bluuebunny/crossref_metadata_2025 huggingface dataset:
STEM
EELS
plasmon imaging (
SEPI
) for mixed phase silicon / silicon‐oxides systems
Authors: Johann Klingsporn Max , Schubert Markus Andreas , Kirner Simon , Kot Dawid , Abou‐Ras Daniel , Stannowski Bernd , Kissinger Gudrun
Published: December 2016

Plasmon imaging using energy filtered transmission electron microscopy (EFTEM) has been a well‐established technique for investigating mixed phase silicon systems for more than a decade [1]. To image the silicon distribution typically an energy window of 4 eV centered at 17 eV is used. With this approach the signal contains significant contributions of the silicon monoxide and dioxide plasmons which deteriorates contrast and prohibits quantitative imaging.

As alternative approach we developed SEPI. A method, based on the combination of scanning transmission electron microscopy (STEM) with electron energy loss spectroscopy (EELS). SEPI allows to separate the contributions of Si, SiO and SiO
2
(see Fig. 1(a)) and, thereby, to map them individually. This was achieved by a spectrum‐by‐spectrum evaluation routine of EELS data cubes including the extraction of the single scattering distribution (SSD) and the subsequent fitting with reference spectra of silicon monoxide and dioxide and the analytical Drude model for silicon.

In this work we present the successful application of SEPI for investigations of three silicon / silicon oxides systems. All measurements were performed on FEI Tecnai Osiris microscope equipped with a FS‐1 electron energy spectrometer.

In Fig. 1(b) the silicon nanostructure of a nanocrystalline hydrogenated SiO
x
(nc‐SiO
x
:H) layer deposited on a silicon wafer using PECVD is shown. During the last years nc‐SiO
x
:H was under investigation for several applications in silicon thin film solar cells [2], as it offers high electronic conductivity compared to other silicon alloys. The electrical properties are commonly explained by the presence of silicon nanofilaments [3], which can be seen in Fig. 1(b).

In Fig. 2, a line scan across the interface of a 14.5 nm thick silicon oxide layer on a silicon wafer is shown. The oxide layer was thermally grown at 900 °C partially using HCl atmosphere. The distribution of the three components Si, SiO, and SiO
2
demonstrate that between the silicon substrate and the SiO
2
layer an intermediate SiO layer exists.

Fig. 3 (a) shows the oxygen distribution measured using energy dispersive X‐ray spectroscopy (EDX) of an oxygen precipitate in silicon. Oxygen precipitates in silicon are generated by precipitation of the supersaturated interstitial oxygen during thermal processing. Their stoichiometry was under discussion for decades and the compositions found were ranging from SiO
2
to SiO. Recently, it was shown that the center of the precipitate consists of SiO
2
[4]. The SiO plasmon ratio distribution of the oxygen precipitate, shown in Fig. 3 (b), demonstrates that the oxygen precipitate is also surrounded by an SiO layer similar to the oxide layer.
Switching mechanism of
DNA
replication fork complex revealed by single particle analysis
Authors: Mayanagi Kouta , Ishino Sonoko , Takafuji Mika , Mitsuoka Kaoru , Shirai Tsuyoshi , Kiyonari Shinichi , Nishida Hirokazu , Kohda Daisuke , Morikawa Kosuke , Ishino Yoshizumi
Published: December 2016

A number of proteins are involved in DNA replication, which is essential for the inheritance of genetic information. These proteins assemble to form a huge complex, called replisome, and accomplish each function through highly regulated manner. Electron microscopic single particle analysis is one of the most powerful methods to study such complex system, which is difficult to study by X‐ray crystallography.

DNA replication in archaea and eukaryotes is executed by family B DNA polymerases, which exhibit full activity when complexed with the DNA clamp, proliferating cell nuclear antigen (PCNA). PCNA has a trimeric ring structure that encircles the DNA, and increases the processivity of the bound DNA polymerase by tethering it to the DNA. It is known now, that PCNA also interacts with multiple partners to control DNA replication, DNA repair, and cell cycle progression, and works not only as the platform, but also as the conductor for the recruitment and release of these factors. However, the molecular architectures as well as the mechanism of the regulation of these replication factors are not known in detail.

