Abstract: We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series.

Abstract: Directed assembly of gold nanorods through the use of dithiolated molecular linkers is one of the most efficient methodologies for the morphologically controlled tip-to-tip assembly of this type of anisotropic nanocrystals. However, in a direct analogy to molecular polymerization synthesis, this process is characterized by difficulties in chain-growth control over nanoparticle oligomers. In particular, it is nearly impossible to favor the formation of one type of oligomer, making the methodology hard to use for actual applications in nanoplasmonics. We propose here a light-controlled synthetic procedure that allows obtaining selected plasmonic oligomers in high yield and with reaction times in the scale of minutes by irradiation with low fluence near-infrared (NIR) femtosecond laser pulses. Selective inhibition of the formation of gold nanorod n-mers (trimers) with a longitudinal localized surface plasmon in resonance with a 800 nm Ti:sapphire laser, allowed efficient trapping of the (n – 1)-mers (dimers) by hot spot mediated photothermal decomposition of the interparticle molecular linkers. Laser irradiation at higher energies produced near-field enhancement at the interparticle gaps, which is large enough to melt gold nanorod tips, offering a new pathway toward tip-to-tip welding of gold nanorod oligomers with a plasmonic response at the NIR. Thorough optical and electron microscopy characterization indicates that plasmonic oligomers can be selectively trapped and welded, which has been analyzed in terms of a model that predicts with reasonable accuracy the relative concentrations of the main plasmonic species.

Abstract: Introducing artificial pinning centers is a well established strategy to trap quantum vortices and increase the maximal magnetic field and applied electric current that a superconductor can sustain without dissipation. In case of spatially periodic pinning, a clear enhancement of the superconducting critical current arises when commensurability between the vortex configurations and the pinning landscape occurs. With recent achievements in (ultrafast) optics and nanoengineered plasmonics it has become possible to exploit the interaction of light with superconductivity, and create not only spatially periodic imprints on the superconducting condensate, but also temporally periodic ones. Here we show that in the latter case, temporal matching phenomena develop, caused by stroboscopic commensurability between the characteristic frequency of the vortex motion under applied current and the frequency of the dynamic pinning. The matching resonances persist in a broad parameter space, including magnetic field, driving current, or material purity, giving rise to unusual features such as externally variable resistance/impedance and Shapiro steps in current-voltage characteristics. All features are tunable by the frequency of the dynamic pinning landscape. These findings open further exploration avenues for using flashing, spatially engineered, and/or mobile excitations on superconductors, permitting us to achieve advanced functionalities.

Abstract: Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.

Abstract: The crystal structure of the K6.4Nb28.2Ta8.1O94 pseudo-tetragonal tungsten bronze-type oxide was determined using a combination of X-ray powder diffraction, neutron diffraction and transmission electron microscopy techniques, including electron diffraction, high angle annular dark field scanning transmission electron microscopy (HAADF-STEM), annular bright field STEM (ABF-STEM) and energy-dispersive X-ray compositional mapping (STEM-EDX). The compound crystallizes in the space group Pbam with unit cell parameters a = 37.468(9) A, b = 12.493(3) A, c = 3.95333(15) A. The structure consists of corner sharing (Nb,Ta)O6 octahedra forming trigonal, tetragonal and pentagonal tunnels. All tetragonal tunnels are occupied by K(+) ions, while 1/3 of the pentagonal tunnels are preferentially occupied by Nb(5+)/Ta(5+) and 2/3 are occupied by K(+) in a regular pattern. A fractional substitution of K(+) in the pentagonal tunnels by Nb(5+)/Ta(5+) is suggested by the analysis of the HAADF-STEM images. In contrast to similar structures, such as K2Nb8O21, also parts of the trigonal tunnels are fractionally occupied by K(+) cations.

Abstract: Lithium-ion (Li-ion) batteries that rely on cationic redox reactions are the primary energy source for portable electronics. One pathway toward greater energy density is through the use of Li-rich layered oxides. The capacity of this class of materials (>270 milliampere hours per gram) has been shown to be nested in anionic redox reactions, which are thought to form peroxo-like species. However, the oxygen-oxygen (O-O) bonding pattern has not been observed in previous studies, nor has there been a satisfactory explanation for the irreversible changes that occur during first delithiation. By using Li2IrO3 as a model compound, we visualize the O-O dimers via transmission electron microscopy and neutron diffraction. Our findings establish the fundamental relation between the anionic redox process and the evolution of the O-O bonding in layered oxides.

