bluuebunny/crossref_metadata_2025 huggingface dataset:
EELS
Observation on Spontaneously Grown Ag@Titanium Oxide Core Shell Nanowires
Authors: Song Jenn‐Ming , Tsai Chi‐Hang , Chen Shih‐Yun , Gloter Alexandre
Published: December 2016

To enhance functionality and usability of 1‐D nanomaterials, the synthesis of composite nanowires such as core‐shell nanowires is a good solution. Ag‐TiO
2
core‐shell nanowires have attracted much attraction, because Ag nanowires have unique properties of high surface plasmon resonance as well as good electrical conductivity, while TiO
2
is an ideal material as photocatalysts. In the absence of oxide precursors, templates, inoculants and surfactants, this study successfully prepared vertical Ag nanowires with a spontaneous ultra‐thin TiO
2
shell (~0.5 nm) on TiO
2
substrate using a one step process. STEM/EELS results demonstrate that this oxygen‐deficient TiO
2
layer is formed through the oxidation of Ti which is released from the substrate and segregated to the nanowire surface simultaneously with crystal growth of the nanowires (Fig. 1). The EELS spectra suggest that the valence of Ti ions in this spontaneous oxide layer is between Ti
3+
and Ti
4+
.
Dislocation and microstructure analysis of tungsten
Authors: Horvath Barbara , Dai Yong , Lee Yongjoong
Published: December 2016

The demand for neutron scattering and imaging techniques for material characterization under controlled conditions is continuously growing over the last couple of years. For such measurements large scale neutron facilities are needed and the European Spallation Source (ESS) will soon be the world's most powerful neutron source, build in Lund, Sweden [1]. Here, neutrons are produced through a spallation process in tungsten, which due to its high atomic number has a high neutron production density and localized neutron production. The use of tungsten avoids issues related to corrosion effects related to water cooling and it is relatively environmentally friendly compared to other target materials. Its disadvantages, however, are its low ductility and a high ductile‐to‐brittle transition temperature. Tungsten is the most critical non‐structural material and its integrity during operation is essential for maintaining helium circulation and retaining of transmutation elements, therefore it must operate reliably and predictably for the planned lifetime of the target. In order to estimate the target life, reliable data is needed on the mechanical properties of tungsten, both in unirradiated and irradiated conditions. Dedicated irradiation programs were established to examine the behavior of tungsten under representative operational conditions, which studies are performed in PSI.

In this current study, in order to evaluate the properties of irradiated tungsten, initially as a comparison we must observe the microstructure and mechanical properties of unirradiated tungsten. Evaluating the microstructure of the unirradiated tungsten material normally would not be complicated; such transmission electron microscopy (TEM) samples can be created relatively easily by cutting 3 mm discs and then thinning them by jet polishing. However, in this case we developed samples in a more complex way, with the use of focused ion beam (FIB) and then flash electrochemical polishing the lamella in order to establish a method where in the future the irradiated tungsten samples can also be examined safely. Thanks to FIB, with the reduction of the sample size the activity of the sample also gets reduced dramatically, ensuring safe handling. The sample is lifted out internally inside the FIB by a micromanipulator and a 8 x 8 μm
2
and 200 nm thick lamella is created. Then, by flash polishing (in 0.5% NaOH, 2 °C) this lamella is more thinned down to the thickness of approx. 60 nm, which is necessary to remove the FIB induced damages on the surface of the lamella. Electron microscopy observation is performed with a JEOL 2010 type TEM operated at 200 keV and equipped with EDX. Bright field (BF and weak‐beam dark field (WBDF) imaging conditions were used at (g, 4g) or (g, 5g), while g=110. In order to obtain quantitative information of the dislocations, they are counted on several low magnification pictures on different areas of the sample.
Low‐loss
STEM
‐
EELS
analysis of beam‐sensitive lithium‐ion negative electrodes
Authors: Boniface Maxime , Quazuguel Lucille , Moreau Philippe , Boucher Florent , Guyomard Dominique , Bayle‐Guillemaud Pascale
Published: December 2016

Silicon represents one of the most promising anode materials for next generation lithium‐ion batteries. However its colossal volume expansion (up to 300%) upon electrochemical reaction with lithium repeatedly exposes fresh surfaces to electrolyte solvent oxidation
1‐2
. This leads to very high irreversible capacities, compounded by the fact that parts of the silicon‐based electrodes are progressively disconnected from both electrical and ionic transport networks as the solid electrolyte interface (SEI) accumulates. Deeper insight into these degradation phenomena is critical to engineer adequate electrodes and/or electrolytes.

Characterization of these electrodes has so far mostly focused on either bulk or surface analysis, both lacking spatial resolution. Little is known about the SEI's morphology in silicon nanoparticles (SiNPs) aggregates that make the electrode, or about the evolution of these nanoparticles themselves with cycling. Attempts to characterize this system through electron microscopy have been severely limited by the radiolysis and sputtering damage, respectively, undergone by the SEI and lithium‐silicon alloys (Li
x
Si).

