bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping the plasmonic modes of silver nanoparticle aggregates
Authors: Diaz‐Egea Carlos , Abargues Rafael , Martínez‐Pastor Juan P , Sigle Wilfried , van Aken Peter A. , Molina Sergio I
Published: December 2016

The optical properties of the noble metal nanoparticles (NPs) are dominated by localized surface plasmon resonances (LSPR) [1]. A spherical NP suspended in vacuum would present a LSPR mode that can be modelled as a dipole, hence called dipolar mode. When NPs are close enough to each other, they couple splitting the plasmonic modes of the same order and creating two new modes, the bonding dipolar plasmonic mode (BDP), and the antibonding dipolar plasmonic mode (ADP) [2]. The BDP is a low‐energy mode while the ADP resonates at a value slightly higher than the dipolar mode of a sphere. The exact energy value for both modes depends on the inter‐particle distance, being smaller as they are closer to each other [3]. It also depends on the aspect ratio of the group with lower energy values as the aspect ratio gets larger [4]. The third conditioning factor is the geometric shape of the cluster. In the same way that triangular NPs have plasmonic modes at lower energies than a sphere [5], a triangular or rhomboidal shaped group of NPs shows plasmonic modes at smaller energies than a spherical one [6].

In this work, silver NPs were created and were forced to cluster. Samples were taken at different stages of the aggregation process. They were analyzed at a large scale by UV‐Vis spectroscopy (UV‐Vis) and at nanometre scale by energy‐filtering transmission electron microscopy (EFTEM). The individual, dipolar mode was clearly identified for isolated NPs corresponding to the early stages of the clustering process. As bigger clusters are created, the collective modes become more apparent.

This work was supported by the Spanish MINECO (projects TEC2014‐53727‐C2‐1‐R, 2‐R and CONSOLIDER INGENIO 2010 CSD2009‐00013), Generalitat Valenciana (PROMETEOII/2014/059) and Junta de Andalucía (PAI research group TEP‐946). The research leading to these results has received funding from the European Union Seventh Framework Program [FP/2007/2013] under Grant Agreement No. 312483 (ESTEEM2) and H2020 Program (PROMIS ITN European network).
Electron‐beam‐induced structural phase transition related to oxygen vacancy ordering in epitaxial
L
a2/3
S
r1/3
M
nO3 films
Authors: Yao Lide , Majumdar Sayani , Äkäslompolo Laura , Inkinen Sampo , Qin Qi Hang , van Dijken Sebastiaan
Published: December 2016

Functional oxides with a perovskite crystal lattice of type ABO
3
may possess corresponding oxygen‐deficient modulation structures, which can be used to tailor material properties including magnetism, ferroelectricity, and superconductivity. One prototypical example is the brownmillerite crystal structure of type ABO
2.5
[1‐5], which due to its high ionic conductivity could find applications in solid oxide fuel cells, oxygen‐separation membranes, gas sensors and other devices requiring anion diffusion. Brownmillerites have been derived from perovskite materials using topotactic reduction [1], optimized film growth [2,3], and oxygen getters [4]. Here, we demonstrate that the evolution of the perovskite‐brownmillerite phase transition can be fully controlled and monitored in epitaxial La
2/3
Sr
1/3
MnO
3
(LSMO) films using electron‐beam irradiation in a transmission electron microscope (TEM) [5].

Atomic‐scale real‐time TEM imaging reveals that the structural transition is driven by an incessant ordering of electron‐beam induced oxygen vacancies in every second MnO
x
plane. This local depletion of oxygen reduces the coordination of Mn cations, causing a vertical displacement of the La/Sr ions. A map of the out‐of‐plane lattice spacing corroborates this point (Figure 1(b)). Over‐irradiation of the brownmillerite phase induces a second transition to a perovskite‐like structure with disordered oxygen vacancies and a significantly enhanced out‐of‐plane lattice compared to the original LSMO film (Figure 1(c)). Additional information on the distribution of oxygen vacancies in the three structural phases of LSMO is obtained by HRTEM under negative Cs imaging (NCSI) conditions [6]. Compared to the original perovskite LSMO (see Figure 2(a) and inset), the NCSI contrast from brownmillerite LSMO (Figure 2(b) and inset) manifests a depletion of oxygen and predominant tetrahedral coordination of Mn in every other MnO
x
layer. The modulation structure disappears when the LSMO crystal transforms into the oxygen‐deficient perovskite‐like structure with enhanced out‐of‐plane lattice parameter (Figure 2(c) and inset). In this case, the oxygen is randomly distributed, which is facilitated by oxygen diffusion from MnO
6
octrahedra to MnO
4
tetrahedra during the second structural phase transition. Electron energy loss spectroscopy and energy‐dispersive x‐ray spectroscopy further confirm our findings [5].

