Abstract: Strain is an important method to tune the properties of topological insulators. For example, compressive strain can induce superconductivity in Bi2Se3 bulk material. Topological insulator nanostructures are the superior candidates to utilize the unique surface states due to the large surface to volume ratio. Therefore, it is highly desirable to monitor the local strain effects in individual topological insulator nanostructures. Here, we report the systematical micro-Raman spectra of single strained Bi2Se3 nanoribbons with different thicknesses and different surface facets, where four optical modes are resolved in both Stokes and anti-Stokes Raman spectral lines. A striking anisotropy of the strain dependence is observed in the phonon frequency of strained Bi2Se3 nanoribbons grown along the ⟨112̅0⟩ direction. The frequencies of the in-plane Eg2 and out-of-plane A1g1 modes exhibit a nearly linear blue-shift against bending strain when the nanoribbon is bent along the ⟨112̅0⟩ direction with the curved {0001} surface. In this case, the phonon deformation potential of the Eg2 phonon for 100 nm-thick Bi2Se3 nanoribbon is up to 0.94 cm–1/%, which is twice of that in Bi2Se3 bulk material (0.52 cm–1/%). Our results may be valuable for the strain modulation of individual topological insulator nanostructures.

Abstract: The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer.

Abstract: Based on first-principles calculations, we study the structural stability of the H and T phases of monolayer MoS2 upon Li doping. Our calculations demonstrate that it is possible to stabilize a distorted T phase of MoS2 over the H phase through adsorption of Li atoms on the MoS2 surface. Through molecular dynamics and phonon calculations, we show that the T phase of MoS2 is dynamically unstable and undergoes considerable distortions. The type of distortion depends on the concentration of adsorbed Li atoms and changes from zigzag-like to diamond-like when increasing the Li doping. There exists a substantial energy barrier to transform the stable H phase to the distorted T phases, which is considerably reduced by increasing the concentration of Li atoms. We show that it is necessary that the Li atoms adsorb on both sides of the MoS2 monolayer to reduce the barrier sufficiently. Two processes are examined that allow for such two-sided adsorption, namely, penetration through the MoS2 layer and diffusion over the MoS2 surface. We show that while there is only a small barrier of 0.24 eV for surface diffusion, the amount of energy needed to pass through a pure MoS2 layer is of the order of similar or equal to 2 eV. However, when the MoS2 layer is covered with Li atoms the amount of energy that Li atoms should gain to penetrate the layer is drastically reduced and penetration becomes feasible.

Abstract: The self-assembly of nanoparticles into clusters and the effect of the different parameters of the competing interaction potential on it are investigated. For a small number of particles, the structural organization of the clusters is almost unaffected by the attractive part of the potential, and for an intermediate number of particles the configuration strongly depends on the strength of it. The cluster size is controlled by the range of the interaction potential, and the structural arrangement is guided by the strength of the potential: i.e., the self-assembled cluster transforms from a faceted configuration at low strength to a spherical shell-like structure at high strength. Nonmonotonic behavior of the cluster size is found by increasing the interaction range. An approximate analytical expression is obtained that predicts the smallest cluster for a specific set of potential parameters. A Mendeleev-like table is constructed for different values of the strength and range of the attractive part of the potential in order to understand the structural ordering of the ground-state configuration of the self-assembled clusters.

Abstract: Recent experimental studies showed that formation of a two-dimensional crystal structure of nitrogenated holey graphene (NHG) is possible. Similar to graphene, NHGs have an atomically thin and strong crystal structure. Using first-principles calculations, we investigate the structural, phononic, and thermal properties of monolayer NHG crystal. Our charge analysis reveals that the charged holey sites of NHG provide a reactive ground for further functionalization by adatoms or molecules. We also found that similar to graphene, the NHG structure has quite high-frequency phonon modes and the presence of nitrogen atoms leads to the emergence of additional vibrational modes. Our phonon analysis reveals the presence of three characteristic Raman-active modes of NHG. Furthermore, the analysis of constant-volume heat capacity showed that the NHG structure has a linear temperature dependence in the low-temperature region. The strong lattice structure and unique thermal properties of the NHG crystal structure are desirable in nanoscale device applications.