In this work we demonstrate the possibility to map major SEI and electrode components such as lithium carbonate (Li
2
CO
3
), lithium fluoride (LiF) and lithium oxide (Li
2
O) as well as quantifying lithium‐silicon alloys compositions
4
and Si crystallinity from a single dataset by combining scanning transmission electron microscopy and low‐loss electron energy loss spectroscopy
5
(STEM‐EELS) (fig. 1). The low‐loss part of the EEL spectrum is considerably more intense than its high energy counterpart and contains both the Li K‐edge and plasmons. Fine tuning of the experimental parameters allows us to acquire low‐loss spectrum images with good signal‐noise ratios within timeframes compatible with minimal sample degradation. Plasmons can then either be used as unique molecular signatures for the SEI, or directly for quantification in the case of Li
x
Si compounds (fig. 2 inset). This can yield unique insight into electrode degradation phenomena through careful data processing (MLLS, Drude model fit…). Large spectrum images can be acquired within short timeframes (~10 ms/voxel), making this method a powerful and practical diagnostics tool for battery electrodes and other beam‐sensitive nanostructured systems.

Results on electrodes disassembled from full cells at their 1
st
, 10
th
and 100
th
charge and discharge, with a limited capacity of 1200 mAh/g, shed light on the SEI's deposition mechanism and morphological as well as chemical evolution along cycling for different electrolytes. Strong correlations were observed between the SEI's local chemistry and our nanoparticles cycling performance (fig. 2). Lithiation was also observed to proceed preferentially along grain boundaries, resulting in different behaviours between mono‐ and polycrystalline silicon powders.
Single particle
EM
study of the E1 helicase from Papillomavirus in complex with
DNA
Authors: Coscia Francesca , Ryzhenkova Ksenia , Chaban Yurij , Sanders Cyril , Orlova Elena V
Published: December 2016

The papillomaviruses (PV) are small dsDNA tumour viruses of significant medical importance and the prototype of the group is bovine PV (BPV‐1). PVs encode one highly conserved replication enzyme, E1, that acts as an initiator and a helicase. E1 forms hexamers and unwinds double stranded DNA (dsDNA) into single stranded DNA (ssDNA) products using the energy of ATP hydrolysis. However, how the helicase engages the replication fork at the molecular level is unclear. BPV‐1 E1 is comprised of four domains: a regulatory domain (residues 1‐158), a sequence specific
ori
DNA binding domain (OBD, residues 159‐299) and the C‐terminal half (residues 300‐605, E1HD) that has helicase activity and is further divided into the oligomerisation domain (OD, residues 308‐378) and the AAA+ ATP
ase
domain. A C‐terminal acidic tail domain (AT, residues 579‐605) is required for helicase processivity (Figure A). We have obtained structures of the full length E1 helicase (E1FL) in complex with a DNA replication fork with and without DNA labelling with protein tags. The 5’ end of dsDNA and the 5’ ssDNA end of the fork were labelled and helicase structures studied using single particle electron microscopy.

Negatively stained images (with 2% uranyl acetate) of E1FL/DNAfork/Fab /Streptavidin were taken and the structure obtained at a resolution of~ 20 Å (Figure B). We are currently working on the native structure by cryoEM (Figure C). The 3D reconstruction of E1FL (Figure D) has a three‐tier organisation with well‐defined domains (N‐terminal, DBD, OD, and AAA+). Domains were localised by docking of available atomic structures. The 3D structure of the E1/ labelled DNA fork confirmed the triple ring organisation with an internal small chamber above the helicase motor domain where DNA unwinding appears to take place. Interestingly, dsDNA enters into the chamber via a side tunnel above the helicase motor domain, with the 5́‐ssDNA strand leaving through a narrow tunnel located on the opposite side, while the 3́‐ssDNA is pulled through the hexamer's central tunnel (Figure D). Our findings are confirmed by DNA footprint experiments and FRET experiments. Recently we analysed a cryoEM structure of the E1FL in complex with a DNA fork at subnanometer resolution that reveals the same structural organization and provides more detail on the interaction with DNA.

Our structural studies demonstrate that the process of DNA separation takes place inside the E1FL complex rather than on the exterior surface of E1. In the light of our results we suggest that the current ‘steric exclusion’ model for strand separation should be revised. A molecular understanding of E1 function will be essential to shed light on the early phase of DNA replication and will assist in the understanding of E1 as a therapeutic target of viral DNA replication.
High resolution
EDS
study of Ba2Y1+xNb1‐xO6‐δ sintered compounds
Authors: Hassine Mohamed Ben , Iakovleva Anastasia , Ashtiani Paul Haghi , Dezanneau Guilhem
Published: December 2016

We present here the study of Ba
2
Y
1+x
Nb
1‐x
O
6‐δ
(x = 0, 0.05, 0.1, 0.15, 0.2) compounds with potential application as ion‐conducting materials in Solid Oxide Fuel Cells and/or Proton Conducting Fuel Cells. Yttrium is used here as an acceptor‐doping element in substitution to niobium to create oxygen vacancies by charge compensation. Nanopowders have been prepared by a freeze‐drying route and dense ceramics were obtained after shaping and treatment at high temperature. X‐ray diffraction analysis shows that single phase compounds are obtained for
x
values equal or below 0.2. Transport properties indicate that, in spite of a significant concentration of oxygen vacancies, the ion conductivity remains low in oxidative atmosphere. A higher conductivity is observed in humidified hydrogen showing that the material gets partially reduced in such conditions.