We have been focusing our interest on the mechanism of synthesis and maturation of Okazaki fragments during lagging strand DNA replication in which three replication factors, i.e. DNA polymerase, Flap endonuclease, DNA ligase, are playing essential roles (Fig. 1A‐C). As all of these 3 enzymes are known to interact with PCNA trimer, a switching mechanism between these factors has been proposed, called PCNA tool belt model, which is considered to increase the efficiency of these sequential reactions (Fig 1D). Recent biochemical study, on the other hand, suggests a sequential switching mechanism of these factors. Little is known regarding the switching mechanism, due to the lack of the structural data of these complexes.

We have investigated the three‐dimensional structure of the core components of the replisome, such as DNA polymerase B(PolB)‐PCNA‐DNA, and DNA ligase‐PCNA‐DNA ternary complexes, by single particle analysis (2‐ 3). Besides the authentic interaction through a PCNA‐interacting protein box (PIP‐box), we could find a novel contact between both polymerase‐PCNA and ligase‐PCNA. Mutant analysis showed that these contacts are involved in the regulation of the replication factors, such as the switching between the polymerizing and editing modes of the PolB. Our results, showing that both factors interacting with two subunits of the PCNA trimer ring, were inconsistent with the standard tool belt model. However, the third PCNA subunit was still free in both complexes, thus we analyzed the complex structures with two replication factors bound to a PCNA ring, in order to investigate the switching mechanism between them in more detail.
Combining
TEM
and
APT
for a better understanding of super high efficiency Cu(In,Ga)Se2 thin film solar cells
Authors: Castro Celia , Raghuwanshi Mohit , Pareige Philippe , Duguay Sébastien , Cadel Emmanuel , Witte Wolfram , Jackson Philip , Hariskos Dimitrios , Kessler Friedrich , Buecheler Stephan , Carron Romain , Avancini Enrico , Bissig Benjamin , Tiwari Ayodhya
Published: December 2016

The Sharc25 EU H2020 project aim is to push the efficiency of Cu(In,Ga)Se2 (CIGS) thin film solar cells to their maximum theoretical limit. Sharc25 consists in a large consortium to take under consideration both theoretical and experimental aspects. One of the strategies to achieve this goal is to improve and understand the CIGS absorber material deposited by co‐evaporation.

The polycrystallinity of the CIGS absorber layer is one of the key elements which plays a crucial role in its efficiency. We combine here atom probe tomography (APT) (Fig. 2) and transmission electron microscopy (TEM) to study the distribution of alkali elements at sub‐nanometer scale and with statistic relevancy. 3D APT atomic mapping of grain boundaries (GB) is here completed by systematic STEM‐EDS analyses of GB all along the CIGS absorber layer (Fig. 1). Issues on samples preparation for APT and TEM will be also discussed.

This project has received funding from the
European Union's Horizon 2020 research and innovation programme
under grant agreement No 641004
Im2Cr
: An efficient tool for crystallographic indexing of
HR(S)TEM
images
Authors: Silva André , Carbó‐Argibay Enrique , Proença Alberto , Stroppa Daniel
Published: December 2016

Transmission Electron Microscopy (TEM) and Scanning TEM (STEM) have been widely used to characterize nanostructured materials with atomic resolution, and significant advances on their experimental setup greatly extended the current pool of analysis possibilities at the nanoscale. The exploration of advanced (S)TEM characterization capabilities and their reproducible application to reach a suitable sampling is often restricted by the extensive data analysis procedures required to reliably interpret experimental results and to extract quantitative information. Even routine tasks such as nanoparticles crystallographic indexing from electron diffraction patterns or from high resolution (S)TEM images are mostly carried out manually by the users, resulting in a reduced TEM characterization yield and significant user bias.

