bluuebunny/crossref_metadata_2025 huggingface dataset:
An artificial neural network based algorithm for three‐dimensional quantitative imaging in optical microscopy
Authors: Van den Broek Wouter , Jiang Xiaoming , Koch Christoph T.
Published: December 2016

In [1] an algorithm was proposed, inverse dynamical photon scattering (IDPS), which uses as a forward model the propagation of the optical wave through the sample and the objective lens with the multislice method. By recasting the forward model as an artificial neural network (ANN), an error metric can be chosen, and the derivatives of this metric with respect to the unknown values of the discretized object become available at the low computational cost of one extra pass through the ANN. These gradients are deployed in a derivative‐based optimization scheme to retrieve a three‐dimensional reconstruction of the specimen; Polak‐Ribière conjugate gradients (PRCG) and alternate directions augmented Lagrangian (ADAL) are opted for. IDPS is implemented on the graphics processing unit.

IDPS is verified using the open source data from [2,3], where two stacked 1995 US Air Force resolution test charts, 110 mm apart, were adopted as specimen. This dataset is acquired with a microscope with a numerical aperture (NA) of 0.1. An LED array is placed sufficiently far away to consider each individual LED to illuminate the specimen with a spatially coherent plane wave. Nine bright‐field and 284 dark‐field images are recorded with LEDs up to 0.44 illumination NA, providing an effective NA of 0.54. Since the central wavelength of the LEDs is 643 nm, the 0.54 NA corresponds to a lateral resolution of 1.20 µm. The resolution of the reconstructions is evaluated as the center‐to‐center distance of the bars in the smallest element in the resolution target that is still discernible: 2.76 µm for element 4 of group 8, and 1.38 µm for element 4 of group 9.

Given that results are obtained from an initial guess of zero, no preprocessing steps such as light field refocusing are necessary. The free choice of error metric is important as the standard choice of sum of squared differences (SSD) leads to a high amount of resolution‐limiting noise, see Fig. 1, and to erratic behavior in the
R
‐factor. The alternative sum of normalized absolute differences (SNAD) yields a better‐behaved and lower
R
‐factor, as well as a better resolution (see Fig. 2). This poses a problem for Gerchberg‐Saxton‐type algorithms since they can be thought of as implicitly minimizing SSD [1].

Estimation of certain nuisance parameters—the focal value and illumination angle in this case—together with the specimen itself, improves the result by decreasing the
R
‐factor and diminishing cross‐talk between layers. Combined with a total variation regularization of the object, achieved by the ADAL approach, a reconstruction with the same resolution and considerably smoother and strongly diminished spurious oscillations is obtained, as is shown in Fig. 3. [4]
Revealing chromatin at different microscopy resolutions
Authors: Schöfer Christian
Published: December 2016

Chromatin in cell nuclei is formed by DNA associated with nucleosomes which consist of the core histone proteins (H2A, H2B, H3, H4). These play a crucial role in genome organization and are well‐known regulators of a variety of biological processes occurring at the DNA template such as transcriptional activity. The histone subtype H3 exists in several varieties. Whereas most varieties are synthesized during S‐phase of the cell cycle, the variant H3.3 is expressed throughout interphase and has been associated with transcriptionally active chromatin [1]. These differences suggest diverging roles of these variants in chromatin organization and function.

Here, we expressed histone H3 variants in normal and malignant cells and compared the nuclear expression patterns at different resolution levels using conventional epifluorescence and confocal microscopy, structured illumination imaging (SIM) and electron microscopy (Fig. 1).

We observed differing distribution patterns of the histone H3 variants within interphase cell nuclei (Fig. 2). In addition, we found distinct banding patterns after expression of histone H3.3 in mitotic chromosomes. Together this indicates differences in functions of these chromatin constituents in the interphase nucleus [2]. Surprisingly, the highly transcribed ribosomal genes within nucleoli were not labelled with histone H3.3 suggesting a difference in nucleosomal architecture or nucleosomal dynamics in active ribosomal genes to genes transcribed into mRNA molecules. In summary, we could demonstrate that histone H3 variants show diverging expression patterns in interphase nuclei and in mitotic chromosomes.
Combining
SEM
with
AFM
for in situ Correlative Microscopy
Authors: Kleindiek Stephan , Dadras Massoud , Schock Klaus , Lieb Andreas , Renka Gregor
Published: December 2016

With the large amount of current research and development focused on nano wires, carbon nano tubes, and other nano scale materials, imaging these materials has become a large part of the challenges involved.

The two most prominent methods for imaging at the nano scale are Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). These complimentary methods utilize fundamentally different principles for generating imagery ‐ SEM exploits the interaction of electrons with matter, while AFM is based on physical interaction of a sharp tip with the sample surface.

Both approaches have strengths and weaknesses. The SEM's strength is to quickly generate images with a large range of magnifications, making it easy to locate the area of interest. Additionally, the SEM beam can be used to characterize materials beyond mere imaging (e.g. EDX elemental mapping, etc.). Beyond that, the use of Focussed Ion Beams (FIB) enhances the ability for modification or preparation of samples.

However, scanning beams do not yield 3D information, e.g. “invisible” contamination layers or the precise surface structure of novel materials such as solar cells.