High resolution STEM images and EDS chemical mapping show very well order of Y and Nb in Ba
2
YNbO
6
compound (x = 0), however when x = 0.1 a pronounced cationic exchange is observed between Y and Nb (Figure 1). Based on these results and Molecular Dynamics calculations, we noticed that the Y on Nb site induce an oxygen vacancies created by Yttrium doping. When the doping level is low, a long range diffusion would suppose that oxygen vacancies also locate close to Niobium atoms which does not seem to be possible in this material. Thus, the only way for oxygen vacancies to participate to long range ion diffusion is to percolate from a site close to a Y dopant to another site close to a Y dopant.

These results were presented at an international conference EMRS Warsaw (2015) and gave rise to a publication that is being prepared.
Defects and strain analysis of
GaAs/Si
nanostructures from high‐resolution
HAADF‐STEM
images
Authors: Kozak Roksolana , Prieto Ivan , Skibitzki Oliver , Dasilva Yadira Arroyo‐Rojas , Rossell Marta , Erni Rolf , Schroeder Thomas , von Känel Hans
Published: December 2016

The increasing demand for high‐performance, ultra‐small size electronics and photonics requires the development of new nanostructured materials. Promising candidates for this purpose are monolithically integrated GaAs nanocrystals, selectively grown by metal organic vapor phase epitaxy (MOVPE), on top of Si nano‐tips and nano‐pillars (Fig. 1,2) with ~ 60 nm and ~ 40 nm diameter, respectively. Growth on substrate nanopatterns eliminates threading dislocations similar to “aspect ratio trapping” in submicron trenches and pits [1]. It may even prevent plastic strain relaxation by misfit dislocations in contrast to the growth of thin films on planar substrates by taking advantage of the compliant substrate effects [2]. Consequently, it is important to study the local atomic defects at the GaAs/Si interface and their evolution with changing shape/size of the substrate pattern, and to analyze the residual elastic strain of the grown crystals by means of the scanning transmission electron microscopy (STEM) technique in order to find the maximum crystal size below which elastic relaxation is favorable.

STEM investigation of the GaAs/Si nanostructures has been performed on lamellas prepared by focused ion beam (FIB). From the analysis of aberration‐corrected high‐resolution high‐angle annular dark‐field (HAADF) STEM images the presence of 60º misfit dislocations (MDs), as well as 90º and 30º Shockley misfit partial dislocations (MPDs) at the GaAs/(001)Si tip interface has been revealed (Fig. 3). The latter generate extrinsic and intrinsic stacking faults, respectively, which propagate through the entire crystal. Gliding of a group of 30º Shockley MPDs along parallel successive slip planes produces a nanotwin. In the GaAs crystals grown on (001) Si pillars two intrinsic stacking faults, lying in {111}‐type planes, meet at the interface and build a V‐shaped defect (Fig. 4). According to the literature [3], such V‐shaped configuration of stacking faults suggests their formation upon island coalescence. These stacking faults border at the interface a stair‐rod dislocation, which is formed by the interaction of two 30º Shockley MPDs located in the Si pillar. Among the observed defects, the most efficient ones for relaxing misfit strain are 60º MDs, whereas 30º MPDs release strain only partially. Geometrical phase analysis (GPA) [4] has been also applied to estimate the misfit strain in the GaAs crystals.
Investigation of pristine Li1.2Ni0.13Mn0.56Co0.13O2 by advanced
TEM
Authors: Wiktor Christian , Liu Hanshuo , Jiang Meng , Wu Yan , Yang Xingyi Yang , Botton Gianluigi A.
Published: December 2016

Layered Li‐transition metal (TM) oxides are very promising materials for new Li ion battery cathodes. Compounds with an increased content of Li and Mn are particularly interesting because they exhibit a high capacity of 200‐300 mAhg
−1
even after an initial drop in capacity during the first charging cycle.[1] The structure of such compounds and their capacity degradation over multiple cycles is not fully understood due to the complexity of the crystallographic phases, the ambiguities in the diffraction data and the presence of additional phases.

The investigated compound Li
1.2
Ni
0.13
Mn
0.56
Co
0.13
O
2
is derived from LiNi
0.33
Mn
0.33
Co
0.33
O
2
, (NMC). Due to the higher capacity of the Li‐rich compound, it will be referred to as high energy NMC (HENMC).[2] The chemical formula of HENMC can be rewritten as Li
2
MnO
3
· LiNi
0.33
Mn
0.33
Co
0.33
O
2
which implies that this compound is a mixture of trigonal NMC and monoclinic Li
2
MnO
3
. In NMC, there are two different cation layers which are exclusively occupied by Li and TM respectively. In Li
2
MnO
3
one third of the TM sites are occupied by Li. HENMC must be either a phase mixture with distinct domains of the two oxides or a solid solution of the two, with “Li rich” positions in the TM layers and an overall reduced, monoclinic symmetry (Figure 1).[3] The exact nature of HENMC and similar materials is crucial to understand the de‐lithiation processes during charging cycles.

The layered structure and its relation to other phases was investigated with a combination of electron diffraction in bright‐field and scanning modes with high resolution transmission electron microscopy (HRTEM) and high‐angle annular dark‐field scanning TEM (HAADF‐STEM) imaging. Due to the high structural similarity of NMC and Li
2
MnO
3
, all lattice distances which can be found for NMC can also be found for Li
2
MnO
3
; as seen in the respective electron diffraction patterns (Figure 2). HAADF‐STEM imaging reveals the presence of Li‐rich positions in the TM layers as indicated by a lower intensity of the related atom columns (Figure 3). Due to the stacking faults of the TM layers, the interpretation of contrast in any other orientation becomes by far less intuitive as we will demonstrate. A LiTM
2
O
4
spinel phase is found on the surface quite frequently. Its relation to the bulk phase was derived from high resolution images. STEM‐EELS revealed the presence of surface reduction due to oxygen depletion in HENMC.