This work was supported by the Academy of Finland (Grant Nos. 260361 and 252301) and by the European Research Council (ERC‐2012‐StG 307502).
Nanograin formation due to premelting in free‐standing thin films
Authors: Rani Pooja , Subramaniam Anandh , TEWARI RAGHVENDRA , Vishwanadh Bathula , Bhattacharyya Somnath
Published: December 2016

The melting point of metals decreases on the formation of nano‐crystals. Premelting of surfaces and grain boundaries has also been reported. The current study pertains to annealing of solutionized Cu‐2wt.%Fe alloy thin film samples in the temperature regime of 200–300°C. Transmission electron microscopy specimens have been used as free‐standing thin films and the annealing of the samples are performed by two methods: (i) in‐situ in a TEM, (ii) ex‐situ after sealing the samples in vacuum. In the in‐situ annealing treatment the power to the heater was switched off after annealing, while the ex‐situ samples were quenched in water. Formation of nanocrystals with grain size of about 6 to 10 nm is observed in both kinds of samples after annealing and is occurs after 10 minutes of annealing at 250°C in the in‐situ sample. Given that the solidus temperature of the alloy is 1064°C, these observations represent fast changes in a short period of time. We postulate that the samples have undergone surface premelting followed by solidification. Due to rapid quenching of the molten layer on the substrate of the same materials, nano‐crystals on the surface are observed
Direct Visualization of Magnetic Skyrmion by Aberration‐Corrected Differential Phase Contrast Scanning Transmission Electron Microscopy
Authors: Matsumoto Takao , So Yeong-Gi , Kohno Yuji , Sawada Hidetaka , Ikuhara Yuichi , Shibata Naoya
Published: December 2016

Magnetic skyrmion is a topologically protected quantum spin texture. It is so stable and expected to be utilized for future memory devices featuring ultralow energy consumption. However, influences of structural defects in real materials remain to be elucidated in such practical applications. Since magnetic skyrmion is a nano‐scale magnetic structure, visualization techniques with very high spatial resolution are essential to investigate such influences of nano‐scale structural defects, such as edges, dislocations and grain boundaries on magnetic skyrmion. Here, we present the direct visualization of magnetic skyrmion lattice in a thin film specimen of FeGe
1‐x
Si
x
by aberration‐corrected differential phase‐contrast scanning transmission electron microscopy (DPC‐STEM) taking advantages of a segmented annular all‐field (SAAF) detector [1] connected via photomultiplier tubes with a high‐speed numerical processer.

Polycrystalline FeGe
1‐x
Si
x
was grown from FeGe
0.8
Si
0.2
ingot by conventional solid‐state reaction annealed at 900 °C for 100 hours. A thin film specimen was fabricated from a bulk crystal by using an Ion Slicer (EM‐9100IS, JEOL, Ltd.). For DPC STEM observations, we used a STEM (JEM‐2100F, JEOL, Ltd.) equipped with a probe‐forming aberration corrector (CEOS, GmbH) and a Schottky field emission gun operated at 200 kV. This microscope was equipped with a SAAF detector. We used a double‐tilt liquid‐nitrogen cooling specimen holder (Model 636, Gatan, Inc.). Analysis of DPC STEM images was done either online by using a direct reconstruction system [2] implemented as an application of LabView software (National Instruments, Inc.) running on Windows or offline by using a program written in Digital Micrograph Scripting language (Gatan, Inc.).

Figure 1a shows a schematic diagram of electron‐optical system of DPC STEM used in the present study. In‐plane magnetization can be mapped by analyzing the Lorentz deflection of electron beam using segmented annular detector as schematically shown in Fig. 1b. As shown in Fig. 2a, a set of four images is selected from sixteen images obtained by the segmented detector. Such images are first converted into two images corresponding to a horizontal and a vertical component image of Lorentz deflection (Fig. 2b). Finally, the two Lorentz deflection images are analyzed to show a in‐plane magnetization vector, intensity, and magnetic helicity images as shown in Fig. 2c. Figure 3 demonstrates the live reconstruction of in‐plane magnetic field and intensity of a magnetic skyrmion lattice. A unique structural relaxation mechanism in a magnetic Skyrmion domain boundary core, revealed by the technique for the first time [3], will be presented in detail.
Determination of elemental ratio in an atomic column by
STEM‐EELS
Authors: Haruta Mitsutaka , Hosaka Yoshiteru , Ichikawa Noriya , Saito Takashi , Shimakawa Yuichi , Kurata Hiroki
Published: December 2016

The elemental signals do not necessarily localize at atomic‐column positions because the spatial resolution of an EELS signal is constrained by the delocalization of inelastic scattering and electron channeling process. These complexities make it difficult to perform quantitative analysis with atomic resolution. When we estimate the exact value of elemental ratio with atomic scale, full quantum mechanical simulations combined with experimental result are necessary. On the other hand, if there is a criterion about accuracy of experimental result about elemental ratio for an atomic column without simulation, it would be very useful.

In this study, atomic‐resolution quantification of the elemental ratio of Fe to Mn at octahedral and tetrahedral sites in brownmillerite Ca
2
Fe
1.07
Mn
0.93
O
5
(Fig. 1) is demonstrated using STEM‐EELS. It is known that Fe and Mn ions are nearly all ordered but not fully ordered, i.e., a small number of Fe and Mn ions reside in octahedral and tetrahedral sites, respectively. It was found that a considerable oversampling of the spectral imaging data yields a spatially resolved area that very nearly reflects atomic resolution (~1.2 Å in radius) for Fe and Mn L
2,3
‐edge (Fig. 2). And the average relative compositions of Fe to Mn within the region were 17.7 to 82.3 ± 13.1 in octahedral sites and 80.7 to 19.3 ± 9.9 in tetrahedral sites. The actual atomic ratio was estimated by calculating the mixing of signals from nearest‐neighbor columns using simple simulation based on multislice technique. It was concluded that the ratio of Fe to Mn was 14 to 86 at octahedral sites. It agrees well with the previous neutron diffraction experiment (14.4 to 85.6) which can correctly decide such information for bulk sample [1]. On the other hand, the experimental value and the estimation value from tetrahedral site have relatively large error compare with the result of neutron diffraction experiment (92.2 to 7.8). This means that an experimental oversampling SI data of Fe and Mn
L
2,3
‐edge from octahedral site in perovskite‐like structure is probably interpreted with an uncertainty of approximately 10% without simulation.
Novel in vivo imaging techniques to visualise renal morphology and function in acute kidney injury
Authors: Liang Xiaowen , Wang Haolu , Gravot Germain , Liu Xin , Roberts Michael
Published: December 2016