The AFM's main advantage lies in its ability to obtain 3D information, the downsides are that it is hard to find the target area and image generation is slow.

Combining these two tools into one setup ‐ putting an AFM inside an SEM ‐ gives quick access to a more complete data set. Additionally, FIB‐milled or FIB‐deposited structures can be characterized using this combination of tools in a FIB/SEM system.

The utility of this combination of tools is demonstrated with several examples where locating the area of interest purely by AFM or light microscopy would have been highly impractical.
Structural Verification of Magnetite Nanocrystals in
PVDF
‐fibers by Scanning Electron Nano Diffraction (
SEND
)
Authors: Wirch Nelly , Slabu Ioana , Theissmann Ralf , Krüger Maria , Weirich Thomas E.
Published: December 2016

Incorporation of inorganic nanocrystals in polymer fibers is always a challenging process with two major requirements,
i.e
. the particles should be homogenously distributed in the polymer matrix and the nanomaterial properties must be kept during the processing of the fibers. These criteria become even more demanding if the final product is intended for later medical application, where the material must comply with the high safety standards. However, the incorporated total nanoparticle concentration in polymer fibers is usually very low, which implies that certification of the unaltered crystal structure of the nanomaterial cannot be achieved by conventional XRD methods. Within the present study we demonstrate that
Scanning Electron Nano Diffraction
(SEND) [1] in a STEM is a suitable alternative technique to XRD for handling this issue. Thus the SEND method was applied on magnetite (Fe
3
O
4
) nanocrystals incorporated in melt spinned polyvinylidene fluoride (PVDF) fibers for verifying the inverse spinel structure of the iron oxide particles. The diffraction experiments were carried out in a FEI Titan S/TEM @ 300 kV using ultrathin cross section samples received from ultramicrotomy on resin embedded nano magnetite loaded PVDF‐fibers. Within one measuring campaign a total number of 100 diffraction patterns were recorded from sample regions ranging from 21x21 nm
2
to 34x41 nm
2
in size. Interplanar spacings and angles between the diffraction spots were determined from 12 unambiguous indexed zone axis patterns and used for verifying the structure of magnetite and for calculation of the cubic lattice parameter. Hence evaluation of 90 unique indexed interplanar spacings in the range between 4.8 Å and 1.0 Å yielded a lattice parameter of
a
= 8.36(9) Å for the cubic unit cell with
Fd‐3m
symmetry.
Spin polarisation with electron Bessel beams?
Authors: Schattschneider Peter , Grillo Vincenzo , Schachinger Thomas , Löffler Stefan
Published: December 2016

Despite the statement of Bohr and Pauli that Stern‐Gerlach based spin separation for electrons cannot work [1], it has been argued that spin separation or filtering of electrons is possible in particular geometries [2,3]. The argument has been debated, see e.g. [4], and it seems that the effect exists but is too small to be exploited with present day technology. As of now, no Stern‐Gerlach design of a spin polarizer for free electrons was successful. On the other hand, an unexpected intrinsic spin‐orbit coupling (SOC) in relativistic vortex electrons was discovered, and it was proposed to use this effect to construct a spin filter for free electrons [5]. Recently, it has been shown [6] that crossed electric and magnetic quadrupole fields correspond to so‐called q‐plates which are used in laser optics for spin‐to‐orbital moment conversion (STOC). In combination with electron vortex beams, this opens the possibility to couple the spin of free electrons to the spatial degree of freedom, and so design a spin filter [7]. However, the realisation of such devices is hampered by severe geometric constraints.

Here, we propose a different approach exploiting the magnetic fields created by the lenses already present in conventional TEMs. The vector potential of a round magnetic lens in the TEM has cylindrical symmetry over the propagation axis. This is equivalent to an optical q‐plate. Such a field can be used as a STOC device quite similar to the optics case because the total angular momentum J= L + S is a constant of motion. Thus, it seems that electron microscopes are intrinsic spin polarizers. Basic considerations show that a vortex beam of order one passing a standard magnetic round lens (the objective lens in the present case) is intrinsically spin polarized. As shown in Fig. 1, the vortex in plane A can be seen as a continuous line of point sources (red dot) on the ring aperture, each of which results in a tilted plane wave in B. Classically, the momentum p of the particle in A is tilted by the Lorentz force to p’ at B (grey arrows). The spin vector (red arrows) performs a precession in the magnetic field when going from A to B. Conservation of the total angular momentum J=L+S creates small contributions of Bessel beams J
0
or J
2
, depending on the original spin polarisation in plane A, which are superimposed onto the dominant J
1
beam in plane B. This spin‐to‐orbit coupling allows spin filtering because J
0
and J
2
have different radial profiles.

In the limit of infinitely small detectors on axis, the spin polarisation tends to 100 %. Increasing the detector size, the polarisation decreases rapidly, dropping below 10
−5
for standard settings of medium voltage microscopes. For extremely low voltages, the figure of merit increases by two orders of magnitude, approaching that of existing Mott detectors (Fig. 2).