This work thus provides structural information about the synthesized material in its pristine state to facilitate understanding the changes the material undergoes during the (de‐)lithiation segments of electrochemical cycling. Further investigations on such effects are currently being carried out and will be discussed.
Optimizing electron channeling contrast imaging condition in scanning electron microscope
Authors: Han Luyang , Gamm Bjoern
Published: December 2016

The electron channeling contrast imaging (ECCI) is a technique that makes use of the influence of back scattered electrons (BSE) by the relative orientation of crystalline lattice and incident electron beam [1]. The ECCI in scanning electron microscope (SEM) is especially useful to image the crystallographic defects such as dislocations, stacking faults and twin boundaries [2]. In this contribution the amount of channeling contrast in the total BSE signal is quantified and its dependence on different working conditions is explored.

An example of the ECCI on an epitaxial GaN thin film is shown in Figure 1. The sample is investigated using ZEISS GeminiSEM 500 FE‐SEM with a PIN‐diode BSE detector under the objective lens. By adjusting the strength of the scanning coil it is possible to move the pivot point of scanning electron down to the surface of the sample, forming the selected area channeling pattern (SACP) [1]. The intensity variation of BSE signal can be extracted by the line profile across the Kikuchi line, shown as the red dotted line in the figure. The relative variation of BSE signal in SACP with respect to average signal can thus be used as a quantification of channeling contrast.

The amount of channeling contrast is influenced by the properties of incident electron beam and the detector. In principle, the energy and convergence angle of the incident electron beam determines the channeling pattern itself, while the position and energy response of the detector influence the amount of channeling contrast. In this study a large parameter space is explored to optimize the channeling contrast, including electron beam energy, working distance, convergence angle and position of detectors. As an example, the influence of electron beam energy to channeling contrast is summarized in Figure 2. The SACPs are shown in the right part of the figure. The position of the lines as well as intensity variations within the pattern changes significantly between different energies. However, quantification of the channeling contrast shows a clear trend of increasing channeling contrast at lower electron beam energy.
In‐situ electrical measurements of Graphene Nanoribbons fabricated through Scanning Transmission Electron Microscopy
Authors: Vicarelli Leonardo , Heerema Stephanie J. , Dekker Cees , Zandbergen Henny
Published: December 2016

We recently demonstrated a controllable and reproducible method to obtain suspended monolayer graphene nanoribbons with atomically defined edge shape [1]. Our method exploits the electron‐beam of a Scanning Transmission Electron Microscope (accelerated at 300 kV) to create vacancies in the lattice by knock‐on damage and pattern graphene in any designed shape. The small beam spot size (0.1 nm) enables close‐to‐atomic cutting precision, while heating graphene at 900 K during the patterning process avoids formation of beam‐induced Carbon deposition and allows self‐repair of the graphene lattice. Self‐repair mechanism is essential to obtain well‐defined (zig‐zag or armchair) edge shape and, if the electron beam dose is lowered, to perform non‐destructive imaging of the graphene nanoribbons.

Drawing the electron‐beam path with a software script, we were able to obtain reproducible graphene nanoribbons with sub 10 nm width. Using an in‐house built microscopy holder equipped with electrical feedthroughs, we performed 2 and 4 wire measurements on several graphene nanoribbons, with different number of layers. Wide nanoribbons (width> 50 nm) exhibited ohmic behaviour, with conductivity linearly proportional to the width. Narrower ribbons (10 nm < width < 50 nm) displayed non‐linear current‐voltage (IV) relationship at low temperature (4 K, ex‐situ), possibly indicating the opening of a band gap. The narrowest ribbon was 1.5 nm wide, with strong non‐linear IV also at room temperature.

Electrical measurements were also performed in the high temperature range (300 K – 900 K), from which we concluded that thermal generated carriers give the main contribution to electrical conductivity above room temperature.
Electron tomography with sub‐5‐second temporal resolution for dynamic in situ transmission electron microscopy
Authors: Migunov Vadim , Leary Rowan K. , de la Mata María , Russo‐Averchi Eleonora , Tütüncüoglu Gözde , Morral Anna Fontcuberta i , Arbiol Jordi , Dunin‐Borkowski Rafal E.
Published: December 2016

Electron tomography (ET) is an important technique for the study of the three dimensional morphology, structure and chemical composition of nanoscale materials in the transmission electron microscope (TEM). Although ET is potentially a powerful tool for
in situ
three‐dimensional TEM studies of catalytic reactions, growth processes, phase transformations, switching mechanisms and defect nucleation, motion and interactions, its application to dynamic experiments has been limited, since typical acquisition times for tilt series are typically tens of minutes or longer [1].

We have recently demonstrated the rapid acquisition of a tomographic tilt series comprising approximately 3500 images between +30° and −70° in only 3.5 s, as shown in Fig. 1) [2]. Here, we apply the technique to the three‐dimensional imaging of the thermal segregation of an InAs V‐shaped nanomembrane [3]. The membrane was heated
in situ
in an FEI Titan TEM up to a temperature of 420 °C. Changes in membrane morphology were tracked by acquiring images on a Gatan K2‐IS camera at 400 frames per second while continuously tilting the specimen between +60° and −65°. Each tilt series (i.e., one rotation in one direction) was acquired in approximately 4.3 s and comprised ~1700 frames. Selected frames are shown in Figs 2 and 3.