This work presents Im2Cr, a new software tool to aid the crystallographic indexing of nanostructured materials using high resolution (S)TEM images. Im2Cr implementation aims for a minimal user interaction, supporting the detection of zone‐axis oriented particles, and including an efficient peak detection process applied to the images Fourier Transform (FT). With basis on the FT peaks distances and relative angles, crystallographic indexation is carried out autonomously via comparison with a list of candidate structures named by the user, and a ranking of the best matching combinations of crystallographic structures and viewing zone axes is generated.

Im2Cr was successfully tested for robustness and execution efficiency in a wide range of High Resolution (S)TEM images from crystalline nanomaterials, with domain size ranging from 4 to 100 nm. The autonomous indexation with preset parameters has a very high success rate, and runs in a small fraction of typical (S)TEM images acquisition time by taking advantage of the inherent hardware parallelism. Alternatively, the user can operate Im2Cr in a semi‐autonomous mode and control relevant parameters related to the region of interest (ROI) selection on the (S)TEM image and on the FT peaks detection. Im2Cr promising results point to the possibility of real‐time image analysis with reduced user interaction, allowing for an increased (S)TEM characterization yield and also enabling the interpretation of complex images, such as those from nanocrystalline materials imaged in high‐order zone axis orientations.
Epitaxy of
G
a
N
nanowires on graphene
Authors: Kumaresan Vishnuvarthan , Largeau Ludovic , Madouri Ali , Glas Frank , Zhang Hezhi , Oehler Fabrice , Cavanna Antonella , Babichev Andrey , Gogneau Noelle , Tchernycheva Maria , Harmand Jean‐Christophe
Published: December 2016

Nitride nanowires (NWs) are today actively explored as an active material for a large number of optoelectronic devices (light emitting diodes, photodetectors, solar cells). The NWs are usually grown on bulk crystalline substrates (Si, sapphire) but these substrates impose their properties which may not be adapted to the device functionality (low electrical or thermal conductivity, opacity, weigh, rigidity, cost,…). Recently, graphene has been proposed as an attractive candidate to grow III‐V semiconductor NWs [1]. Graphene is transparent, flexible and it has high thermal and electrical conductances and it can be synthesized at low cost on large areés. Furthermore, graphene films are easily transferable to almost any carrier substrate, including amorphous and/or flexible materials.

In this study, epitaxial growth of GaN nanowires on graphene is demonstrated using molecular beam epitaxy without any catalyst or intermediate layer. We have grown GaN NWs on isolated mono‐crystalline graphene flakes transfered onto SiO2/Si carrier substrates. The nanowires grow vertically and X‐Ray diffraction (XRD) show that the nanowires have grown along their c‐axis. We have observed by SEM that locally, the NW factes have the same in‐plane orientation over several µm². The 10‐10 facets of the NWs have been determined by high angle annular dark field scanning transmission electron microscopy (HAADF‐STEM). Cross‐sections have been prepared by focussed ion‐beam (FIB). HAADF images of NW‐graphene/silica interface show that the base of the NWs is defect‐free. Selected area electron diffraction (SAED) patterns taken from different zones show identical patterns indicating that the nanowires from all the zones have same in‐plane orientation. Since it is well established that the hexagonal periphery of the graphene flakes corresponds to zig‐zag edges of the graphene lattice, we can conclude that the epitaxial relationship is 11‐20 GaN parallel to the graphene zig‐zag. It leads to an apparent mismatch of 29% between the graphene and the GaN wurtzite structure. This value is very large. We show that an in‐plane super cell coincidence between 4 unit cells of graphene and 3 unit cells could lead to a more favorable mismatch of ‐3.1%. The optical properties of NWs arrays have been probed by photoluminescence spectroscopy.
Direct comparison of differential phase contrast and off‐axis electron holography for the measurement of electric potentials by the examination of reverse biased Si p‐n junctions and III‐V samples
Authors: Haas Benedikt , Cooper David , Rouviere Jean‐Luc
Published: December 2016