Our findings may lead to new desings of spin filters, an attractive option in view of its inherent combination with the electron microscope, especially at low voltage.
Nanoscale characterization of Co and Co‐B catalytic coatings before and after catalytic tests for the sodium borohydride hydrolysis
Authors: Beltrán Ana M , Paladini M , Godinho V , Arzac G.M. , Jimenez de Haro M.C. , Fernández A
Published: December 2016

The use of hydrogen as a potential future energy carrier is limited due to the problems of its storage. Hydrolysis of hydrogen storage materials such as sodium borohydride (NaBH
4
, SB) has been one of the most investigated approaches for hydrogen generation. SB is stable in dry air and combines lightweight with high hydrogen content (10.8 wt%).

Although spontaneous, the SB hydrolysis (reaction 1) needs catalysts to occur at appreciable rates. Co has demonstrated to be a good choice because its compromise between activity and cost. However, its major drawback is related to stability: these materials deactivate upon cycling. Despite the great number of works reporting Co and Co‐B based catalysts, the nature of the active phase and deactivation mechanisms are still under intense discussion.

We have recently reported the preparation of supported Co metallic catalysts as thin films by magnetron sputtering for sodium borohydride hydrolysis [1]. Magnetron sputtering is a very versatile technique used in this work to fabricate Co and CoB catalytic coatings under different deposition conditions and supported on different substrates (i.e. silicon and polymeric membranes). In this work we have been able to study by electron microscopy the catalytic coatings as grown on the wires of the polymeric membranes. The structural and compositional characterization by SEM and (S)TEM techniques has been performed before and after the catalytic tests (19 wt% SB in NaOH 4 wt%, 90 min reaction time). Fig. 1 and 2 show the SEM morphology of a Co thin film on the polymeric membrane before and after the catalytic test, respectively, showing the growth of a new layer onto the catalysts upon operation. Further nano‐analysis of the structure and compositional distribution have been performed by (S)TEM techniques coupled to EELS. They also reveal the formation of fiber/nanoflake‐like nanostructures onto the catalytic coatings (Fig. 3 and Fig. 4). Compositional analysis have pointed out the formation of Co‐borates and most likely cobalt oxide/hydroxide nanoflakes (i.e. CoO(OH)) which could be the origin of the leaching and deactivation mechanisms of the Co‐based catalysts for the investigated reaction.
Aberration corrected environmental
STEM
(
AC ESTEM
) for atom‐by‐atom analysis of nanoparticle catalyst activation and deactivation mechanisms
Authors: Boyes Edward , Ward Michael , Martin Thomas , Lari Leonardo , Mitchell Robert , LaGrow Alec , Lloyd David , Wright Ian , Gai Pratibha
Published: December 2016

The core design for the modern ETEM (1, 2), of which there are now some 20 replicates worldwide, has been modified to support full ESTEM functionality and to be compatible with a different basic instrument, in this case the JEOL 2200, with a series of differentially pumped column sections separated by fixed beamline apertures reconfigured for purpose in size and position.  Single atom resolved HAADF imaging and full analytical functionalities, including wide angle electron diffraction, CBDP, EDX and EELS, are enabled under controlled chemical reaction conditions of high temperatures in a continuously flowing gas atmosphere around the supported nanoparticle catalysts samples while retaining sub‐Angstrom resolution and single atom sensitivity for atom‐by‐atom analysis of critical processes.  The novel AC ESTEM machine at York provides new insights into the processes of metal nanoparticle catalyst activation, operational state and deactivation (3) which have economic and other societal importance, including for scientifically informed environmental management.   At typical 2‐20Pa gas pressures the gas supply covers the sample surface with multiple 1000s of monolayers of gas per second and generally fully adequate to continuously flood the surface with gas molecules.  They drive the chemistry under conditions defined in surface science as 'high pressure' (4) and minimise e‐beam driven artefacts.  Catalysis is a massive industry with highly leveraged investments in processes and plants.  However, in many applications, including automotive emission controls (5), it is still relatively inefficient compared to what might be possible with a better informed knowledge base generating strategies to restrain deactivation processes.   The unique to York AC ESTEM supports quantitative atom‐by‐atom analysis of the underlying mechanisms of Ostwald Ripening (OR) through atom detachment, migration and re‐attachment at lower temperatures around constant particle centres of gravity (6,).  This is compared with (and sometimes mixed with) higher temperature modes of particle migration and coalscence (PMC), with local nanostructure attributes in the round influencing local outcomes.  Neither process is found to be sensitive to gas pressure at 2‐20Pa levels.   Both mechanisms have now been studied with new levels of precision using the novel capabilities at York; leading to a better informed understanding of the technical problems and options and helping to specify the enabling developments needed going forward.
Developments in unconventional dark field
TEM
for characterising nanocatalyst systems
Authors: Thirunavukkarasu Gnanavel , Ward Michael R , Gai Pratibha L , Boyes Edward D
Published: December 2016