The reconstruction of time‐dependent (four‐dimensional) tilt series can be performed using two approaches: i) Reconstruction of each individual tilt series and interpolation between each reconstruction in the time domain, resulting in a time resolution that is limited by the acquisition time for each tilt series (i.e., 4.3 s); ii) Model‐based reconstruction, involving tracking of changes between individual frames within each tilt series, resulting in sub‐second temporal resolution. We are presently pursuing both approaches.

We are grateful to Cory Czarnik and Ana Pakzad from Gatan Inc. for making the K2 IS camera available for the experiments and to the European Research Council for an Advanced Grant.
Visualization of aligned collagen fibrils in cartilage by second harmonic generation microscopy
Authors: Finnøy Andreas , Olstad Kristin , Lilledahl Magnus
Published: December 2016

Articular cartilage is located at the bone ends in synovial joints and enables smooth and pain‐free joint motion. Its function is in large part determined by a network of collagen fibrils organized into zones and compartments, but little is known about how this organization is achieved in growing animals [1]. The articular cartilage develops superficially to a layer of temporary growth cartilage. The growth cartilage is responsible for the expansion of the bone ends and is replaced by bone during growth. The interface between the immature articular cartilage and the growth cartilage is histologically indistinguishable [2]. On the other hand, aligned collagen fibrils encapsulate cells in the articular cartilage but not in the growth cartilage, so the immature articular cartilage and the growth cartilage can be distinguished by locating these fibrils with transmission electron microscopy (TEM) in growing animals [1]. However, TEM requires extensive sample preparation and has limited field of view.

Second harmonic generation (SHG) microscopy is a promising image modality that is highly specific to collagen fibrils without any staining [3]. SHG is a coherent nonlinear optical process that is specific for non‐centrosymmetric structures such as collagen fibrils and is characterized by frequency‐doubling of light. In contrast to fluorescence, the SHG intensity and radiation direction is highly sensitive to the arrangement of collagen fibrils. In addition, as the arrangement of fibrils can vary at different length scales, this sensitiveness can depend on the size of the focal volume.

The aim of this study was to examine if the aligned fibrils encapsulating cells could be visualized by SHG microscopy without any staining in order to locate the immature articular cartilage of a growing animal.

The cartilage located at the distal femur of growing piglets was imaged by detecting the forward and backward directed SHG. Focusing objectives with different numerical aperture (NA), i.e. focal volume, were used to examine the collagen fibrils at different length scales. The results demonstrated that the ratio of forward to backward SHG was dependent on the NA and that the dependence on the NA varied with distance from the articular surface (Figure 1). The high forward to backward ratio at low NA near the articular surface (Figure 2) was interpreted to represent the aligned fibrils characterizing the articular cartilage. The gradual transition between the immature articular cartilage and the growth cartilage was therefore clearly visualized by SHG, and SHG microscopy is therefore a promising technique to study the development of the collagen matrix in articular cartilage.
Decontamination capacity of a fish after trophic contamination with gold nanoparticules: ultrastructural study
Authors: Mesmer‐Dudons Nathalie , Chongaud Aurore , Mornet Stephane , Feurtet‐Mazel Agnès , Maury‐Brachet Régine , Baudrimont Magalie
Published: December 2016

Nanomaterials represent today a major economic and technological issue, because of their innovating properties rising from their nanometric size (1 to 100 nm) and in particular of their chemical compositions, sizes, specific surfaces and varied surface qualities. These nanomaterials are present in sectors as varied as building, car industry, chemistry, energy or health, and therefore can be found in natural ecosystems without knowing yet their potential impacts.

In this context, trophic transfer of gold nanoparticles (AuNPs) between periphytic biofilms and a periphytophage fish
Hypostomus plecostomus
as final consumer has been studied in laboratory. Histological analyses have been performed at the two trophic levels with a particular focus on transmission electronic microscopy (TEM) observations in fishes.

In upstream running waters, periphytic biofilms are constituted by the association of micro‐organisms secreting an organic polymermatrix. Diatoms (brown microalgae) as a major component of these biofilms ensure a great part of the primary productionin the upstream running watersand are at the basis of their food web.

A contamination of these microorganisms by AuNPs could be vector of a trophic transfer of these nanomaterials along the trophic chain. Thus we determined if a trophic transfer of AuNPs was possible between natural periphytic biofilms and the fish
Hypostomus plecostomus
.
H. Plecostomus
is a tropical benthic fish with a ventral mouth modified into suction cup and adapted to graze the periphytic biofilms.

Analyses of gold bio‐accumulation in fishes were performed after 7 days of contamination, followed by a period of depuration of 14 days. These analyses were supplemented by an observation of AuNPs localization in tissues and cells by TEM and the toxic effects of AuNPs were also observed in them.