In this presentation we will compare differential phase contrast (DPC) [1] and off‐axis electron holography [2] for the measurement of electrostatic potentials in semiconductor devices. DPC uses the lateral shifts of a convergent electron beam to determine the field in the sample whereas for electron holography the changes in potential is encoded in interference fringes that are formed using a biprism [1]. To fairly assess the relative sensitivity of the different techniques on the same specimen, a symmetrically doped p‐n junction with a dopant concentration of 1 x 10
19
cm
‐3
has been measured as a function of reverse bias applied in situ in the TEM. Figure 1(a) and (b) shows maps acquired by DPC of the p‐n junction with 0V and 4V reverse bias applied. At 0V, it is difficult to see the presence of the junction whereas for a reverse bias of 4 V the space charge region is now visible. Profiles acquired from across the junction for various reverse bias voltages can be seen in Figure 1(c). Electron holograms were acquired and Figure 1(d) and (e) show reconstructed phase images of the junction at zero bias and 4 V reverse bias. Even though a low magnification has been used to obtain a large field of view at the expense of sensitivity, the junction is clearly visible in both of the phase images. Corresponding electric field profiles that have been calculated from the potential maps are shown in Figure 1(f). These results show that off‐axis electron holography has a significantly better sensitivity than DPC. However the advantages of using DPC is that a large field of view has been obtained and it is not necessary to examine a region close to vacuum.

These techniques have also been applied to an InGaN/GaN system. Figure 2(a) shows a HAADF STEM image of the specimen. Figure 2(b) shows a potential map and (c) profile acquired by off‐axis electron holography with a spatial resolution of 5 nm. When using DPC, sub‐nanometer spatial resolution is expected and maps of the electric field in the InGaN layers can be observed in Figures 2(d) and (e). Here the specimen has been tilted onto and away from a zone axis and a large variation in the measured signal is observed which is visible in Figure 2(f). In this presentation will discuss the effects of diffracted beams on the measured DPC signal. We will also discuss the advantages and disadvantages of using DPC and electron holography for the measurement of electrostatic fields in a range of different doped and III/V semiconductor specimens and show improvements that have been applied.
Imaging molecular sieve 3A
Authors: Algara‐Siller Gerardo , Lunkenbein Thomas , Schlögl Robert , Willinger Marc Georg
Published: December 2016

The framework of many zeolites has been studied using different TEM techniques even though these materials are easily damaged by the electron beam
1
. Until now the mechanisms for radiation damage in zeolites are not fully understood due to the complexity of their structure except for some works which have given a general indication on its origin
1‐4
. Despite the fact that each work used different zeolites it can be derived from them that the main factors for the stability of a zeolite under the electron beam are the Si/Al ratio, the size of cations and the water content. In this work we present the investigation of molecular sieve 3A (LTA framework) by HRTEM, with a Si/Al ratio of 1, and Na and K cations (Sigma Aldrich). Although the Si/Al ratio is unity i.e. the material is highly sensitive to electron irradiation
2
our results show that with electron dose rates up to 1000 e/nm
2
s the atomic structure of such material can be obtained (observation timespan ~1200 s) independent of the electron energy (80 keV, 200 keV or 300 keV). The latter indicates that by using an electron energy above 80 keV electronic exitations (e.g. radiolysis) and knock‐on damage are simultaneously taking place during electron irradiation thus no dominance of either radiation mechanism, these results are in agreement with previous findings reported by Ugurlu et al.
4
. Although the structure of zeolite could be obtained, damage invariable occurred during recording, however, at a slow rate. In conclusion, these results are one step foward for the understanding of radiation damage mechanisms in molecular sieves, and a step towards imaging the cation positions.
A Study of Heavy Ion Irradiation‐Induced Segregation at Grain Boundaries in Alloy 800H
Authors: Jun Hua Lim Joven , Burke M Grace
Published: December 2016