Recent methods of dark field TEM are being explored to extent the information and frequency of data capture in dynamic in‐situ experiments on nanocatalyst systems under reaction conditions (1). The broad need is for a faster frame rate than can conveniently be achieved with HAADF STEM imaging, starting from the similarly expressed goals for tomography of Bals et al (2) and gentle high resolution by Zhang et al (3). Beam stop spiders described in (2,3) and other geometries including displaced aperture arcs stopping the central beam have been explored. FIB fabricated custom devices have been introduced into a custom mechanism using regular 3mm apertures for easier customisation. This is primarily inserted into the high contrast (lower) objective aperture position on our modified JEOL 2200FS with aberration correctors for both TEM image and STEM probe. The preliminary results with the new applications are encouraging with 0.2nm lattice images recorded from larger (~10nm) particles (Fig.1) and sensitivity down to a few atoms (Fig.2) recorded using 1 second exposures, rather than requiring 10x that for direct STEM methods. The aim is to be able to track individual migrating atoms and nanoparticles with sufficient frequency to have confidence for each one in their source and endpoint to better inform our understanding of key coarsening mechanisms (4) which lead to catalyst inefficiencies, including in environmental emission controls (5). This requires analysis at sufficient frequency that the mean atom/nanoparticle movement is significantly less than the spacing between sites.
In vitro hemocompatibility of thin films materials for direct blood contact
Authors: Major Roman , Trembecka‐Wojciga Klaudia , Lackner Jurgen M , Plutecka Hanna
Published: December 2016

The main objective of the study was modified surface thin film materials deposited on polymer substrate constituting the microenvironment for the uptake and controlled differentiation of stem cells the controlled share caused by residual stress and optimized stiffness of the surface using the plasma methods.

Plasma surface modification method generating a controlled part of residual stress in the coating affect the formation of the surface topography in the form of a nano‐ wrinkles similar to the niches in the tissue environment where stem cells are stored. Niches like structures can catch stem cells from blood flow and prevent their rapid differentiation. Topography and stiffness of the surface of the coating allow for targeted cellular differentiation. The properly formed full confluence of the endothelial cells effectively inhibits blood clotting processes.

The challenge of the work was to develop the surfaces which would mobilize and activate stem and progenitor cells. The idea was to produce the surface containing the niche like structures, the most appropriate structure for the stem cells. The coatings were developed with controlled residual stresses participation, proper microstructure (Fig. 1) and mechanical properties. Controlled share of residual stress created nano‐wrinkles, similar to the niches where stem cells reside in the natural conditions. The creation of stress generated wrinkles did not lead to delaminating of the coating from the substrate. The coating adhered well to the substrate, and wrinkles provided the cellular microenvironment (Fig. 2). The microstructure and mechanical properties were the key factor that determined the controlled cellular differentiation. The differentiation of stem cells was carried out for endothelial cells formation. The following scientific problems were studied: the anchoring mechanisms of the coating to the polymeric substrate, the effect of ion methods for surface modification towards the microenvironment creation for the stem cells and blood‐ material interaction.
Heterogeneous interfacial chemical nature and bonds in an
Al
matrix composite reinforced with
W
‐coated diamond particles
Authors: Gang Ji , Zhanqiu Tan , Yinggang Lu , Dominique Schryvers , Zhiqiang Li
Published: December 2016

Over the last decade, a diamond particle reinforced Al matrix, namely diamond/Al, composite has been developed for thermal management applications, mainly in the microelectronic industry. This composite has demonstrated an excellent combination of a Thermal Conductivity (TC) as high as 600 W/mK and a Coefficient of Thermal Expansion (CTE) lower than 10 ppm/K, being compatible with that of electronic components. However, considering the TC (~ 1800 W/mK) of the diamond particles incorporated, it is clear that the overall TC enhancement has not been completely exploited in the composite. One then points at the diamond/Al interface, which should provide good adhesion as well as maximal Interfacial Thermal Conductance (ITC) in order to facilitate thermal exchange across the diamond/Al interface.

Our analytical modelling has recently predicted that introduction of a W interface nanolayer is one of the most efficient ways to achieve high ITC, which provides a practical guide for interface engineering. Accordingly, a cost‐effective sol‐gel process has been tentatively used to deposit the W coating for diamond surface metallization. Compared with the diamond/Al counterpart, TC of the composite with such a W nanolayer improved more than 20 %. In this work, Scanning Transmission Electron Microscopy (STEM)/Energy‐Dispersive X‐ray spectroscopy (EDX) and Precession Electron Diffraction (PED) have been performed in order to investigate interface configurations of a W‐coated diamond/Al composite. The aim is to study the effect of interface formation, reaction and diffusion on the ITC.

The results indicate that the deposited W coating is discontinuous, and consists of nanoparticles with a size in the range 30‐400 nm and homogenously covering the surface of the diamond particle (Figs. 1a and 1b). The average coating thickness is estimated to be around 200 nm (Fig. 1c). A STEM/ADF image in Fig. 1d shows that the formed diamond/Al interface has a heterogeneous configuration at the nanoscale where Al grain contrasts and a particle with high Z contrast are revealed. STEM/EDX mapping in Fig. 2 displays a W and Al rich interfacial particle. Visible O traces can be related to fine microstructural features. Alternatively, a 'clean' diamond/Al interface is tightly‐adhered and is not rich in O (Fig. 3). As shown in Fig. 4, PED zone‐axis patterns recorded from the W and Al rich particles are indexed to be the Al
12
W phase (Cubic,
I2/m‐3,
No. 204). Such different chemical nature of the bonds at the interface can have a pronounced effect on the local ITC [1,2].
Microscopic study of friction layer and the distribution of components in automotive brake pads
Authors: Dedkova Katerina , Peikertova Pavlina , Wilhelmi Tamara , Morbach Marcus , Kukutschova Jana
Published: December 2016