The results showed a trophic transfer of AuNPs between biofilms and fish, with a significant gold bioaccumulation in several organs (heart, spleen, liver, muscles). TEM observations revealed also a concentration of AuNPs in the spleen of the fish, localized especially in the erythrocytes and an important destructuration of the muscle fibers. After depuration, AuNPs totally disappeared from the erythrocytes, but were concentrated in the melanomacrophages, along with a recuperation of the muscles fibers, suggesting an important capacity of this fish to detoxify this type of nanoparticles.
Traditional and modern methods in tardigrade analysis
Authors: Hyra Marta , Czernekova Michaela , Student Sebastian , Poprawa Izabela
Published: December 2016

Tardigrada (also known as water bears) are microscopic, cosmopolitan invertebrates that are closely related to Arthropods. They are widespread in marine and brackish, freshwater, terrestrial habitats throughout the world, and they can be found in hot springs, Himalaya mountaintops, under the ice layer and even in ocean sediments. These animals are well known due to their unbelievable abilities that allow them to survive in extreme environments (such as temperatures ranging from −272°C to 151°C, pressure, dehydration, radiation, toxins, outer space, etc.). Although there are many more researches that are focused on tardigrades, this Phylum is still not very well known. Since knowledge about tardigrades has contributed to the discovery of dry vaccines, it seems that the research conducted on these animals is valuable.

In our research we focused on the traditional and modern methods that are used in the analysis of tardigrades. From the traditional methods, we used light microscopy, transmission and scanning electron microscopy as well as histo‐ and immunohistochemical methods. We also present a new method that is used in invertebrate analysis SBEM (
serial block‐ face scanning electron microscopy
), which had not previously been used for analysis of invertebrates. SBEMis a method that generates high resolution three‐dimensional (3D) images from the two‐dimensional (2D) images that are obtained by scanning the block‐face of an analysed sample. It was invented by Winfried Denk in 2004 to analyse the connectivity of the axons in the human brain. In this method, a microscope that connects the scanning electron microscopy, transmission electron microscopy and microtome into one tool is used.
Atom‐Resolved
STEM
Imaging Using a Segmented Detector
Authors: Seki Takehito , Sanchez‐Santolino Gabriel , Lugg Nathan , Ishikawa Ryo , Findlay Scott D. , Ikuhara Yuichi , Shibata Naoya
Published: December 2016

In scanning transmission electron microscopy (STEM), differential phase contrast (DPC) imaging has been developed to visualize the local electromagnetic field distribution in materials at medium resolution [1, 2]. The electromagnetic field deflects the incident electron beam, and this deflection can be measured by taking the difference between signals detected in opposing detector segments. Recent rapid progress in high‐sensitive segmented detectors has enabled DPC STEM imaging to be performed at atomic‐resolution [3]. However, DPC STEM images are sensitive to thickness and defocus, because dynamical scattering strongly affects DPC imaging of crystals in zone axis orientations [4]. It thus remains a challenge to develop a practical imaging technique at atomic‐resolution with the segmented detector.

Fig. 1 shows images of SrTiO
3
simultaneously obtained by different segments on a new segmented annular all field detector (SAAF2) installed in an aberration‐corrected STEM (JEOL JEM‐300F, 300kV). The relative orientation of the detector and the crystal structure is shown in Fig. 2. The images were at a defocus value of −3.7 nm relative to the defocus condition giving maximum contrast in annular dark field (ADF) imaging. These 512×512 pixel images were recorded with a dwell time of 38 µs per pixel, so the total imaging time is about 10 seconds. Each segment image can be qualitatively interpreted by electron beam deflection due to electric field from nuclei, including from the light oxygen atomic columns, though dynamical effects should be taken into account. According to image simulations, the DPC image appearance is largely unchanged with sample thickness if a defocus value is selected to obtain the highest contrast DPC image. This suggests that DPC STEM imaging at atomic resolution with a proper defocus value may be a new robust imaging mode that enables visualization of atomic column positions, including for light elements. Furthermore, this new imaging mode may contain information on charge redistribution due to charge transfer or orbital hybridization.

In addition, we have found that the detector is sensitive enough to allow both segmented annular dark field imaging and DPC STEM imaging of single atoms to be performed. The details will be discussed in the presentation.
Soft
X
‐Ray cryo‐tomography reveals ultrastructural alterations of the host cell during Hepatitis
C
infection
Authors: Perez‐Berna Ana Joaquina , Rodríguez Maria Jose , Sorrentino Andrea , Chichon Francisco Javier , Friesland Martina , Carrascosa Jose Lopez , Gastaminza P , Pereiro Eva
Published: December 2016

Chronic hepatitis C virus (HCV) infection causes severe liver disease in millions of humans worldwide. Pathogenesis of HCV infection is strongly driven by a deficient immune response of the host, although intersection of different aspects of the virus life cycle with cellular homeostasis is emerging as an important player in the pathogenesis and progression of the disease.

Cryo soft X‐ray tomography (cryo‐SXT) was performed to investigate the ultrastructural alterations induced by the interference of hepatitis C virus (HCV) replication with cellular homeostasis. Native, whole cell, three‐dimensional maps were obtained in HCV replicon‐harboring cells and in a surrogate model of HCV infection at 40nm resolution. Tomograms from HCV‐replicating cells show blind‐ended endoplasmic reticulum (ER) tubules with pseudo spherical extrusions and marked alterations of mitochondrial morphology that correlated topologically with the presence of ER alterations, suggesting a short‐range influence of the viral machinery on mitochondrial homeostasis.