Environmentally‐Assisted Cracking (EAC) of structural components in a nuclear reactor core of light water reactors (LWRs) and water‐cooling systems in fusion reactors is of concern in that it can directly influence on the safety of a nuclear reactor. Previous studies showed that one of the many factors that governing the EAC of a structural component is the changes of the chemical composition of the grain boundaries of the material used after exposed to neutron radiation [1]. This phenomenon is also known as irradiation‐assisted stress corrosion cracking (IASCC). The changes of the chemistry of grain boundaries induced by irradiation, i.e. radiation‐induced segregation (RIS), and the increase in irradiation‐induced defects can promote hardening of the material, thereby affecting the resultant mechanical and environment‐sensitive behaviour. With long‐term (~80 years) reactor operation under consideration for power generation, Alloy 800H is one of the candidate alloy systems that may be used in the next generation advance light water nuclear energy system [2]. One of the reasons for this choice is that Alloy 800H is code‐certified for high temperature (up to 760 °C) use in nuclear power systems [3]. Also, the high Ni and Cr concentrations in the alloy provide good resistance to void swelling and corrosion in light water environments [4].

In this study, RIS in ion‐irradiated Alloy 800H was investigated. A commercial grade Alloy 800H was subjected to simultaneous Fe
++
and He
++
ion‐beam irradiation to simulate the effect of neutron irradiation‐induced segregation. The alloy was irradiated to a dose of 16.6 dpa at temperature of 440°C using the facility at University of Michigan Ion Beam Laboratory, Ann Arbour, Michigan. The microstructural characterisation was performed using a spherical aberration‐corrected FEI Titan G2 80‐200 with Super X EDX (ChemiSTEM™) operated at 200kV and equipped with a GIF Quantum 965 EELS to provide independent compositional analyses of the intergranular segregation induced during ion irradiation. Scanning transmission electron microscopy (STEM) – Electron Energy Loss Spectroscopy (EELS) analyses show that the grain boundaries in Alloy 800H are enriched with Ni, Si and Ti after irradiation, as shown in Figure 1. Fe and Cr depletion was also detected at the same grain boundary, as shown in Figures 2 and 3. Apart from that, a denuded zone with no chemical‐related irradiation‐induced defects decorating along the grain boundary was observed. However, diffraction contrast imaging shows that a high number density of the irradiation‐induced dislocation loops was observed along the grain boundary. This observation and its implications for the alloy will be further discussed.
Aberration corrected
CVD‐TEM
for in‐situ growth of
III–V
semiconductors
Authors: Wallenberg Reine , Jacobsson Daniel , Thelander Kimberly Dick , Gustafsson Joacim , Dogel Stas
Published: December 2016

We will show the first results from a newly designed Environmental TEM with cold FEG emitter, aberration corrector, heating stage and a free choice of up to nine different gaseous reactants to produce heterostructures in‐situ during real‐time observation and analysis.

Observing growth of semiconductors on an atomic scale, under MOCVD or CVD‐like conditions, will bring valuable information and understanding of the possibilities and limitations for making devices, solar cells and LED:s from nanowires. We have constructed a 300 kV Environmental TEM, with cold FEG emitter, heating stage and a free choice of up to nine different gaseous reactants to produce heterostructures in‐situ.

The use of an aplanatic B‐COR image corrector provides space in the objective lens polepiece for a heating stage reactor with gas inlets, while still achieving an 86 pm point resolution (in vacuum). The gas inlets are designed to give a total pressure of up to10 Pa, which is sufficient to grow nanowires at a reasonable speed. The gas handling system will allow switching between the different gases at will, or through programmed sequences.

Changes and defects in the crystal structure, and the effect on the outer shape of the nanowires can be followed by combinations of conventional HREM imaging, STEM‐DF and STEM‐BF, as well as SE‐imaging. Simultaneous analysis by XEDS will provide chemical changes along the growth path.
STEM
and
EELS
investigation of graphene nanoribbons epitaxially grown over
S
i
C
Authors: Gloter Alexandre , Palacio Irene , Celis Arlensiu , Nair Maya Narayanan , Zobelli Alberto , Sicot Muriel , Malterre Daniel , Berger Claire , Heer Walt De , Conrad Ed , Taleb Amina , Tejeda Antonio
Published: December 2016