Brake pad is a complex, multicomponent system consisting of reinforcing agents, abrasives, lubricants, binders, fillers and in some cases elemental metals. Numerous mechanical properties of this system are required and are related to the distribution of components in its volume. Friction layer is in contact with cast iron disc and distribution of single components there is crucial for the braking process. Due to high pressure and temperature achieved, various changes of chemistry and morphology during braking process occur. In this study commercially available automotive brake pads and newly developed brake pads modified with kaoline were investigated using light optical digital microscopy and scanning electron microscopy with EDS which enabled to create maps of elemental distribution. New unused brake pads and pads after AK master braking procedure were investigated. Combination of two microscopic techniques provided detailed information about the structure and its changes in such a complex system as brake pad is. This information will help to understand the process of friction layer formation and wear particles emissions.
Engineering the Contrast Transfer through the
Cc/Cs
Corrected 20–80
kV
SALVE
Microscope
Authors: Börrnert Felix , Biskupek Johannes , Lee Zhongbo , Linck Martin , Hartel Peter , Müller Heiko , Haider Maximilian , Kaiser Ute
Published: December 2016

Modern aberration‐corrected transmission electron microscopy (AC‐TEM) is able to routinely image sample structures with true atomic resolution with a resolution better than 1 Å. Unfortunately, the energy of the electrons used for imaging accelerated with voltages of 200–300 kV damages the samples under observation. Especially, light elements suffer severe damage via the knock‐on mechanism [1–3]. To avoid this kind of sample damage, imaging at lower acceleration voltages of 60–80 kV became popular recently to undercut the threshold for knock‐on damage and thanks to geometrical aberration correction, an image resolution of below 2 Å can be maintained. One interest when performing atomic resolution microscopy of thin and/or light‐element materials lies in interfaces and defects and there, the aforementioned damage threshold is significantly lowered calling for even lower imaging electron energies [4,5].

In TEM at acceleration voltages of 30 kV and lower, in addition to the spherical aberration, the chromatic aberration coefficient of the imaging lens limits the resolution. The chromatic aberration can be corrected by using a C
c
/C
s
corrector [5] or it can be minimized by employing a monochromator for the primary electrons [6].

In this contribution, we discuss the optimum imaging parameters for the contrast transfer through the 20−80 kV C
c
/C
s
corrected SALVE (sub angstrom low voltage electron microscope) instrument. This includes the influence of a partially adjustable positive fifth order spherical aberration. Positive and negative phase contrast transfer are compared with the help of graphene images taken at different electron acceleration voltages; in the example in Figure 1 imaging has been performed at 30 kV at positive and negative atom contrast; as can be seen from the Fourier transform inserted, frequencies up to (107 pm)
−1
have been transferred [7].
Structure and viability of atypical morphological forms of
L
yme disease spirochetes
Authors: Vancová Marie , Rudenko Nataliia , Maryna Golovchenko , Strnad Martin , Bílý Tomáš , Grubhoffer Libor , Nebesářová Jana
Published: December 2016

Spirochetes Borrelia burgdorferi sensu lato are the causative agents of Lyme disease transmitted by the hard ticks of the genus Ixodes. Spirochetes are motile bacteria with typical flat‐wave morphology. These features are crucial for efficient dissemination and evasion of immune responses. However, several reports described presence of non‐motile atypical morphologies, e.g. rod‐shaped forms, looped/ring shaped forms and spherical/cystic forms called round bodies (RBs). These forms were observed in the cerebral cortex of patient with chronic Lyme neuroborreliosis [1]. Recently, we proved long term survival of Borrelia in patients after extended antibiotic treatment by successful isolation of live spirochetes [2].

Now, we would like to answer questions, (i) whether RBs represent resistant forms of persisting Lyme disease spirochetes and (ii) whether the transformation of flat‐waved spirochetes into RBs forms influences the capability to withstand unfavourable environmental conditions.

For this purpose, we studied morphology and three dimensional arrangements of spirochetes isolated from patients by transmission electron microscopy and electron tomography on serial resin sections and negatively stained spirochetes. Next, using a modification of our novel approach combining cryo‐fluorescence and cryo‐scanning electron microscopy, we interconnect viability assay with visualization of morphology at high resolution [3]. Viability of GFP expressing spirochetes in a response to host sera was assessed using propidium iodide exclusion method. Obtained results confirmed different susceptibility to different host sera, previously described by our colleagues [4]. We confirmed the formation/viability of RB forms under specific conditions.
Investigating lattice strain in Au nanodecahedrons
Authors: Goris Bart , De Beenhouwer Jan , De Backer Annick , Zanaga Daniele , Batenburg Joost , Sanchez‐Iglesias Anna , Liz‐Marzan Luis , Van Aert Sandra , Sijbers Jan , Van Tendeloo Gustaaf , Bals Sara
Published: December 2016