Abstract: We study the effects of the rippling of a graphene sheet on quasiparticle dispersion. This is achieved using a generalization to the honeycomb lattice of the momentum average approximation, which is accurate for all coupling strengths and at all energies. We show that even though the position of the Dirac points may move and the Fermi speed can be renormalized significantly, quasiparticles with very long lifetimes survive near the Dirac points even for very strong couplings.

Abstract: We performed single particle deformation experiments on silica-coated gold nanorods under femtosecond (fs) illumination. Changes in the particle shape were analyzed by electron microscopy and associated changes in the plasmon resonance by electron energy loss spectroscopy. Silica-coated rods were found to be more stable compared to uncoated rods but could still be deformed via an intermediate bullet-like shape for silica shell thicknesses of 14 nm. Changes in the size ratio of the rods after fs-illumination resulted in blue-shifting of the longitudinal plasmon resonances. Two-dimensional spatial mapping of the plasmon resonances revealed that the flat side of the bullet-like particles showed a less pronounced longitudinal plasmonic electric field enhancement. These findings were confirmed by finite-difference time-domain (FDTD) simulations. Furthermore, at higher laser fluences size reduction of the particles was found as well as for particles that were not completely deformed yet.

Abstract: The effect of an electron-hole puddle on the electrical transport when governed by snake states in a bipolar graphene structure is investigated. Using numerical simulations we show that information on the size and position of the electron-hole puddle can be obtained using the dependence of the conductance on magnetic field and electron density of the gated region. The presence of the scatterer disrupts snake state transport which alters the conduction pattern. We obtain a simple analytical formula that connects the position of the electron-hole puddle with features observed in the conductance. The size of the electron-hole puddle is estimated from the magnetic field and gate potential that maximizes the effect of the puddle on the electrical transport.

Abstract: Fulfillment of the promise of transparent electronics has been hindered until now largely by the lack of semiconductors that can be doped p-type in a stable way, and that at the same time present high hole mobility and are highly transparent in the visible spectrum. Here, a high-throughput study based on first-principles methods reveals four oxides, namely X2SeO2, with X = La, Pr, Nd, and Gd, which are unique in that they exhibit excellent characteristics for transparent electronic device applications – i.e., a direct band gap larger than 3.1 eV, an average hole effective mass below the electron rest mass, and good p-type dopability. Furthermore, for La2SeO2 it is explicitly shown that Na impurities substituting La are shallow acceptors in moderate to strong anion-rich growth conditions, with low formation energy, and that they will not be compensated by anion vacancies VO or VSe.

Abstract: Studying protein interactions is of vital importance both to fundamental biology research and to medical applications. Here, we report on the experimental proof of a universally applicable label-free homogeneous platform for rapid protein analysis. It is based on optically detecting changes in the rotational dynamics of magnetically agitated core-shell nanorods upon their specific interaction with proteins. By adjusting the excitation frequency, we are able to optimize the measurement signal for each analyte protein size. In addition, due to the locking of the optical signal to the magnetic excitation frequency, background signals are suppressed, thus allowing exclusive studies of processes at the nanoprobe surface only. We study target proteins (soluble domain of the human epidermal growth factor receptor 2 – sHER2) specifically binding to antibodies (trastuzumab) immobilized on the surface of our nanoprobes and demonstrate direct deduction of their respective sizes. Additionally, we examine the dependence of our measurement signal on the concentration of the analyte protein, and deduce a minimally detectable sHER2 concentration of 440 pM. For our homogeneous measurement platform, good dispersion stability of the applied nanoprobes under physiological conditions is of vital importance. To that end, we support our measurement data by theoretical modeling of the total particle-particle interaction energies. The successful implementation of our platform offers scope for applications in biomarker-based diagnostics as well as for answering basic biology questions.

