bluuebunny/crossref_metadata_2025_split huggingface dataset:
How nanoparticles disturb the lipid bilayer vesicles
Authors: Er‐Rafik Meriem 
Published: December 2016

Meriem Er‐Rafik*,(1),Khalid Ferji (2), Olivier Sandre (2), Carlos M. Marques (1), Jean‐Francois Le Meins (2), Marc Schmutz (1)

Institut Charles Sadron, Université de Strasbourg‐CNRS UPR 22, 67034 Strasbourg, France

Laboratoire de Chimie des Polymères Organiques (LCPO), Université de Bordeaux, CNRS, 33607 Pessac, France

Innumerous molecules and particles, from simply water to complex proteins or self‐assembled small liposomal carriers, can frequently interact with the cell membrane with possible modification on it. Despite a constant increase of the variety of new particles or molecular assemblies, due to rapid progress in nanotechnology, the molecular features determining how is the membrane behaviour with respect to a given molecule are not yet elucidated.
Here, we will present a new mechanism of the lipid bilayer of liposomes behaviour in presence of nanoparticles investigated by cryo‐electron tomography. Cryo‐electron microscopy is a relevant technique allowing not only to inspect the structure of the membrane, by resolving for instance the two leaflets of the bilayer, but reveals also geometric features of nanoparticles such as size and shape that play an important role for the potential interaction with lipid bilayer (fig. 1). Cryo‐electron tomography resolve in 3D space the relative positions of particles and membranes, providing insight into the interplay between particle‐lipid interactions and the ensuing bilayer transformations.
The complex structure of catalyst particles used in fluid catalytic cracking
Authors: Krumeich Frank , Diaz Ana , Menzel Andreas , Holler Mirko , Guizar‐Sicairos Manuel , Sanchez Dario Ferreira , Grolimund Daniel , van Bokhoven Jeroen , Shu Yuying , Cheng Wu‐Cheng 
Published: December 2016

The refining of crude oil by conversion of its heavy fraction into gasoline and light olefins represents an important industrial process providing a valuable source for fuel and basic chemicals. The catalyst for this reaction, the so‐called fluid catalytic cracking (FCC), is a complex composite of multiple components, including zeolites, clay, and various minor additives with certain catalytic or structural functions. The many reaction and regeneration cycles during long‐term operation change the structure of the FCC particles, leading to a decrease of their catalytic activity. To understand this deactivation, it is essential to derive a three‐dimensional model of an individual catalyst particle, to quantify the porosity, and to identify metal deposition and other structural changes happening during the process. In addition to 3D imaging with high resolution X‐ray tomography [1], we here present the results obtained with different electron microscopy methods that were applied to gain information about the local structure and the elemental distribution with high resolution.
The commercially‐deactivated FCC catalyst studied here is a mixture of a La‐exchanged zeolite type Y, metakaolin clay, an aluminum silicate, and comprises almost spherical particles with diameters between ca. 50 and 100 micrometer (Fig. 1a). For the investigation of the particles' internal structure, cross‐sections were prepared. The spheres were embedded in a resin and the obtained cylindrical blocks cut into slices. For TEM and STEM investigations, these slices were mechanically thinned and finally ion‐milled till a hole in the center was generated [2].
SEM images of these cross‐sections reveal a porous and partly fibrous interior structure that is surrounded by a dense wall (Fig. 1b) which is iron rich according to EDXS mapping, (Fig. 1c). The HAADF‐STEM image (Fig. 2a) was taken at the rim of such a particle. The outermost layer at the left appears bright, dense and two to five micrometer thick. It mainly consists of silicon oxide enriched with iron (Fig. 2b‐d). The loss of porosity in the outermost layer during the catalytic operation originates from the formation of a dense phase there. Furthermore, the EDXS mappings reveal areas in the inner part of the particles that contain mainly Ti, Si and Al. This finding agrees with the results of x‐ray diffraction studies that identified zeolite and titanium oxide in addition to a small amount of crystalline aluminum silicate.
It can be concluded that an equilibrated FCC particle as investigated here is covered by a dense newly‐formed iron‐enriched silicon oxide layer while a freshly prepared, catalytically more active FCC particle has a highly porous outermost shell [3].
Multi scale tomography of materials for Li‐ion battery electrodes
Authors: Maire Eric , Douillard Thierry , Etiemble Aurélien , Roiban Lucian , Vanpeene Victor 
Published: December 2016

