FEI Titan G3 50-300 PICO

The FEI Titan G3 50-300 PICO is a unique fourth generation transmission electron microscope which has been specifically designed for the investigation of a wide range of solid state phenomena taking place on the atomic scale and thus necessitating true atomic resolution analysis capabilities. For these purposes, the FEI Titan G3 50-300 PICO is equipped with a Schottky type high-brightness electron gun (FEI X-FEG), a monochromator unit, and a Cs probe corrector (CEOS DCOR), a Cs-Cc achro-aplanat image corrector (CEOS CCOR+), a double biprism, a post-column energy filter system (Gatan Quantum 966 ERS) as well as a 16 megapixel CCD system (Gatan UltraScan 4000 UHS). Characterised by a TEM and STEM resolution well below 50 pm at 200 kV, the instrument is one of the few chromatically-corrected high resolution transmission electron microscopes in the world. Typical examples of use and technical specifications for the instrument are given below

Nanoscale X-ray investigation of magnetic metallofullerene peapods

Endohedral lanthanide ions packed inside carbon nanotubes (CNTs) in a one-dimensional assembly have been studied with a combination of high resolution transmission electron microscopy (HRTEM), scanning transmission X-ray microscopy (STXM), and X-ray magnetic circular dichroism (XMCD). By correlating HRTEM and STXM images we show that structures down to 30 nm are resolved with chemical contrast and record X-ray absorption spectra from endohedral lanthanide ions embedded in individual nanoscale CNT bundles. XMCD measurements of an Er$_3$N@C$_{80}$ bulk sample and a macroscopic assembly of filled CNTs indicates that the magnetic properties of the endohedral Er3+ ions are unchanged when encapsulated in CNTs. This study demonstrates the feasibility of local magnetic X-ray characterization of low concentrations of lanthanide ions embedded in molecular nanostructures

Vacuum Rabi splitting of a dark plasmonic cavity mode revealed by fast electrons

Recent years have seen a growing interest in strong coupling between plasmons and excitons, as a way to generate new quantum optical testbeds and influence chemical dynamics and reactivity. Strong coupling to bright plasmonic modes has been achieved even with single quantum emitters. Dark plasmonic modes fare better in some applications due to longer lifetimes, but are difficult to probe as they are subradiant. Here, we apply electron energy loss (EEL) spectroscopy to demonstrate that a dark mode of an individual plasmonic bowtie can interact with a small number of quantum emitters, as evidenced by Rabi-split spectra. Coupling strengths of up to 85meV place the bowtie-emitter devices at the onset of the strong coupling regime. Remarkably, the coupling occurs at the periphery of the bowtie gaps, even while the electron beam probes their center. Our findings pave the way for using EEL spectroscopy to study exciton-plasmon interactions involving non-emissive photonic modes

Geometric reconstruction methods for electron tomography

Electron tomography is becoming an increasingly important tool in materials science for studying the three-dimensional morphologies and chemical compositions of nanostructures. The image quality obtained by many current algorithms is seriously affected by the problems of missing wedge artefacts and nonlinear projection intensities due to diffraction effects. The former refers to the fact that data cannot be acquired over the full $180^\circ$ tilt range; the latter implies that for some orientations, crystalline structures can show strong contrast changes. To overcome these problems we introduce and discuss several algorithms from the mathematical fields of geometric and discrete tomography. The algorithms incorporate geometric prior knowledge (mainly convexity and homogeneity), which also in principle considerably reduces the number of tilt angles required. Results are discussed for the reconstruction of an InAs nanowire

Line Defects in Molybdenum Disulfide Layers

Layered molecular materials and especially MoS2 are already accepted as promising candidates for nanoelectronics. In contrast to the bulk material, the observed electron mobility in single-layer MoS2 is unexpectedly low. Here we reveal the occurrence of intrinsic defects in MoS2 layers, known as inversion domains, where the layer changes its direction through a line defect. The line defects are observed experimentally by atomic resolution TEM. The structures were modeled and the stability and electronic properties of the defects were calculated using quantum-mechanical calculations based on the Density-Functional Tight-Binding method. The results of these calculations indicate the occurrence of new states within the band gap of the semiconducting MoS2. The most stable non-stoichiometric defect structures are observed experimentally, one of which contains metallic Mo-Mo bonds and another one bridging S atoms

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

Plasmaabscheidung von mikrokristallinem Silizium: Merkmale und Mikrostruktur und deren Deutung im Sinne von Wachstumsvorgängen

The microstructure of microcrystalline silicon ($\mu$c-Si:H) grown in a low-temperature ($\lesssim$ 400 °C) PECVD process was investigated in dependence on the process parameters and the choice of the substrate material. For characterization, Raman spectroscopy, X-ray diffraction, atomic force microscopy and transmission electron microscopy were applied. lt is shown that a stationary growth is observed in the long term structural evolution of the thin films. The characteristics of this stationary growth can be described in relation to the crystallinity of the microcrystalline samples, irrespective of the details of plasma processing and the nature of the substrate. This also applies for the initially homoepitaxial growth on Si(100), which transforms to disordered growth under similar structural changes when compared to low-temperature MBE growth. A catalytic role of hydrogen during grain epitaxy is suggested therefore and existing models for the growth of μc-Si:H are extended in order to explain for the formation of {111} facets, planar defects on {111} planes and a preferred crystallographic orientation. The present study evidences limitations for tailoring the structural properties of $\mu$c-Si:H according to technical demands. E.g. the columnar morphology and the formation of structural defects limit the extent of coherent crystalline domains. Their sizes cannot be influenced significantly by the choice of the plasma parameters and the substrate material