-ray and neutron powder diffraction data in combination with HAADF-STEM images reveals that nanoparticles of SrO are exsolved from the system during the reaction, with the change in cation stoichiometry accommodated by the inclusion of n > 1 (Co/Ru)nOn+1H2n ‘perovskite’ layers into the Ruddlesden-Popper stacking sequence. This novel pseudo-topochemical process offers a new route for the formation of n > 1 Ruddlesden-Popper structured materials. Magnetization data are consistent with a LaSr3Co1+Ru2+O4H4 (Co1+, d8, S = 1; Ru2+, d6, S = 0) oxidation/spin state combination. Neutron diffraction and μ+SR data show no evidence for long-range magnetic order down to 2 K, suggesting the diamagnetic Ru2+ centers impede the Co-Co magnetic exchange interactions.