Increasing energy capacity, power density and cycle life of Li‐ion batteries requires optimizing the composite electrodes microstructure. 3D simulation analysis and modeling have shown that the amount, the size, the shape, the tortuosity and the specific surface area of pores and particles are all key parameters for the improvement of electrode performance.
Recently, the 3D morphologies of various anodes and cathodes for Li‐ion batteries have been evaluated by FIB/SEM and X‐Ray Computed Tomography (XRCT). In addition, 3D imaging softwares allow automatic processing and quantifying measurements by finite element calculations or other numerical models. XRCT is non destructive but routine procedures are limited to rather poor spatial resolution. Combined Focused Ion Beam (FIB) and Scanning Electron Microscopy (SEM) is destructive but has recently emerged as an established technique for the three‐dimensional imaging at high spatial resolution, inaccessible with laboratory X‐ray tomography. Electron TEM tomography is finally an option to improve the spatial resolution down to several nanometers.
This paper will give examples of different materials used for Li‐ion battery electrodes, analyzed at different scales with all these different 3D tomography techniques. It will be shown that static characterisation of the prestine materials gives the initial morphology of the electrodes.
Samples can then be analysed after electrical cycling and this shows the degradation mechanisms. Some methods even allow to do the observation in operado.
Actin‐dependent mechanisms during vesicle fusion link exo‐ and endocytosis in synapses
Authors: Arpino Gianvito , Näreoja Tuomas , Sopova Elena , Shupliakov Oleg 
Published: December 2016

During the synaptic vesicle fusion at the active zone a fusion pore is formed that results in a formation of an Ω‐shape intermediate structure (Ω‐profile) at the plasma membrane for releasing contents, followed by closure (called kiss‐and‐run) or merging of the Ω‐profile into the plasma membrane (called full fusion). Ω‐profile closure limits vesicular content release and cargo delivery, but recycles vesicles economically. In contrast, Ω‐profile merging allows for rapid, complete content release and cargo delivery, but couples exocytosis to classical endocytosis, involving membrane invagination, Ω‐profile formation and fission, for retrieving merged vesicles. In other words, Ω‐profile merging defines the mode of fusion (full fusion instead of kiss‐and‐run) and the mode of endocytosis (classical endocytosis instead of kiss‐and‐run) [1‐3]. Despite these fundamental roles, the mechanism underlying Ω‐profile merging is unclear in neurons, in which vesicles are less then 50 nm in diameter and fusion takes place rapidly after calcium influx.
Giant presynaptic nerve terminals in lamprey that allow intracellular microinjections of active compounds were used in our experiments to investigate the role of actin dynamics during the synaptic vesicle fusion in synapses. Compounds perturbing the actin dynamics, such as latrunculin A and cytochalasin D, phalloidin and non‐dissociable profilin‐actin directly tagged with fluorescence or along with a fluorescent carrier to monitor microinjections, were introduced into giant synapses stimulated at 5 Hz and 20 Hz and studied by confocal and electron microscopy. Phalloidin labeling was observed at the synaptic active zone and a large number of omega‐shaped membrane invaginations with dimensions corresponded to the size of synaptic vesicles and larger were observed at active zones in synapses microinjected with compounds disrupting actin polymerization as compared to control synapses, injected with dextran or GST and stimulated at the same rate (Fig. 1). In synapses simulated at 20 Hz a larger number of vesicles was observed at active zones at sites of microinjection supporting that SV release was inhibited.
Our results indicate that actin dynamics is involved at stages when synaptic vesicle merges with the active zone and when its membrane relocates to the periactive zone for endocytosis.
Imaging of Electron Beam Triggered Phase Transformations and Chemical Reactions of Organic Molecules by Aberration‐Corrected Low‐Voltage Transmission Electron Microscopy
Authors: Biskupek Johannes , Chamberlain Thomas , Skowron Stephen , Besley Elena , Khlobystov Andrei , Kaiser Ute 
Published: December 2016