Introduction

The medical uses of optical imaging are revolutionizing medicine; optical imaging is undergoing explosive growth fuelled by advances in high‐sensitivity detectors. These light based systems utilise multiphoton microscopy (MPM) to provide high resolution and quantitative imaging of cellular metabolism in
in situ
and
in vivo
biological tissues and organs – in space (three dimensions), in time, in spectra, and in fluorescence anisotropy (i.e. a total of 6 dimensions). MPM allows
in vivo
visualisation of intact kidney tissue at the single cell resolution, which is solved a long‐standing critical technical barrier in renal research to study several complex and inaccessible cell types and anatomical structures. In this study, MPM was employed to visualise morphology changes and study the functions of acute kidney injury (AKI).

Methods

Glycerol‐inducedAKI model (elevated serum creatinine) can be used to mimic rhabdomyolysis, which was developed in male C57BL/6 mice (8–12 weeks) byintramuscular injection of50% (v/v) glycerol /PBS (10 ml/kg) into the left hind leg. The control mice were injected by PBS using the same method. After 24 hours, kidneys were exposed to image using MPM for morphology examination in both groups. Since Rhodamine 123 (RH123) is a marker to measure P‐glycoprotein (P‐gp) transporter function, it was intravenously injected into control and AKI mice and imaged by MPM to evaluate the P‐gp transporter function. Using a bolus injection of FITC labelled inulin, rapid quantification of glomerular filtration rate (GFR) was determined in both groups by directly imaging of inulin clearance from glomerulus. A LaVision Biotec Nikon MPM was used to image RH123 excretion from tubules. GFR was measured using a DermanInspect system equipped with the ultrashort (85 fs pulse width, 80 MHz repetition rate) pulsed mode‐locked tunable Ti:sapphire laser (Mai Tai, Spectra Physics, 25 Mountain View, USA).

Results

The MPM imagesdirectly showed morphology changes in AKI mice compared to control group, where acute injury of tubular cells as indicated by reduced autofluorescence and cellular vacuolation (Fig.1). Intravital imaging showed that RH123 was rapidly excreted from tubules in control group but slowly eliminated from AKI model (Fig. 2), indicating P‐gp transporter dysfunction in glycerol‐induced AKI. As shown in Fig, 3, reduced glomerular permeability was also observed in AKI model, where FITC‐labelled inulin (red color) was quickly cleared from glomerular at 30 mins after injection in control group, while fluorescence from FITC‐labelled inulin was retained in glomerular in AKI model.

Conclusion

This advanced imaging techniquecan be used to rapiddiagnosis and quantification of AKIinduced morphology andfunctional changes.
Quantitative compositional mapping on the nanoscale over large fields of view in thin film solar cells from earth abundant elements
Authors: Thersleff Thomas , Giraldo Sergio , Xie Haibing , Pistor Paul , Saucedo Edgardo , Leifer Klaus
Published: December 2016

Solar power is projected to become the largest single global source of electricity generation by 2050, with photovoltaic devices constituting the majority of this market share [1]. Next generation materials based on material systems with direct band gaps fabricated in thin films are predicted to make considerable contributions to this market with the promise of significantly reducing materials costs and solar cell bulk. At present, one of the most promising thin film absorber material is CuIn
x
Ga
(1‐x)
Se
2
(CIGS), which has been shown to achieve a solar conversion efficiency in the laboratory of 21.7% [2]. However, the high cost of the raw materials in this system has driven research to find more cost effective alternatives [3].

One such alternative material system based on the crystallographic kesterite family Cu
2
ZnSn(S,Se)
4
promises to be highly cost competitive due to the use of earth abundant elements. However, this system is currently less mature than CIGS with a record solar conversion efficiencies of 12.6% [4] or 11.6% [5] if no sulphur is used. The challenges impeding improvement are related to chemical and nanoscale structural inhomogenities that lead to a reduction in the open circuit voltage of the system [6]. A full understanding of these defects and, hence, progression in fabrication of these materials thus requires a characterization technique capable of spatially mapping out compositional, structural, and electronic trends with nanoscale spatial resolution.