The three dimensional (3D) structural characterization of nanoparticles is crucial in materials science since many properties heavily depend on size, surface to volume ratio and morphology. In addition, the ability to investigate the crystal structure is just as essential because the presence of defects and surface relaxation will directly affect plasmonic or catalytic properties. A well‐known example of strained nanoparticles are the so‐called “nanodecahedra” or “pentagonal bipyramids”. Such particles consist of five segments bound by {111} twin boundaries, yielding a crystallographic forbidden morphology. Therefore, measuring strain fields in nanodecahedra by transmission electron microscopy (TEM) has been the topic of several studies. However, it is important to note that such studies are based on 2D projections, hereby neglecting the 3D nature of the lattice strain. [1,2] Here, we will quantify the lattice strain in 3D based on high resolution electron tomography reconstructions. [3]

Therefore, a continuous tilt series of 2D projection images was acquired using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) and a dedicated alignment procedure was applied. These projection images are then used as an input for a model based tomography reconstruction algorithm. A major disadvantage of conventional reconstruction techniques is that a continuous volume is reconstructed hampering the extraction of atom coordinates without the use of dedicated post‐processing methods. [4] We could overcome this limitation by assuming that the 3D atomic potential can be modelled by 3D Gaussian functions. This hypothesis significantly simplifies the reconstruction problem to a sparse inverse problem, yielding the coordinates of the individual atoms as a direct outcome of the reconstruction.

Visualizations of the final 3D reconstruction, obtained for a Au nanodecahedron containing more than 90,000 atoms, are presented in Figure 1.a–c along different viewing directions. Since the coordinates of the atoms are a direct outcome of the reconstruction, it becomes straightforward to calculate the 3D displacement map. We computed derivatives of the displacement map in such a manner that 3D volumes were obtained corresponding to ε
xx
and ε
zz
. Slices through the resulting ε
xx
and ε
zz
volumes are presented in Figure 1.d and Figure 1.f. Furthermore, the variation of the lattice parameters was investigated along x and z based on the same slices (Figure 1.e and Figure 1.g). Both along the x and z direction a systematic outward expansion of the lattice can be observed. The expansion along z is limited to a few of the outer atomic layers and shows an asymmetry (Figure 1.f–g) that is likely related to the fact that the decahedron is deposited on a carbon support.
In situ scanning and transmission electron microscopy experiments developed at the University of Picardy: a versatile approach optimized for the study of lithium‐ion batteries and extended to the observation of plant tissues
Authors: Dupont Loic , Demortiere Arnaud , Davoisne Carine , Jamali Arash , Dachraoui Walid , Giannini Mattia , Miart Fabien , Grouther Damien MC , Brydson Rick
Published: December 2016

Over the past fifteen years, the Platform of Electron Microscopy at the University of Picardy Jules Verne (PME UPJV) has been developing
in situ
scanning electron microscopy techniques to successfully observe polymer [1] and solid or liquid electrolyte lithium‐ion batteries cycling in the scanning electron microscope (figure 1).
In situ
Electron Microscopy techniques allow to spot the slightest textural, chemical or structural modification of lithium‐ion electrodes, interfaces and active materials. Consequently, such innovative studies help electrochemists to design batteries with better performance through the selection/synthesis of the appropriate electrode materials and the control of the electrode/electrolyte interfaces upon cycling.

However, considering the ‘resolution limit’ of the SEM, electrochemists working on lithium‐ion batteries tend towards
in situ
transmission electron microscopy to fulfill their ambition of atomic‐scale observations of electrochemical cycling. Nevertheless, there are several technological bottlenecks in using such techniques. For instance restrictions imposed by the limited sample size and thickness (less than 100nm) and the requirement of high vacuum necessitate the use of adapted strategies (all‐solid‐state batteries, ionic liquid as electrolyte, STM or liquid bias TEM holder)[2,3,4]. To address these issues, we undertook two different approaches: cycling all‐solid‐state microbatteries with a Nanofactory STM holder [5] (figure 2) and cycling liquid electrolyte batteries with a Protochips liquid/bias Holder.

We are extending now the application of these developed methods at PME UPJV to perform
in situ
analysis of samples from another branch of natural science: Plant Biology (from seeds to biorefinery). The
in situ
electron microscopy analyses will be performed to characterize the role of plant specialized cell layers (figure 3) and lignocellulosic biopolymers and examine their modification as a result of seed germination, enzymatic modifications, micromechanical tests as well as plant pathogen interactions.
Measurement of mechanical properties gradient on impact‐based transformed surfaces: Nano‐mechanical testing in graded micro‐structured α‐iron
Authors: TUMBAJOY‐SPINEL David , DESCARTES Sylvie , BERGHEAU Jean Michel , JOAO Sergio SAO , GUILLONNEAU Gaylord , MICHLER Johann , KERMOUCHE Guillaume
Published: December 2016