Both mitochondrial and ER alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved direct‐acting antivirals (DAAs) for the treatment of chronic HCV infection. In addition to providing structural insight into cellular aspects of HCV pathogenesis our study illustrates how cryo‐SXT is a powerful three‐dimensional wide‐field imaging tool for the assessment and understanding of complex cellular processes in a setting of near native whole hydrated cells. Our results also constitute a proof of concept for the use of cryo‐SXT as a platform that enables determining the potential impact of candidate compounds on the ultrastructure of the cell that may assist drug development at a preclinical level.
Generation of super‐oscillatory electron beams beyond the diffraction limit
Authors: Remez Roei , Tsur Yuval , Lu Peng‐Han , Tavabi Amir H. , Dunin‐Borkowski Rafal E. , Arie Ady
Published: December 2016

In 1873, Ernst Abbe discovered that the imaging resolution of conventional lenses is fundamentally
limited by diffraction
, which, since then, has been overcome using a variety of different approaches in optical microscopy. In electron microscopy, thanks to remarkable developments in aberration corrected electron optics, the resolution of transmission electron microscopes (TEMs) and scanning TEMs (STEMs) has reached the sub‐Ångström regime. However, it is still limited by instrumental stability, residual higher‐order aberrations and the
diffraction limit
of the electron‐optical system. Recently, a concept termed super‐oscillation, which is analogous to the idea of super‐directive antennas in the microwave community [1], was proposed [2, 3] and applied in light optics for far field imaging of sub‐wavelength, barely‐resolved objects beyond the diffraction limit [4]. A super‐oscillating function is a band‐limited function that is able to oscillate faster locally than its highest Fourier component and thereby produce an arbitrarily small spot in the far field.

Here, we demonstrate experimentally for the first time a super‐oscillatory electron beam whose characteristic probe size is much smaller than the Abbe diffraction limit. Figure 1(a) shows scanning electron microscopy (SEM) images of a conventional grating mask (left) and a super‐oscillation off‐axis hologram (right) that have the same outer diameters (10 µm). The masks were fabricated by focused ion beam milling 200‐nm‐thick SiN membranes coated with 150 nm Au. The masks were inserted into the C2 aperture plane of a probe‐corrected  FEI Titan 80‐300 (S)TEM. Owing to the probe aberration corrector and relatively small numerical aperture (convergence semi‐angle), diffraction‐limited spots could be easily obtained from the conventional grating (Fig. 1, left), while a super‐oscillatory electron probe, which was generated at the first diffraction order (Fig. 1, right), produced a much smaller hot‐spot in the center. The size of the super oscillation hot‐spot is approximately one third of that of the diffraction‐limited spot. It could theoretically be decreased further, even below the de‐Broglie wavelength of the electrons, by varying the ratio between the inner and outer radii.

Further applications of such super‐oscillatory electron wave functions, e.g. enhanced STEM imaging, will be presented.
The corrosion of Zr(Fe,Cr)2 Secondary Phase Particles within Zircaloy‐4 under Simulated Nuclear Reactor Conditions
Authors: MacLaren Ian , Annand Kirsty J. , Gass Mhairi
Published: December 2016

Using Scanning Transmission Electron Microscopy (STEM) coupled with Dual Electron Energy Loss Spectroscopy (DualEELS), the corrosion and incorporation of Secondary Phase Particles (SPPs) into the oxide layer of Zircaloy‐4 material has been investigated.

Primarily, this work has focussed on studying Zr(Fe,Cr)
2
particles, and tracking their changes in morphology as they undergo oxidation.

It has been seen that these precipitates typically present themselves as very faceted structures within the α‐Zr metal matrix, and exhibit the hexagonal Laves phase structure. At this point, the body of the SPP tends to contain more Cr than Fe, however, Fe is often seen to segregate to the outside rim of the particle, and occasionally also to sit preferentially in regions within the body of the particle, resulting in Fe enriched areas, as can be seen in Figure 1.

Upon oxidation of the SPP, an out‐of‐plane expansion is seen to occur due to the volume expansion on the formation of the oxide, often resulting in particles that are quite elliptical in cross section with the major axis in the out‐of‐plane direction, as depicted in Figure 2. It can be seen that the elemental distribution does not remain homogeneous, as in the original SPP, and, at this point, three principal phases have been identified in the oxidised SPPs. The first thing to oxidise (i.e. the cap of the precipitate) is very Cr‐rich and is probably mainly Cr
2
O
3
with some Fe substitution – this must consume a reasonable proportion of the Cr in the SPP. Subsequently, the main body of the particle itself is found to oxidise to a Zr, Cr oxide with an approximate 3:2 ratio of Zr:Cr, and very little Fe content. The result of the formation of this majority phase and the rejection of the Fe is the precipitation of veins of Fe‐rich material. Early in the process, this Fe remains at least partially metallic. Even when the SPP is well encapsulated in the oxide scale, Fe‐rich veins have been observed to be very low in oxygen.