In this contribution, we present our progress towards the development of a methodology that will allow researchers to directly address these challenges with nanometer spatial resolution over micron sized areas of sample. We accomplish this through two stages. First, a sample preparation methodology enabling a very large field of view while retaining a reasonable lamellae thickness utilizing the Focused Ion Beam is presented. Preliminary results of this methodology are presented in figure 1, revealing a field of view of many microns over a sample that is under 80 nm thick in the absorber layer. Second, we employ correlative EDX and EELS spectroscopic imaging techniques over large areas, focusing on features such as grain boundaries and pores. The simultaneous use of both spectroscopy techniques allows for two independent quantitative assessments of composition, reducing systematic errors. It also assists in the identification and elimination of artifacts that may arise through the data treatment. The result is large area maps with optimized uncertainties from a materials system containing many difficult and overlapping spectroscopy edges. These techniques are then applied to state‐of‐the‐art samples with very high efficiencies [7].
Quantitative analysis of
A
l
N
/
S
i
C
interfaces in
A
l
G
a
N
/
G
a
N
heterostructures grown on
S
i
C
Authors: Gkanatsiou Alexandra , Lioutas Christos B. , Frangis Nikolaos
Published: December 2016

Wide band gap semiconductors, such as SiC and GaN, exhibit many attractive properties: a unique combination of the wide band gap, high breakdown field, high saturation velocity and the ability to form high quality AlGaN/GaN heterostructures with good transport properties make them ideal candidates for high power and high frequency applications. Hexagonal silicon carbide materials (SiC) are considered to be promising candidates for electronic devices as the third generation key materials for transistors. A typical example of a high performance device is the Al
x
Ga
1‐x
N/GaN heterostructure used as a high electron mobility transistor (HEMT) [1‐2].

As 6‐inch SiC wafers are being introduced into the market, a decrease of the substrate off‐cut for SiC heteroepitaxy is desirable to reduce the manufacturing costs [3‐4]. Therefore, multilayer (5 layers) and multicomponent structures (based on GaN and related materials) were grown on 6H‐SiC (with a misorientation of 1 deg. off from the (0001) plane) substrates using the MOVPE method, for high power applications. The layers were grown epitaxially, as it was confirmed from the corresponding electron diffraction patterns. Several types of interfaces were observed between the layers that either ran parallel to the interface or formed V‐shaped defects (e.g. the SiC/AlN, GaN/AlN, GaN/AlGaN interfaces etc.). Moreover, High Resolution TEM (HRTEM) images showed the existence of steps in the 6H‐SiC/AlN interface. A typical HRTEM image where an atomic scale step is observed is shown in Fig. 1.

In this study, quantitative analysis of the 6H‐SiC/AlN interface is presented based on experimental HRTEM micrographs, showing and proving the steps sites, the layers' sequence and any strain relaxation situation existing. A structural model based on this analysis is proposed and simulated HRTEM images are also obtained. The corresponding atomic models proposed are found to describe well the 6H‐SiC/AlN interface, with the corresponding computer simulation images coinciding with the experimental HRTEM images. An example is shown in Fig. 2, illustrating the monolayer step observed in the 6H‐SiC/AlN interface. In Fig. 3, a characteristic plot shows the phase shift of the fitting of the intensity's distribution along a line that corresponds to the projection of a close‐packing layer revealing the stacking sequence and therefore the starting position of the AlN epilayer. Moreover, the comparison of the sequence clearly shows the height of the step and any alteration on the stacking sequence between the two parts of the image. Finally, the computer simulated image, as shown in Fig. 4, coincides well with the HRTEM image shown in Fig. 1.
In situ
TEM
nanocompression of
MgO
nanocubes and mechanical analysis
Authors: Issa Inas , Amodeo Jonathan , Joly‐Pottuz Lucile , Réthoré Julien , Esnouf Claude , Garnier Vincent , Morthomas Julien , Masenelli‐Varlot Karine
Published: December 2016

In this study, we propose an innovative mechanical observation protocol of nanoparticles in the 100 nm size range. It consists of
in situ
TEM nano‐compression tests of isolated nanoparticles. Load–real displacements curves, obtained by Digital Image Correlation, TEM images (BF, DF and WBDF) are analyzed and these analyses are correlated with Molecular Dynamics simulations. Elementary process that governs the deformation mechanism of nanoparticles can be identified. A constitutive law with the mechanical parameters (Young modulus, Yield stress…) of the studied material at the nano‐scale can be obtained.

In situ
TEM nano‐compression tests were performed on ceramic MgO nanocubes. Magnesium oxide is a model material and its plasticity is very well known at bulk. The MgO nanocubes show large plastic deformation, more than 50% of plastic strain without any fracture. Calculations of Schmid factors of possible slip systems in MgO under solicitation direction coupled with analysis of WBDF images, performed
in situ
in TEM nanocompression tests, contribute to full characterizations for dislocations in MgO nanocubes under uniaxial compression. Correlation of TEM images and stress‐strain curves, obtained by DIC, allows the observation and description of dislocations activities and processes along the compression test. Coupling these analyses with MD simulations, the elementary process that governs the deformation mechanism of single crystal MgO nanocubes under uniaxial compression could be identified. In
Figure 1
, contrast appears in the cube when a change on the curve is observed. This contrast band may be attributed to a ½ dislocation that nucleate at surface and slip along {110} plan as obtained by MD calculations and by TEM analysis on possible dislocations in active slip systems near the diffraction condition in these TEM observations (as we are always near [001] zone axis) as shown in
Figure 2
.