Abstract: The n = 3-6 members of a new perovskite-based homologous series Bi(3n+1)Ti7Fe(3n-3)O(9n+11) are reported. The crystal structure of the n = 3 Bi10Ti7Fe6O38 member is refined using a combination of X-ray and neutron powder diffraction data (a = 11.8511(2) A, b = 3.85076(4) A, c = 33.0722(6) A, S.G. Immm), unveiling the partially ordered distribution of Ti(4+) and Fe(3+) cations and indicating the presence of static random displacements of the Bi and O atoms. All Bi(3n+1)Ti7Fe(3n-3)O(9n+11) structures are composed of perovskite blocks separated by translational interfaces parallel to the (001)p perovskite planes. The thickness of the perovskite blocks increases with n, while the atomic arrangement at the interfaces remains the same. The interfaces comprise chains of double edge-sharing (Fe,Ti)O6 octahedra connected to the octahedra of the perovskite blocks by sharing edges and corners. This configuration shifts the adjacent perovskite blocks relative to each other over a vector (1/2)[110]p and creates S-shaped tunnels along the [010] direction. The tunnels accommodate double columns of the Bi(3+) cations, which stabilize the interfaces owing to the stereochemical activity of their lone electron pairs. The Bi(3n+1)Ti7Fe(3n-3)O(9n+11) structures can be formally considered either as intergrowths of perovskite modules and polysynthetically twinned modules of the Bi2Ti4O11 structure or as intergrowths of the 2D perovskite and 1D anatase fragments. Transmission electron microscopy (TEM) on Bi10Ti7Fe6O38 reveals that static atomic displacements of Bi and O inside the perovskite blocks are not completely random; they are cooperative, yet only short-range ordered. According to TEM, the interfaces can be laterally shifted with respect to each other over +/-1/3a, introducing an additional degree of disorder. Bi10Ti7Fe6O38 is paramagnetic in the 1.5-1000 K temperature range due to dilution of the magnetic Fe(3+) cations with nonmagnetic Ti(4+). The n = 3, 4 compounds demonstrate a high dielectric constant of 70-165 at room temperature.

Abstract: Hybrid nanostructures composed of metal nanoparticles and metal-organic frameworks (MOFs) have recently received increasing attention toward various applications due to the combination of optical and catalytic properties of nanometals with the large internal surface area, tunable crystal porosity and unique chemical properties of MOFs. Encapsulation of metal nanoparticles of well-defined shapes into porous MOFs in a core-shell type configuration can thus lead to enhanced stability and selectivity in applications such as sensing or catalysis. In this study, the encapsulation of single noble metal nanoparticles with arbitrary shapes within zeolitic imidazolate-based metal organic frameworks (ZIF-8) is demonstrated. The synthetic strategy is based on the enhanced interaction between ZIF-8 nanocrystals and metal nanoparticle surfaces covered by quaternary ammonium surfactants. High resolution electron microscopy and tomography confirm a complete core-shell morphology. Such a well-defined morphology allowed us to study the transport of guest molecules through the ZIF-8 porous shell by means of surface-enhanced Raman scattering by the metal cores. The results demonstrate that even molecules larger than the ZIF-8 aperture and pore size may be able to diffuse through the framework and reach the metal core.

Abstract: Nanoscale Zr-based metal organic frameworks (MOFs) UiO-66 and UiO-67 were studied as potential anticancer drug delivery vehicles. Two model drugs were used, hydrophobic paclitaxel and hydrophilic cisplatin, and were adsorbed onto/into the nano MOFs (NMOFs). The drug loaded MOFs were further encapsulated inside a modified poly(epsilon-caprolactone) with d-alpha-tocopheryl polyethylene glycol succinate polymeric matrix, in the form of microparticles, in order to prepare sustained release formulations and to reduce the drug toxicity. The drugs physical state and release rate was studied at 37 degrees C using Simulated Body Fluid. It was found that the drug release depends on the interaction between the MOFs and the drugs while the controlled release rates can be attributed to the microencapsulated formulations. The in vitro antitumor activity was assessed using HSC-3 (human oral squamous carcinoma; head and neck) and U-87 MG (human glioblastoma grade IV; astrocytoma) cancer cells. Cytotoxicity studies for both cell lines showed that the polymer coated, drug loaded MOFs exhibited better anticancer activity compared to free paclitaxel and cisplatin solutions at different concentrations.

Abstract: The recent discovery of electron vortex beams carrying quantised angular momentum in the TEM has led to an active field of research, exploring a variety of potential applications including the possibility of mapping magnetic states at the atomic scale. A prerequisite for this is the availability of atomic sized electron vortex beams at high beam current and mode purity. In this paper we present recent progress showing that by making use of the Aharonov-Bohm effect near the tip of a long single domain ferromagnetic Nickel needle, a very efficient aperture for the production of electron vortex beams can be realised. The aperture transmits more than 99% of all electrons and provides a vortex mode purity of up to 92%. Placing this aperture in the condenser plane of a state of the art Cs corrected microscope allows us to demonstrate atomic resolution HAADF STEM images with spatial resolution better than 1 Angstrom, in agreement with theoretical expectations and only slightly inferior to the performance of a non-vortex probe on the same instrument.