Abstract: Technical progress in the fields of X-ray sources, optics and detectors is constantly enhancing the pace of data acquisition in XRF imaging. This enlarges the size of the hyperspectral datasets and the number of their sub-parts. This paper describes the challenges in processing large XRF datasets featuring several million pixels/spectra and the strategies developed to overcome them. During the investigation of historical paintings by scanning macro-XRF the main challenges are the correct identification of all spectral features in a dataset and its timely processing. For the identification of spectral features different approaches are discussed, i.e. the use of sum spectra, maximum pixel spectra and of chi(2)(r) maps. For the time-efficient, artefact-free evaluation of XRF imaging data, different software packages are evaluated and intercompared (AXIL, PyMCA, GeoPIXE and the in-house written datamuncher). The process of data evaluation is illustrated on a large dataset (3.4 MPixels) acquired during the investigation of a version of Caravaggio's Supper at Emmaus (143 x 199.5 cm(2)). This 17th century painting is currently the largest object entirely scanned with macroscopic XRF.

Abstract: Scanning nano-focused X-ray diffraction and high-angle annular dark-field scanning transmission electron microscopy are used to investigate the crystal structure of ramp-edge junctions between superconducting electron-doped Nd1.85Ce0.15CuO4 and superconducting hole-doped La1.85Sr0.15CuO4 thin films, the latter being the top layer. On the ramp, a new growth mode of La1.85Sr0.15CuO4 with a 3.3° tilt of the c-axis is found. We explain the tilt by developing a strain accommodation model that relies on facet matching, dictated by the ramp angle, indicating that a coherent domain boundary is formed at the interface. The possible implications of this growth mode for the creation of artificial domains in morphotropic materials are discussed.

Abstract: A thorough investigation of three-dimensional kagome lattices of group IV elements is performed with first-principles calculations. The investigated kagome lattices of silicon and germanium are found to be of similar stability as the recently proposed carbon kagome lattice. Carbon and silicon kagome lattices are both direct-gap semiconductors but they have qualitatively different electronic band structures. While direct optical transitions between the valence and conduction bands are allowed in the carbon case, no such transitions can be observed for silicon. The kagome lattice of germanium exhibits semimetallic behavior but can be transformed into a semiconductor after compression.

Abstract: Surface chemistry plays a pivotal role in regulating the morphology of nanoparticles, maintaining colloidal stability, and mediating the interaction with target analytes toward practical applications such as surface-enhanced Raman scattering (SERS)-based sensing and imaging. The use of a binary ligand mixture composed of 1,4-benzenedithiol (BDT) and hexadecyltrimethylammonium chloride (CTAC) to provide gold nanostars with long-term stability is reported. This is despite BDT being a bifunctional ligand, which usually leads to bridging and loss of colloidal stability. It is found however that neither BDT nor CTAC alone are able to provide sufficient colloidal and chemical stability. BDT-coated Au nanostars are additionally used as seeds to direct the encapsulation with a gold outer shell, leading to the formation of unusual nanostructures including semishell-coated gold nanostars, which are characterized by high-resolution electron microscopy and electron tomography. Finally, BDT is exploited as a probe to reveal the enhanced local electric fields in the different nanostructures, showing that the semishell configuration provides significantly high SERS signals as compared to other coreshell configurations obtained during seeded growth, including full shells.

Abstract: We study ballistic transport of Dirac fermions in silicene through arrays of barriers, of width d, in the presence of an exchange field M and a tunable potential of height U or depth-U. The spin-and valley-resolved conductances as functions of U or M, exhibit resonances away from the Dirac point (DP) and close to it a pronounced dip that becomes a gap when a critical electric field E-z is applied. This gap widens by increasing the number of barriers and can be used to realize electric field-controlled switching of the current. The spin p(s) and valley p(v) polarizations of the current near the DP increase with Ez or M and can reach 100% for certain of their values. These field ranges widen significantly by increasing the number of barriers. Also, ps and pv oscillate nearly periodically with the separation between barriers or wells and can be inverted by reversing M.