Size‐effect on dislocation processes could be obtained in MD simulations and in experiments. MD results show that in MgO nanocubes smaller than 8 nm, the deformation occurs through dislocation nucleation at surfaces and edges/corners and dislocation starvation process is observed simultaneously with stress drop, as shown in
Figure 3
(snaps 1, 2 & 3). However larger nanocubes show dislocation interactions and junctions formation rather than dislocation starvation as shown in
Figure 3
(snaps 4 & 5). Experimental results show that these two processes co‐exist in MgO nanocubes in the size range [60–450] nm. However, TEM images and stress‐strain curves show that there is predominance of dislocation starvation mechanism in smaller nanocubes (Figure 4 show a WBDF of a large nanocube after compression where persistent dislocations and dislocations networks assume that dislocation interactions process predominate in larger nanocubes rather dislocation starvation.
High‐Resolution Phosphorescence Lifetime Imaging of Oxygen in 3
D
Tissue Models
Authors: Papkovsky Dmitri , Zhdanov Alexander , Dmitriev Ruslan
Published: December 2016

Molecular oxygen (O2) plays a multitude of important roles in cell and tissue function and (patho)physiology. Real‐time quantitative imaging of O2 by phosphorescence quenching method enables detailed mechanistic studies of cell and tissue physiology, responses to hypoxia, drug treatment and other stimuli. We applied high‐resolution Phosphorescence Lifetime Imaging Microscopy (PLIM) to study several different 3D tissue models: multi‐cellular spheroids, excised animal tissue and cultured organoids. To achieve efficient, stable passive staining of the cells and tissues, we have designed a panel of cell‐penetrating phosphorescent nanosensors with variable surface charge and spectral characteristics, and a small molecule O2 probe, Pt‐Glc, which provides fast and in‐depth staining of most cell models. Using Pt‐Glc and PLIM we studied cultures of PC12 (rat pheochromocytoma) and HCT116 (human colon cancer) cell spheroids, intestinal organoids and ex vivo brain, colon, bladder and vessel tissue samples. We showed that cell aggregates of >50 um size are significantly deoxygenated under ambient O2, but remain viable and respond to treatment with compounds affecting metabolism. For the neurospheres from embryonic rat brain, standard protocol was developed for O2 imaging by PLIM, multiplexed with immunofluorescence of cell type, proliferation and death markers. In giant umbrella cells of mouse bladder epithelium we observed marked intracellular gradients of O2 of up to 40‐50 mM across the cell or 0.6 mM/mm, which may play physiological roles in tissue function. We found decreased respiration in the colonocytes in dextran sulfate sodium (DSS)‐induced colitis mouse colon tissue. These results demonstrate the utility of cell‐penetrating O2 probes and PLIM method for life science research.
Probing localized strain in solution‐derived
YBCO
nanocomposite films
Authors: Guzman Roger , Gazquez Jaume , Mundet Bernat , Callado Pablo , Soler Laia , Jareño Julia , Coll Mariona , Obradors Xavier , Puig Teresa
Published: December 2016

The investigation of the atomic structure of individual defects is critical to the understanding and precise controlling of the physical properties of materials. And although defects are sometimes detrimental to functionality, in high temperature superconductors (HTS) are necessary for providing pinning of magnetic flux and allowing high currents to be carried. Moreover, a strong enhancement on the vortex pinning in HTS YBa
2
Cu
3
O
7
(YBCO) films is also found to be controlled by nanostrain [1], which is attributed to elastic distortions of the crystal lattice at the nanoscale level. Using aberration‐corrected Scanning Transmission Electron Microscopy (STEM) we explore the complex defect landscape of YBCO nanocomposite thin films. Combining High Angle Annular Dark Field (HADDF) with Low Angle Annular Dark Field (LAADF) and local strain analyses we are able to map and quantify the lattice deformations associated to the defects, which will ultimately determine their self‐assembling behavior as well as their mutual interaction. Our atomic scale investigation shows that the presence of mainly randomly oriented nanoparticles generates incoherent interfaces within the epitaxial YBCO matrix, which drastically increases the density of defects, yielding a ramified network of inhomogeneously distributed nanostrained regions where the crystalline perfection of the superconductor is perturbed. Finally, we will compare the microstructure of conventional high‐quality solution‐derived trifluoroacetate‐YBCO nanocomposites with new fluorine‐free films based on a novel transientliquid assisted growth method (TLAG), which provides ultra‐high growth rates with a consequent influence on the defects landscape. Accordingly, TLAG envisages an enormous potential for lowcost and high‐performance coated conductors.
Electron tomography based on highly limited data using a neural network reconstruction technique
Authors: Bladt Eva , Pelt Daniel , Batenburg Joost , Bals Sara
Published: December 2016

Gold nanoparticles are studied extensively due to their unique optical and catalytical properties. Their exact shape determines the properties and thereby the possible applications. Electron tomography is therefore often used to examine the three‐dimensional shape of nanoparticles. However, since the acquisition of the experimental tilt series and the 3D reconstructions are very time consuming, it is difficult to obtain statistical results concerning the 3D shape of nanoparticles. We propose a new approach for electron tomography that is based on artificial neural networks, which enables us to reduce the number of projection images with a factor of 5 or more
1
.

The application of neural network filtered backprojection method (NN‐FBP)
2
to electron tomography consists of two phases: (i) a
learning phase
, in which full tilt series and their corresponding reconstructions are used to calibrate the reconstruction algorithm and (ii) a
reconstruction phase
, in which large batches of limited tilt series (i.e. using fewer projection images) are rapidly reconstructed. The parameters of the NN‐FBP are trained by high quality 3D reconstructions, based on 151 projection images, in the learning phase. In the reconstruction phase, a tilt series of only 10 projection images of a gold nanoparticle is used as input. As opposed to previous advanced reconstruction methods, specific prior knowledge is not explicitly used in the NN‐FBP method. Also, since NN‐FBP is based on the efficient Weighted Backprojection algorithm, it is computationally efficient as well, enabling high throughput of 3D reconstructions. We show that the NN‐FBP reconstruction algorithm is able to yield electron tomography reconstructions based on highly limited data with a comparable quality to a reconstruction based on a full data series with a tilt increment of 1° (Figure 1).