Graphene nanoribbons grown on the (1‐10n) and (‐110n) facets of SiC have demonstrated exceptional electronic properties as ballistic transport along their long direction and a band gap in the small direction [1]. In order to understand these electronic properties, we have performed (S)TEM (HAADF, LAADF, ABF, EELS) investigation in combination with STM and ARPES measurements. The (S)TEM have been performed on X‐section sample as it can be schematically seen in the figure 1. Using Cs corrected STEM at 60 keV voltage, the structural aspect of the graphene can be maintained for high resolution investigation and EELS spectromicroscopy. In particular we will describe the origin of the metal‐semiconductor junction as observed in these graphene [2] and this will be discussed in term of curvature effect, quantum confinement on a complex reconstructed step as presented in figure 2 [3].
Spatial resolution and compositional contrast in imaging using the low‐loss electron signal in
SEM
Authors: Bonet Chris , Tear Steven , El‐Gomati Mohamed
Published: December 2016

Nanotechnology places increasing demands on techniques for sample characterisation on the sub‐100 nm length scale. The scanning electron microscope (SEM) is one, widely used, technique for imaging and characterising nanomaterials using the intensity of secondary (SE) or backscattered electron (BSE) emission from a probed region of the nanomaterial to generate spatially resolved contrast in an image. The acquisition of the low‐loss electron (LLE) signal [1] in the SEM provides an alternative method which may offer the advantage of improved spatial resolution compositional imaging.

Spatial resolution and contrast in compositional imaging of the LLE signal has been investigated by means of experimental measurements in a scanning electron microscope and Monte Carlo simulations for the case of a semiconductor superlattice structure comprising Si
0.85
Ge
0.15
of 11.5 ± 0.4 nm separated by pure Si layers at a periodicity of 69.2 ± 0.2 nm. Both continuous slowing down approximation (CSDA) and discrete‐loss based Monte Carlo models were considered (NISTMonte and PENELOPE) and it was found that the calculated contrast values were particularly sensitive to the choice of model in the low‐loss regime. Experimental data were obtained using a purpose‐built low‐energy electron loss detector [2,3] comprising a retarding field analyser with an electron‐optical input lens. The detector was attached to an FEI Sirion FEGSEM. Experimental data indicated that improved contrast was obtained as the maximum loss energy was lowered (fig 1a), and this trend was reproduced by the simulations (fig 1b). The results indicate that the LLE technique is a useful alternative to operating at low primary beam energies when performing compositional imaging on samples which have nanoscale compositional structure. Statistical noise considerations that affect the LLE signal are discussed. In the case of spatial resolution, resolution metrics for compositional imaging are discussed. It was found that the LLE signal shows improved resolution compared with the backscattered electron signal (figs 2 & 3), however CSDA‐based simulations predict better resolutions than simulations based on a discrete loss model. It is found that the energy‐straggling has the most significant influence on the predicted resolution in the low‐loss regime. The simulations suggest that a SEM with a high‐quality small‐diameter probe is required to fully appreciate the resolution benefits of the LLE signal. Experimental data indicates that certain samples (such as those with sub‐surface compositional inhomogeneity or nanoscale topography) benefit from the LLE technique even when the SEM used has a more modest probe diameter.
Study the microstructure of three and four component phases in Al‐Ni‐Fe‐La alloys
Authors: Kolobylina Natalia , Vasiliev Alexander , Lopatin Sergey , Presniakov Mikhail , Bakhteeva Natalia , Ivanova Anna , Todorova Elena
Published: December 2016