In the industry, there are several techniques which improve the service lifetime of materials by increasing the local mechanical properties in the near‐surface. In the case of mechanical surface treatments (such as impact‐based), the material is exposed to repeated mechanical loadings, producing a severe plastic deformation in the surface, and then leading to a local refinement of the microstructure into the affected zone (Tribologically Transformed Surfaces – TTS). The microstructure's transformation is characterized by a progressive increment of the grain size from the surface until the bulk material. Consequently, very interesting physical properties such as high hardness and better tribological properties are exhibit in these mechanically‐induced transformed surfaces. Nowadays, it is well‐known that the grain size gradient generated provokes an evolution on the mechanical properties in the impacted zone over a few tens of microns. However, a simple micro‐hardness test is not quite enough to quantify precisely the engendered variation of mechanical properties due to the heterogeneity of the transformed surface. The main issue of this work is to assess and describe precisely the elastic‐plastic behavior and the distribution of mechanical properties on deformed zones of a model material (pure α‐iron). In our project, a characterization of the transformed microstructure, as well as a statistics measurement of the grain size distribution on the cross‐section of the sample is presented firstly. Afterwards a methodology based on nano‐indentation tests (Figure 1) and in‐situ micro‐pillars compression tests (Figure 2) is implemented to quantify the evolution of mechanical properties starting from the near‐surface. A relation between the hardness gradient and the microstructure evolution is established, as well as a comparison between the properties measured by both techniques is discussed.
Ten years of
EMCD
: what has been achieved
Authors: Schattschneider Peter , Schachinger Thomas , Löffler Stefan
Published: December 2016

Energy loss magnetic chiral dichroism (EMCD), established in 2006 [1] celebrates its 10
th
anniversary. EMCD is the TEM equivalent of the X‐ray magnetic circular dichroism (XMCD) technique routinely applied on synchrotron beam lines for the study of magnetic moments. The EMCD signal is detected as an asymmetry in the energy filtered diffraction pattern, or alternatively as a slight difference in the fine structure of energy loss spectra for particular momentum transfers in the inelastic interaction (Fig. 1). The extremely high spatial resolution of modern TEMs makes EMCD interesting for spintronic and micromagnetic applications. In the last decade, the technique has evolved into a reliable tool demonstrating nm‐resolution, site selectivity and separation of spin and orbital moments via sum rules.

One of the consequences of EMCD is that the outgoing inelastically scattered probe electrons have topological charge. Structurally, they are identical with vortex electrons that can be routinely created in the electron microscope [2]. Such vortices are characterized by a spiraling wavefront and a phase singularity at the center, similar to optical vortices that were first described by Nye & Berry [3]. Owing to their short wavelength, these matter waves can be focused to atomic size. Another novel aspect is their magnetic moment, quantized in multiples of the Bohr magneton, independent of the electron spin. These features make electron vortices extremely attractive as a nanoscale probe for magnetic materials.

The discovery of vortex electron beams has spurred efforts to use them for EMCD because of their intrinsic chirality. It became soon clear that atom‐sized vortices are needed to achieve this goal [4], as shown in Fig. 2. At the time of writing, the closest successful approach to such beams is the shaping of the incident wave front with a Cs corrector such that it matches the point group symmetry of the selected atomic column, revealing EMCD signals with atomic resolution [5]. A promising alternative is the use of holographic vortex filters in the outgoing beam to detect spin polarized transitions [6], as sketched in Fig. 3. Other than in the standard EMCD geometry, this approach does not require a precise alignment of the crystal, and would thus allow the study of nanocrystalline and amorphous materials.
Novel Linkage Technology of the Shared Alignment Sample Holder for Same Area Observations with Electron Microscopy and Scanning Probe Microscopy
Authors: Diestelhorst Ulrich , Yamaoka Takehiro , Ando Kazunori , Hashimoto Yoichiro
Published: December 2016

We developed an innovative air protection sample holder enabling a hermeneutically sealed sample transfer from Hitachi's ion milling instrument to the Field Emission Scanning Electron Microscopes (FE‐SEM) and the environment control high‐vacuum Scanning Probe Microscope (SPM) AFM5300E for a correlative microscopy (Figure 1). In a previous study, we explained the advantages of this sample holder with regard to the analysis of cathode materials in a lithium‐ion battery [1].

Our novel SEM‐SPM linkage system with the shared alignment sample holder enables a software‐based alignment of the same measurement area for a comprehensive analysis of sample surfaces with Hitachi's FE‐SEM SU8200 Series and the new midsize‐sample SPM AFM5500M, characterized by the automation of the cantilever exchange, laser alignment, feedback parameter tuning and data processing (Figure 2). As the XY‐stage of both microscopes drives with high accuracy to the desired area by only registering three specified coordinates of the sample stage, this linkage system facilitates a correlative microscopy of samples that are difficult to align optically. In this study, we used this technology to analyse a multilayer graphene on a SiO
2
substrate. For an observation of graphene, FE‐SEM is one method to explain the relationship between SE contrasts and the thickness of graphene layers. Another method is the Kelvin force microscopy (KFM) explaining the quantitative relationship between surface potentials and topographic heights. Thus, a linkage of both observation methods enables a correlative analysis of SE contrasts, topography and surface potentials.

Figure 3 shows the SE image obtained at a accelerating voltage of 0.5 kV, topography and the KFM image of a multilayer graphene on a SiO
2
substrate measured with the linkage system. The grey island structure with two different contrasts and several lines in the SE image are well aligned with the topography and KFM images. Analysing the topography, we confirmed that SE contrast differences result from single graphene step heights. Furthermore, we have learned that the surface potential of a bilayer graphene is 15–20 mV higher than that of a monolayer graphene.