The decrease in acquisition time and the use of an efficient reconstruction method enables us to examine a broad range of nanostructures in a statistical manner. Using the NN‐FBP approach, the average radius of a batch of 70 nanospheres was obtained. These results confirm the reliability of the NN‐FBP algorithm and demonstrate the possibility of combining electron tomography and statistical measurements (Figure 2).
Superresolution and depth sensitivity in
HRTEM
through structured illumination
Authors: Van den Broek Wouter , Koch Christoph T.
Published: December 2016

In the weak phase object approximation the wave function in the objective lens' back focal plane is a convolution of the illuminating wave, ψ
in
, with the projected potential, V, multiplied with the coherent transfer function, H, i.e. ( ψ
in
* ( 1 + σV ) ) H, with σ the interaction constant and * the convolution operator. Therefore, frequencies from above the cutoff‐frequency in H's objective aperture enter the image formation in aliased form, as is illustrated in Fig. 1a. In this abstract, fully dynamical multislice simulations are carried out to investigate if these higher frequencies can be disentangled and superresolution can be achieved.

Simulations of [112] Si are set up with FDES [1], the supercell is 5.12 nm by 5.12 nm wide and is 5 nm thick on the left side and 2.5 nm on the right‐hand side. The in‐plane sampling distance and the slice thicknesses were set to 0.01 nm. Si in the [112] direction displays dumbbells that are 0.075 nm apart, corresponding to a spatial frequency of 13.3 nm‐1 or 33.4 mrad at an acceleration voltage of 200 kV. The imaging is done with illumination that is structured to have random‐but‐known phases and that is bandwidth limited to 20 mrad, see Fig. 1b and Fig. 2a. The objective lens behind the sample is set to Scherzer conditions with an objective aperture of 20 mrad, a defocus of ‐18.8 nm and a spherical aberration of 94.0 µm, thus yielding a point resolution of 0.125 nm that is clearly insufficient for resolving the dumbbells. Eight images are recorded with the simulation shifted by 0.27 nm between consecutive recordings; the first image is shown in Fig. 2b, the others look similar.

A three‐dimensional reconstruction was set up in IDES [2,3] with three slices 2.5 nm apart and a pixel size of 0.01 nm; amplitude and phase of the impinging wave and the settings of the objective lens were assumed known. Multiple scattering was accounted for by propagating the wave between slices with the Fresnel propagator. A Polak‐Ribière conjugate gradient search was used to minimize an error function that was chosen as the sum of absolute differences between measurement and corresponding data simulated from the current object estimate. Contrary to [2,3] no sparse regularization has been applied. In Fig. 3a the middle slice of the reconstruction is shown, displaying a clear separation of the Si‐dumbbells. Furthermore, the lower slice displayed in Fig. 3b shows that depth sensitivity with a resolution of at least 2.5 nm is achieved as the right‐hand side, which by construction does not contain any atoms in its lower half, indeed does not display any. [4]
In Situ TEM Characterization of Asphaltene Formation in Crude Oil
Authors: Janssen Arne , Zaluzec Nestor , Kulzick Matthew , McMahon Greg , Burke M.G.
Published: December 2016

Asphaltenes are aromatic hydrocarbons and defined as a solubility class as the n‐heptane‐insoluble, toluene‐soluble fraction of a crude oil or carbonaceous material. They are always present in crude oils and influence the oil properties. Phase changes, viscosity, and interfacial properties of crude oils are strongly affected by asphaltenes. Problems arise when asphaltenes are exposed to changes in temperatures, pressure, or composition, and they become insoluble in the oil. When asphaltenes precipitate, they can deposit onto the walls of the pipe, inhibiting the flow of oil and can end up blocking the pipe entirely. Although, the negative impact of asphaltenes to the oil industries is well known, however, the exact mechanism by which asphaltene flocculation and aggregation occurs is still not fully understood.

Over the last decade methods have been developed to characterize and model the mechanisms of asphaltene flocculation, aggregation and precipitation. [1, and references listed therein]. To date, there have been TEM analyses of asphaltenes that have impacted petrochemical research activities [2]. However, the disadvantage is that the asphaltene sample may be altered as a consequence of sample preparation. With the development of commercially available liquid cell holders for
in situ
TEM there is now the opportunity of direct observations of the oil emulsion system at the nm scale in their natural environment.