Abstract: Superconducting YBa2Cu3O7-delta (YBCO) films with artificial BaZrO3 (BZO) nanodots were prepared using a chemical solution deposition method involving hybrid solutions composed of trifluoroacetate-based YBCO precursors and reverse micelle stabilized BZO nanoparticle dispersions. Microemulsion-mediated synthesis was used to obtain nano-sized (similar to 12 nm) and mono-dispersed BZO nanoparticles that preserve their features once introduced into the YBCO solution, as revealed by dynamic light scattering. Phase pure, epitaxial YBCO films with randomly oriented BZO nanodots distributed over their whole microstructure were grown from the hybrid solutions on (100) LaAlO3 substrates. The morphology of the YBCO-BZO nanocomposite films was strongly influenced by the amount of nanoparticles incorporated into the system, with contents ranging from 5 to 40 mol%. Scanning electron microscopy showed a high density of isolated second-phase defects consisting of BZO nanodots in the nanocomposite film with 10 mol% of BZO. Furthermore, a direct observation and quantitative analysis of lattice defects in the form of interfacial edge dislocations directly induced by the BZO nanodots was evidenced by transmission electron microscopy. The superconducting properties (77 K) of the YBCO films improved considerably by the presence of such nanodots, which seem to enhance the morphology of the sample and therefore the intergranular critical properties. The incorporation of preformed second-phase defects (here, BZO) during the growth of the superconducting phase is the main innovation of this novel approach for the all-solution based low-cost fabrication of long-length coated conductors.

Abstract: Oxidative deintercalation of copper ions from the sulfide layers of the layered mixed-valent manganite oxide sulfide Sr2MnO2Cu1.5S2 results in control of the copper-vacancy modulated superstructure and the ordered arrangement of magnetic moments carried by the manganese ions. This soft chemistry enables control of the structures and properties of these complex materials which complement mixed-valent perovskite and perovskite-related transition metal oxides. (C) 2015 Author(s).

Abstract: Many microscopic investigations of materials may benefit from the recording of multiple successive images. This can include techniques common to several types of microscopy such as frame averaging to improve signal-to-noise ratios (SNR) or time series to study dynamic processes or more specific applications. In the scanning transmission electron microscope, this might include focal series for optical sectioning or aberration measurement, beam damage studies or camera-length series to study the effects of strain; whilst in the scanning tunnelling microscope, this might include bias-voltage series to probe local electronic structure. Whatever the application, such investigations must begin with the careful alignment of these data stacks, an operation that is not always trivial. In addition, the presence of low-frequency scanning distortions can introduce intra-image shifts to the data. Here, we describe an improved automated method of performing non-rigid registration customised for the challenges unique to scanned microscope data specifically addressing the issues of low-SNR data, images containing a large proportion of crystalline material and/or local features of interest such as dislocations or edges. Careful attention has been paid to artefact testing of the non-rigid registration method used, and the importance of this registration for the quantitative interpretation of feature intensities and positions is evaluated.

Abstract: The effect of the number of stacking layers and the type of stacking on the electronic and optical properties of bilayer and trilayer black phosphorus are investigated by using first-principles calculations within the framework of density functional theory. We find that inclusion of many-body effects (i.e., electron-electron and electron-hole interactions) modifies strongly both the electronic and optical properties of black phosphorus. While trilayer black phosphorus with a particular stacking type is found to be a metal by using semilocal functionals, it is predicted to have an electronic band gap of 0.82 eV when many-body effects are taken into account within the G(0)W(0) scheme. Though different stacking types result in similar energetics, the size of the band gap and the optical response of bilayer and trilayer phosphorene are very sensitive to the number of layers and the stacking type. Regardless of the number of layers and the type of stacking, bilayer and trilayer black phosphorus are direct band gap semiconductors whose band gaps vary within a range of 0.3 eV. Stacking arrangements that are different from the ground state structure in both bilayer and trilayer black phosphorus exhibit significant modified valence bands along the zigzag direction and result in larger hole effective masses. The optical gap of bilayer (trilayer) black phosphorus varies by 0.4 (0.6) eV when changing the stacking type. The calculated binding energy of the bound exciton hardly changes with the type of stacking and is found to be 0.44 (0.30) eV for bilayer (trilayer) phosphorous.