In conclusion, the linkage system is a tool for a comprehensive analysis of a sample's composition, structure, 3D topography, mechanic and electro‐magnetic properties with the SEM and SPM instruments without any constraints in regard to their performances.
3D Mapping of electric potentials and magnetic fields at the nanoscale using Electron Holographic Tomography
Authors: Wolf Daniel , Lubk Axel , Lichte Hannes
Published: December 2016

Off‐axis electron holography (EH) is a TEM technique that records the phase information of an electron wave transmitted through a thin specimen in an electron hologram. By reconstructing this phase information, it enables electrostatic and magnetic potentials to be mapped quantitatively with high spatial resolution and, when combined with tomography to electron holographic tomography (EHT), in three dimensions (3D) [1,2]. Tomograms obtained by EHT provide the 3D mean inner potential (MIP) distribution of nanoscale materials from which the 3D morphology and the chemical composition can be inferred [3]. Moreover, functional potentials,
e.g
., introduced by doping of impurities in semiconductors, have been successfully revealed in 3D [4]. Recently, we succeeded in the 3D reconstruction of the axial component of the B‐field prevailing in magnetic nanowires [5,6].

EHT as applied on magnetic samples proceeds as follows (see Fig. 1): (1) an electron hologram tilt series (ideally covering a range of 360°) is acquired, (2) the phase image tilt series is reconstructed from the holograms, (3) electric and magnetic phase shifts are separated by computing half of the sum/difference between opposite (180° tilted) projections, and (4) both the electric potential and the B‐field component parallel to the tilt axis are reconstructed with tomographic techniques. Here, we report EHT studies achieved by means of tomography‐dedicated TEM sample holders, in combination with advanced in‐house developed software packages for acquisition, alignment and tomographic reconstruction.

Fig. 2 shows the 3D electric potential reconstruction of a GaAs/AlGaAs core‐multishell nanowire (NW) grown by metalorganic vapour phase epitaxy (MOVPE) using an Au nanoparticle (NP) as catalyst. Such NWs may serve as novel coherent nanoscale light sources (lasers), because they provide an effective gain medium, low‐loss optical waveguiding, and strong optical confinement for axially guided optical modes. The difference in the MIP allows discriminating between GaAs and AlGaAs within the NW. Longitudinal (Fig. 2b) and cross‐sectional (Fig. 2e) 2D slices averaged over a well‐defined thickness reveal not only the GaAs core and the AlGaAs shell, but also a 5nm thin GaAs shell within the AlGaAs, which acts as a quantum well.

Fig. 3 comprises two recent EHT studies revealing the B‐field within a Co nanowire (NW) [5] and a Co
2
FeGa Heusler alloy NW [6] both with spatial resolution higher than 10 nm. The reconstructions of the dominant axial component of the magnetic induction exhibit a small inversion domain at the apex of the Co NW, whereas at the Co
2
FeGa NW, a magnetic dead layer of 10 nm width could be revealed.

The powerful approach presented here is widely applicable to a broad range of 3D electric and magnetic nanostructures and may trigger the progress of novel nanodevices.
On the morphology of
Li2S
deposits in
Li‐S
batteries
Authors: Giannini Mattia , Mastouri Afef , Demortière Arnaud , Dražić Goran , Davoisne Carine
Published: December 2016

Lithium‐Sulfur batteries are thought to be the future of Li‐ion batteries thanks to their high theoretical specific capacity (1675 mAh.g
‐1
) and low‐cost. However, the real‐life application of Lithium‐Sulfur batteries is still hindered by limitations such as the formation of highly insulating and insoluble species at the cathode (e.g. Li
2
S), mechanical instability of the electrodes and capacity fading due to polysulfides shuttle effect [1]. It is crucial for the development of Lithium‐Sulfur batteries to gain a better understanding on the chemical and microstructural changes which take place at the electrodes upon electrochemical cycling.

We will present the results of our SEM and (S)TEM investigation on the microstructural, crystallographic and chemical properties of the species formed at the cathode during galvanostatic cycling at different discharge rates. We have cycled a Carbon/Sulfur composite material using a Swagelok type cell with Li metal anode with 1M LiTFSI‐TEGDME/DIOX electrolyte. All materials were handled in O
2
‐free conditions.

The studied cathode is formed by carbon nanoparticles having 30 to 50 nm diameter and two types of morphology; regular solid and irregular core‐shell‐like. HR TEM imaging associated with spectroscopy techniques show that sulfur forms a uniform, amorphous coating on the carbon particles.

After full discharge at slow rate (C/20), a porous desert‐rose‐like deposit was observed, whereas at faster rate (1C) a particulate conglomerate discharge product was locally concentrated on the C/S composite (Fig. 1); we infer these discharge products to be Li
2
S deposits.

At the nanometric scale, both slow and fast cycling result in the deposition of a 1 to 2 nm thick Solid Electrolyte Interphase (SEI) onto the carbon particles. Moreover, slow cycling promotes the formation of cubic (
Fm
3
m
) Li
2
S nanocrystals up to 30 nm in size (Fig.2).

These observations suggest that fast and slow discharge rates promote the formation of amorphous and crystalline Li
2
S, respectively.