This nanoanalytical approach reveals the true complexity of the oxidation of these intermetallic compounds, and, understanding how these precipitates corrode in simulated nuclear reactor conditions prior to service is crucial in analysing how the addition of these alloying elements affects the macroscopic properties of the material to corrosion.
Lateral resolution of quantitative element analysis of low‐
Z
elements
Authors: Nissen Jörg , Berger Dirk
Published: December 2016

This work is a continuation of the investigation of the lateral resolution for quantitative analysis in a field emission electron probe microanalyser (FE‐EPMA) [1]. Now, these studies are extended from sputtered gold layer to low‐Z elements like aluminium. The aim is to determine the minimum thickness of an aluminium layer, for which a precise element quantification is still possible at a given accelerating voltage. For this purpose, Al‐layers with different thicknesses are deposited on silicon substrates (Fig. 1) by evaporation of thin pure aluminium rods from a tungsten coil. Cross‐section preparation is made by cleaving and subsequent surface polishing by use of a focused Ga‐ion beam (FIB, FEI Helios NanoLab 600). The material of the substrate and the FIB‐protection layer are chosen for minimum fluorescence by Al‐Kα. The X‐ray emitting volume is estimated by Monte Carlo (MC) simulations (Casino v2.48) of the electron scattering in Al for electron energies between the primary energy (15, 8, 7, 5, 4 and 3 keV respectively) and the critical ionization energy of Al‐Kα at 1.559 keV. The density of Al used for the simulation is measured to be (2.68 +/‐ 0.02) g/cm
3
, which is confirmed by thin film measurements evaluated by the software package STRATAGEM. For determination of the lateral resolution, 99% of the simulated electron trajectories were taken into account. Fig. 2 shows the MC simulation for 7 keV and 4 keV primary electron energy indicating a lateral resolution of 790 nm and 285 nm, respectively. For the quantitative WDS analysis, a 3820 nm Al‐layer is used as reference standard measured with a TAP‐crystal and a measurement time of 20 s for the peak and 10 s for the background.

Table 1 summarized the results of the quantitative measurements of the cross‐sectional aluminium layers, so far, and the lateral resolutions appraised from the MC simulation. A quantification result of (100.0 +/‐0.5) wt% Al and a content of silicon and platinum equal to 0 wt% indicates that the source volume of the emitted X‐rays is completely inside the Al‐layer. So far, a layer thickness of about 465 nm can be resolved quantitatively using an accelerating voltage of 4 kV. At 5 keV we found a discrepancy between measurement and simulation, since the latter predicts a better resolution. All measurements with different layer thicknesses will be presented on the poster.
Near atomic structure of flexible filamentous pepino mosaic virus by high resolution cryo‐
EM
Authors: Agirrezabala Xabier , Mendez Francisco , Sanchez‐Piña Maria Amelia , Aranda Miguel Angel , Valle Mikel
Published: December 2016

Flexible filamentous viruses belonging to the
Alphaflexiviridae
family cause from severe to mild diseases in agricultural crops, often reducing yield and crop quality. Viral particles from the Alphaflexiviridae group are formed by a (+)ssRNA molecule encapsidated by single capsid protein (CP) monomers arranged in helical fashion.
Pepino mosaic virus
(PepMV) is a flexible filamentous plant virus belonging to the genus Potexvirus included in the family
Alphaflexiviridae
which genome consists of a ~6.4 kb (+)ssRNA and encodes five proteins.

We report here the structure of intact PepMV virions by cryoEM at 3.9 Å resolution (Agirrezabala et al., 2015). The results and the resolution achieved (Figure 1) allowed the modeling of the CP, the (+)ssRNA and their relative interactions. The CP was modeled starting with the CP from PapMV (Yang et al., 2012), clearly showing a similar folding of the α‐helical domain for the
Alphaflexiviridae
family. The ssRNA is allocated and protected in a continuous groove of high electropositive potential built up by the CP in helical arrangement. The CP polymerize through a flexible N‐terminal arm providing the structural basis for the flexibility of the virus, in similar organization as the observed for BaMV (DiMaio et al., 2015).

Interestingly, the overall structure and organization of CP from PepMV is similar to the organization of nucleoproteins from the
Bunyaviridae
family, a group of enveloped (‐)ssRNA viruses. Common features include: the folding and arrangement of the α‐helical main domain; the groove for the ssRNA; the N‐terminal arm for polymerization; and the relative position between all these elements. Although structural homology between viruses revealed by their atomic structures is common, in the current case, the different nature of capsid protein and nucleoprotein might have profound evolutionary implications.
Investigation of Plasmonic Modes of Gold Tapers by
EELS
Authors: Guo Surong , Talebi Nahid , Sigle Wilfried , Vogelgesang Ralf , Esmann Martin , Becker Simon F. , Lienau Christoph , van Aken Peter
Published: December 2016

Plasmonic tapers have been studied intensively due to the ability of adiabatically coupling the propagating surface plasmon polaritons along their shaft to the nanolocalized plasmons at their apex. Therefore, they can find applications in the fields of sub‐diffraction‐limit nanofocusing, ultrafast photoemission, and near‐field optical microscopy.

We investigate the plasmonic modes of three‐dimensional single crystalline gold tapers by means of EELS (electron energy loss spectroscopy) and FDTD (finite‐difference time‐domain) numerical calculation. We observe a broadband excitation in the proximity of the apex and discrete higher‐order azimuthal plasmonic modes along the taper shaft in the gold taper with an opening angle of ~45°. Interestingly, the energy dispersions of these higher‐order plasmonic modes are roughly proportional to the inverse local radius. The importance of phase‐matching between electron field and radiative taper modes in mesoscopic structure is demonstrated [1]. The role of an alternative mechanism suggested by Schröder et al. [2] was analyzed by systematically studying changes in the dispersion of higher‐order plasmonic modes of gold tapers for different opening angles.