Aluminium alloys play a key role in modern engineering since they are the most used non‐ferrous material. They have been widely used in automotive, aerospace, and construction engineering due to their good corrosion resistance, superior mechanical properties along with good machinability, weldability, and relatively low cost. The progress in practical application has been determined by intensive research and development works on the Al alloys. A new class of Al–REM–TM aluminum alloys (REM indicates rare earth metal and TM is transition metal) was revealed in the end of the last century. These alloys differ from conventional ones by their extraordinary ability to form metal glasses and nanoscale composites in a wide range of compositions. Having low density, these alloys possess unique mechanical characteristics and corrosion resistance. Two as received alloys, namely Al
85
Ni
9
Fe
2
La
4
and Al
85
Ni
7
Fe
4
La
4
were obtained in the form of ingots from melts of corresponding compositions upon cooling in air were studied by scanning/transmission electron microscopy (STEM), energy dispersive X‐ray (EDX) microanalysis and X‐ray diffraction (XRD). The microstructural analyses were performed in a aberration corrected TITAN 80‐300 TEM/STEM (FEI, USA) attached with EDX spectrometer with ultrathin window (EDAX, USA). The specimens for transmission electron microscopy (TEM) were prepared by an electrochemical or ion etching. It was found that the received alloys exhibits along with fcc Al and Al4La (Al11La3) particles, these alloys contain a ternary phase Al3Ni1 Fe isostructural to the Al3Ni phase and a quaternary phase Al8Fe2 NiLa isostructural to the Al8Fe2Eu phase and monoclinic phase Al
9
(Fe,Ni)
2
isostructural to the Al
9
Co
2
. The study by HRSTEM together with a new atomic resolution energy dispersive X‐ray microanalysis method demonstrated that Fe and Ni atoms substituted one another in the Al8Fe2–NiLa quaternary compound. Besides, several types of defects were determined: first ones have a form of a δ ‐layers and they are Al3.2Fe1–Ni ternary compound with a Al3.2Fe structure type. Second ones were point defects, which are La vacancies.

The experimental part of this work was partially done on the equipment of the Resource Center of Probe and Electron Microscopy (Kurchatov Complex of NBICS‐Technologies, NRC “Kurchatov Institute”)
Epitaxial BaTiO3 on Si and SiGe for low power devices: nanoscale characterization of the film and its interface with the semiconductor by
HAADF
and
EELS
in
STEM
Authors: Schamm‐Chardon Sylvie , Magen Cesar , Mazet Lucie , Cours Robin , Frank Martin , Narayanan Vijay , Dubourdieu Catherine
Published: December 2016

Introduction.
In the late 1990s, the success of SrTiO
3
epitaxial growth on Si by molecular beam epitaxy (MBE) opened a path for integrating complex oxides on Si‐based platforms. In particular, ferroelectric perovskite oxides offer promising perspectives to improve or add functionalities on‐chip like low power logic devices or integrated photonics [1]. BaTiO
3
, the prototypical ferroelectric perovskite oxide, is a good candidate for these applications [2, 3]. However, regarding practical devices, integrating a perovskite oxide epitaxially on Si by MBE is still in its infancy. One key point is the control of the crystalline orientation, which determines the polarization orientation within the thin film. Playing with experimental parameters of growth and the composition of the Si
x
Ge
1‐x
semiconductor substrate are means to manipulate the competition between compressive stress from epitaxy and tensile stress from thermal expansion. In order to support MBE growth strategies, aberration‐corrected scanning transmission electron microscopy has been investigated to determine both the strain and the chemical state of epitaxial BaTiO
3
thin films.

Experiment.
BaTiO
3
was epitaxially grown on Si
x
Ge
1‐x
(x=1 and x = 0.20) substrates either using an SrTiO
3
buffer layer to reduce both thermal and lattice mismatches between BaTiO
3
and Si or without any buffer on Si
0;2
Ge
0.8
. The complex oxides were grown by MBE using Sr, Ba and Ti effusion cells. Details on the growth are given in refs [1,4]. BaTiO
3
was grown directly on strained Si
0.8
Ge
0.2
/Si substrates using a barium passivation. STEM‐HAADF images were collected on a FEI Titan Low‐Base 60‐300 probe corrected microscope and the data treated using the geometric phase analysis (GPA). STEM‐EELS data were also acquired with a special attention to Ba, Ti and O elements.