Direct observation of organic single‐molecules in their pristine state using transmission electron microscopy (TEM) is a challenging task because the electron irradiation during high‐resolution imaging can modify the structure under investigation. However, recent advances in low‐voltage aberration‐corrected high‐resolution transmission electron microscopy (AC‐HRTEM) allow atomic resolution even at accelerating voltages as low as 20kV [1] allowing atomic‐resolution imaging even for light‐element materials with knock‐on damage thresholds below 80kV [3]. However knock‐on damage is not the only damaging process. A reduction of the electron beam‐induced charging and radiolysis effects can be obtained by dedicated sample preparation such as embedding the sensitive material into a chemically inert, conducting, and one‐atom thick container such as a carbon nanotube [3] or in between two layers of graphene [4]. By combining dedicated low‐voltage TEM instrumentation with sophisticated sample preparation, electron irradiation‐induced damage mechanisms slow down or can even be completely turned off which even allows imaging of molecules containing hydrogen‐carbon bonds [5].
In this work we apply low voltage AC‐HRTEM not only to image but also to trigger a previously unknown chemical reaction – the polycondensation of perchlorocoronene (PCC), which leads to the formation of graphene nanoribbons, an exciting polymeric structure with significant potential for electronic applications. The multi‐step mechanism of this reaction was determined by AC‐HRTEM and is both complex and difficult to postulate a priori or from macroscopic observations. However our time‐series imaging at the single‐molecule level reveals the nature of key intermediates and follows the pathways of their transformations, thus providing the most direct experience of chemical reactions and demonstrating the physical reality of the elusive steric factor in real space. Figure 1a shows a time series of PCC molecules stacked in single walled carbon nanotube and their electron beam induced changes over time as a product of the accumulated electron dose. A close examination of the experimental images (Figure 1b) indicates that intermolecular reactions are possible only when a PCC molecule can change its orientations with respect to the neighbouring molecules: two non‐parallel molecules are able to join together to form angular species which gradually transform into planar species approximately twice the length of the original PCC molecules.
Sample preparation for in‐situ biasing
TEM
experiments
Authors: Hömpler Udo , Wagner Tolga , Niermann Tore , Lehmann Michael 
Published: December 2016

Knowledge about the potential distribution of semiconductor devices at the nanometer scale is important for the development of new device structures. Electron holography is a technique sensitive to the electrostatic potential with a high spatial resolution up to the sub nanometer scale [1, 2]. The potential especially in semiconductors is highly sensitive to the generation of electron‐hole pairs, damage caused by the electron and ion beam during investigation and preparation [3], and the biasing of the sample. In‐situ Biasing of specimen within the transmission electron microscope (TEM) provides an external stimuli allowing to differentiate between various effects influencing the hologram. A possible investigation is the influence of reverse and forward bias on the width of the depletion region and on the potential difference between p‐ and n‐sides of the diode [4, 5]. For the comparison between the the bulk device and the TEM‐ specimen we monitored the influence of the sample preparation on the electrical behavior.
For these investigations a silicon solar cell was chosen [6]. The used sample geometry is inspired by the experiments of A.C. Twitchett [7]. The first steps are cleaving and grinding of a wedge out of the wafer. Afterwards two copper clamps are bonded with conductive silver on the front and back contacts of the specimen. This is followed by the preparation of a TEM lamella with a focused ion beam (FIB). A sketch of the FIB prepared lamella is shown in Figure 1. The preparation of the biasing sample is finished by bonding of the clamped specimen on a custom build carrier chip with conductive silver. Figure 2 shows the finished sample.
After each preparation step, an IV measurement was performed and the corresponding curves are shown in Figure 3. As result, the influence of the FIB preparation on the whole sample is negligible (solid red and dashed blue). The measurements are not significantly changed before and after inserting the sample holder into the vacuum of the TEM (solid green and dashed orange). In reverse bias direction however a change of the slope after each bonding step is visible. Before bonding the parallel resistance is 70.1 kΩ. After bonding the slope of the current increases. This corresponds to the presence of a parallel resistance. Conductive silver or residues from its solvent might shortcut the device and build a parallel resistance. This parallel resistance decreases from 10.3 kΩ to 1.95 kΩ after the bonding steps.
During investigations within the TEM an influence of the electron beam on the measured shortcut current was recognizable. Illuminating the FIB‐cut lamella portion of the specimen (and partially the thicker parts below it (left of the lamella in Fig. 1) produced a current of ‐2.1 μA, while illuminating the hole near the specimen only produced an current of ‐8.8 nA.
Insight on the fine structure of semiconductor nanowires down to single atom detection: correlation to their physical properties
Authors: Arbiol Jordi , Genç Aziz , Zamani Reza R. , de la Mata María 
Published: December 2016

Nanotechnology allows modifying the structure of nanoobjects down to the atomic scale. Low dimensional quantum structures can be embedded in a nanowire system in order to modify its properties at will. Electronic and optoelectronic devices benefit from the new advances in growth methodologies, with a fine control of the elemental species locally deposited.
In the present work, we will present how an accurate knowledge on the atomic positions, down to single atom detection, may help to deeply understand the improved properties of our complex nanowire heterostructures. We will show how from scanning transmission electron microscopy (STEM), it is possible to obtain precise 3D atomic models that can be used as input for the simulation of its physical properties. Finally, these theoretical properties will be cross‐correlated to the experimental measurements obtained locally on our nanowire systems.
Some of the presented works will include: the effect of the isotope distribution on the phononic behavior of nanowires, the measurement of the internal electric fields in quantum structures and the influence of doping on the compensation of the polarization field, or the influence of polarity and the atomic arrangement on the photonic and electronic properties of single heterostructured nanowires.
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.