Initial
in situ
TEM experiments of asphaltene formation and aggregation were conducted in a FEI Talos F200X TEM operated at 200 keV using the Protochips Poseidon P210 analytical liquid cell holder. A light crude oil with a nominal asphaltene content of 3.7% was mixed with heptane to initiate flocculation of the asphaltenes in the liquid
in situ
TEM cell. Our first results indicate that the aggregation process is driven by the initial formation of 10–20 nm spherical colloids. These colloids cluster to flocculates in a range of several tens to hundreds of nanometers in the oil‐heptane emulsion (Figure 1). The flocculation sequence is in good agreement with the proposed Yen model [1]. Further asphaltene flocculation experiments from different crude oils and their morphology evolution will be compared and discussed. In addition, opportunities and limitations for using
in situ
liquid cell holders for studying asphaltene flocculation in an analytical TEM will be described.
3 dimensional measurements of tuberculosis granulomas using optical clearing techniques
Authors: Francis Robert , Keeble James , Khatri Bhagwati , Dagg Belinda , Ho Mei Mei , MacLellan‐Gibson Kirsty
Published: December 2016

Tuberculosis remains one of the major infectious diseases in the world. Current vaccine testing relies on
in vivo
models including the mouse aerosol challenge model. To determine structural changes in the 3D of granulomas caused by
Mycobacterium tuberculosis
previous observations have relied on serial sectioning with histopathology techniques. However, this has several disadvantages including the possibility of missing or distorting information in the 3D.

Optical clearing techniques may offer a way around this by making the whole organs transparent using chemical procedures, and then imaging by confocal laser scanning microscopy to produce optical sections. Therefore this study aimed to see whether optical clearing techniques can be used to study granulomas in 3D and the structural changes to the surrounding tissue. Results to date have shown that it is possible to optically clear lobes of the mouse lung and to resolve individual nuclei. We now hope to use the same techniques to image
M. tuberculosis
infected lung and to compare with other organs.
Control of octahedral rotations via octahedral connectivity in an epitaxially strained [1
u.c.
// 4
u.c.
]
LaNiO3/LaGaO3
superlattice
Authors: Qi Haoyuan , Kinyanjui Michael , Chen Xiaodan , Biskupek Johannes , Geiger Dorin , Benckiser Eva , Habermeier Hanns‐Ulrich , Keimer Bernhard , Kaiser Ute
Published: December 2016

ABO
3
provskites represent a board spectrum of intriguing functionalities such as metal‐insulator transitions, multiferroicity, colossal magnetoresistance and superconductivity owing to the strong correlation between charge, spin and orbital degrees of freedom [1]. In recent years, heterostructures and superlattices formed by two or more different ABO
3
perovskites have received intense research interest. Due to the electronic and structural reconstructions at the heterointerfaces, novel phenomena may emerge opening the way to novel functionalities that are not accessible in their bulk counterparts [2]. In ABO
3
perovskites, the magnetic and electronic states are strongly coupled to the B‐O‐B bond angles and B‐O bond lengths. Therefore, precise control of the BO
6
octahedral rotations and distortions via epitaxial strain and interfacial octahedral connectivity offers a promising route to tailoring the material properties in a controllable way [3].

In our previous study of a [(4 u.c.// 4 u.c.) ×8] LaNiO
3
/LaGaO
3
superlattice grown on (001) SrTiO
3
by using aberration‐corrected high‐resolution transmission electron microscopy (AC‐HRTEM), we have shown that the response of NiO
6
rotations to epitaxial strain in the LaNiO
3
/LaGaO
3
superlattice is significantly different from that in LaNiO
3
thin films [4]. In LaNiO
3
thin films, epitaxial strain effectively modifies the NiO
6
rotational magnitudes throughout the entire film therefore stabilizing new electronic and magnetic states [3]. However, in the [(4 u.c.// 4 u.c.) ×8] LaNiO
3
/LaGaO
3
superlattice, the [100] and [010] rotational magnitudes of NiO
6
and GaO
6
relax to the bulk values of LaNiO
3
and LaGaO
3
even though the superlattice is still coherently strained.

Here, we investigated the local octahedral rotations in a [(1 u.c.// 4 u.c.) ×13] LaNiO
3
/LaGaO
3
superlattice grown on a (001) SrTiO
3
substrate. Figure 1 shows the atomic models of bulk LaNiO3 and LaGaO3 and the simulated [110] AC‐HRTEM images. Figure 2 represents an experimental AC‐HRTEM image near the surface of the superlattice. We found that, due to the octahedral connectivity at LaNiO3‐LaGaO3 interfaces (see Fig. 1e), the octahedral rotations of NiO
6
adopted the same [100] and [010] rotational magnitudes as the neighbouring GaO
6
till the surface of the superlattice. Our results indicate that in LaNiO
3
based superlattices, the octahedral rotations of NiO
6
can be precisely controlled via interfacial octahedral connectivity when the thickness of the LaNiO
3
layer is reduced to 1 unit cell.
Quantification of particles in samples of a split‐virion influenza vaccine
Authors: Nicolai Marie‐Claire , Deliot Aurelie , Ronzon Frederic , Cotte Jean‐François , Manin Catherine , Nemecek Daniel
Published: December 2016

Influenza is an infectious disease caused by
Orthomyxoviridae
viruses that infect 3‐5 million people worldwide during seasonal epidemics. Influenza vaccines must be produced and administred annually to respond to the high rate of mutations and possible exchange of genomic segments between different strains. The vaccines are produced by a well established prodedure in inoculated embryonated eggs. Influenza virions are purified by sucrose gradient and then split by detergent filtered and inactivated by formaldehyde. Samples of split virions contain mainly HA and NP viral proteins.

To monitor quality of produced vaccines, quantitative information about the oligomerization state and molecular assembly of antigens in produced lots is desirable. We have developed a new approach to determine the size distribution of particles in split‐viron influenza vaccine samples by electron microscopy and could thus interpret elution profiles from the asymmetrical flow field‐flow fractionation (A4F) method. Samples were imaged by negative‐stain electron microscopy using organo‐tungstate stain (nanoW, pH 8.0) at 19,000x magnification (5.59 Å/pix) and 4‐μm defocus (Figure 1). About 40‐60 micrographs were initially filtered to remove variations in background and improve signal‐to‐noise ratio [1]. Individual particles were then segmented by a watershed algorithm [2]. Areas of the segmented 2D projections were determined in ImageJ [3] and plotted as histograms of the size distribution. (Figure 2). This approach is able to distinguish among different oligomeric states of HA and NP subunits in the sample, however all larger assemblies and aggregates are not resolved.

In parallel, we analyzed the same samples by A4F. Elution profiles resolved three peaks of small particles (diameter 200 nm). While the first three peaks correspond to the HA and NP oligomers resolved in the size distribution resolved in the analysis by electron microscopy, the latter peaks reflect presence of large lipid vesicles with embedded HA proteins. Interpretation of the A4F elution profiles allows routine screening and monitoring of produced split‐virion influenza vaccines.

This study has been funded by Sanofi Pasteur.
Correlative
SEM
techniques for resolving complex microstructure of
CoCrFeNiZrx
High Entropy Alloys
Authors: Jelen Andreja , Guim Hwanuk , Dolinšek Janez
Published: December 2016

High‐entropy alloys (HEAs) introduce a new concept of developing advanced metallic materials with properties that conventional alloys, based on one principal element, cannot achieve [1]. Other multi‐component metallic systems are quasicrystals (QCs), complex metallic alloys (CMAs) and bulk metallic glasses (BMGs).

HEAs are multicomponent mixtures of 4 to 9, and occasionally up to 20 chemical elements, in similar concentrations, ranging from 5 to 35 at.% each, where the high entropy of mixing can stabilize disordered solid‐solution phases with simple crystal structures like a body‐centered cubic (bcc), a face‐centered cubic (fcc) and a hexagonal close‐packed (hcp), in competition with ordered intermetallic phases and phase‐segregated mixtures [2]. Though the average crystal structure of a HEA is generally simple, microstructure might be highly complex, as will be shown later in this presentation.

In our research, the HEA series CoCrFeNiZr
x
(x = 0.40, 0.45, and 0.50) has been investigated. Various SEM techniques were employed, including backscattered‐electron (BSE) imaging, EDS point analysis, chemical mapping and EBSD.

The results reveal high complexity of the HEAs' microstructure and helped us to determine the grains' composition. Brief outline is presented in the four figures shown below. Figs. 1 and 2 show BSE SEM images. The coarsest interpretation is that the samples are composed of two different types of microstructures: (1) rounded dark phases and (2) fine interweaving of the light and dark phases. Higher magnification of the image in Fig. 2 shows the “invisible borders”, where the fine microstructure changes its character. EBSD investigations at lower magnification (2.000x) revealed that the “invisible borders” correspond to grain boundaries of larger grains (see Fig. 3 – showing different area than Figs. 1 and 2.), whereas more detailed EBSD results at higher magnification of 10.000x (Fig. 4) explained the fine grain structure inside the main grains. Therefore, grains' sizes at two different scales are present in these samples. The effect of Zr content on the HEA microstructure was thus traceable in great detail.
How dark are dark plasmon modes ‐ a correlative
EELS
and
CL
study on lithographed silver nanodisks
Authors: Schmidt Franz‐Philipp , Losquin Arthur , Hofer Ferdinand , Krenn Joachim R. , Kociak Mathieu
Published: December 2016

Plasmonic nanostructures enable the concentration of light to the deep subwavelength regime and, thus, are the topic of intense fundamental and application oriented research. Nanoparticles acting as optical antennas are well known for their nanoscale mode volumes, due to the excitation of localized plasmon modes. In this context electron energy‐loss spectroscopy (EELS) in a transmission electron microscope (TEM) became a powerful technique as it enables to map the full modal spectrum of plasmon eigenmodes with unprecedented high spatial resolution [1–3]. Beside EELS, Cathodoluminescence (CL) has also recently been used to gain information about the optical response taking advantage of the same high spatial resolution in a TEM [4]. While it is stated that EELS is linked to the full photonic local density of states (LDOS), the CL signal is related to the radiative LDOS [5].

In this work we present a combined EELS/CL study of plasmon eigenmodes on silver nanodisks, using fast electrons in a TEM. In particular we compare the differences of the EELS and CL response using experimental and simulated data. Precise variation of the disk size is achieved by means of electron beam lithography (Figure 1a), enabling a comprehensive study of plasmon excitations on silver nanodisks.

From theoretical considerations it is known, that for certain particle geometries (and therefore for specific surface charge distributions) there exist so called dark modes, which are “invisible” to photons but “visible” to electrons, and therefore can be measured with EELS but not with light [6]. Here we discuss how dark these dark modes are comparing EELS and CL (figure 1b+c). In particular, radial breathing modes (C in figure 1b+c) were predicted to be dark modes [6], although we will show how comparison between EELS and CL can mitigate this statement. Additionally, limitations for the theoretical predictions will be discussed, when the particle size is increased and therefore retardation effects become more important. In this case we show that dark modes are getting brighter. Furthermore symmetry breaking by the excitation source itself, a focused fast electron beam, will be discussed.