Main results.
In a first part, we will first describe the crystalline structure and cationic composition studied at the nanoscale in BaTiO
3
/SrTiO
3
/Si heterostructures. The effect of oxygen pressure will be discussed. We show that the lattice parameter profile evolution within the thickness of the BaTiO
3
films is clearly associated with modifications of the cation stoichiometry within the thickness and that there is a clear impact of the oxygen pressure on both lattice parameter and composition profiles. In a second part, we will discuss the particular epitaxial state of BaTiO
3
grown directly on Ba‐passivated strained Si
0.8
Ge
0.2
.
Layer specific optical band gap measurement at nanoscale in
MoS2
and
ReS2
van der Waals compounds by high resolution electron energy loss spectroscopy
Authors: Krishnan Dileep , Sahu Rajib , Peter Sebastian , Datta Ranjan
Published: December 2016

Atomically thin monolayer transition metal dichalcogenides (TMDs) are a new class of two dimensional nano‐material with promising optoelectronic, energy and novel device applications. One of the important features of many TMDs is that they undergo a crossover from indirect band gap in the bulk to direct band gap in the monolayer form [1]. While the monolayer properties of TMDs are unique (e. g. direct band gap), it may be illusive while fabricating practical devices because the cross over to indirect band gap occurs due to unavoidable electronic packaging and the property could change in close proximity of foreign substance. Therefore, there is an urge to stabilize such novel properties arising from the monolayer in the interface or in the bulk form. With this goal there is a candidate material already reported in the family, i.e. crystalline 1T‐ReS
2
[2]. In this work we have exploited high resolution electron energy loss spectroscopy (HREELS) to perform layer specific direct measurement of optical band gaps of two important van der Waals compounds, MoS
2
and ReS
2
at nanoscale. Areas with mono, bi, tri and multilayers of MoS
2
and ReS
2
have been identified using a electron microscope. The atomic resolution image of mono and multilayer MoS
2
and ReS
2
have been given in figure 2. For monolayer MoS
2
, the twin excitons (1.8 and 1.95 eV) originating at the K point of the Brillouin zone are observed. The band gap values have been deduced after plotting Tauc‐like plots for both direct and indirect band gaps from the EELS absorption spectra. An indirect band gap of 1.27 eV is obtained from the multilayers regions (see figure 1). Indirect to direct band gap crossover is observed which is consistent with the previously reported strong photoluminescence from the monolayer MoS
2
. For ReS
2
the band gap is direct and a value of 1.52 and 1.42 eV are obtained for the monolayer and multilayers, respectively (see figure 1). A direct to indirect band gap transition has been observed in MoS
2
going from monolayer to bilyer but no such transition is observen in ReS
2
The results demonstrate the power of HREELS technique as a nanoscale optical absorption spectroscopy tool.
Local order and conformation of nucleosomes in solution and in interphase nuclei analysed by cryo‐electron microscopy of vitreous sections
Authors: Leforestier Amélie , Lemercier Nicolas , Livolant Françoise
Published: December 2016

Despite spectacular advances in our knowledge of chromosome dynamics and large scale organisation, little is still known about how the 10 nm nucleosome bead‐on‐string fibre is packed in the cell nucleus. While a folding into 30 nm fibres has long been assumed, there is now accumulating evidence that no such structure exists
in situ
(1), except in the cases of chicken erythrocytes and echinoderm sperm cells (2). Our knowledge of the nucleosome structure itself is still limited to crystallographic structures obtained with engineered particles (3). There is also increasing evidence that there would be no unique nucleosome structure but a whole dynamic family with variations of the composition and conformation of the particle (histone variants, post translational modifications, stoichiometry) (4).

Using cryo‐electron microscopy of vitreous sections (CEMOVIS), we explore in parallel the conformation and local ordering of nucleosomes both in the interphase nuclei of human cell lines HT29 (Figure 1A) and KE37 and in concentrated solutions of isolated native particles in presence of low or high added salt concentrations (15 or 150 mM NaCl) (Figure 1B).

In both cases, individual nucleosomes can be identified. Striated patterns, indicative of the presence of piles of stacked particles are observed, but much more locally in cell nuclei (piles of 2 to 4‐5 particles only). We analyse these patterns by comparison with the different projections of the DNA from the canonical crystallographic structure of the nucleosome core particle (2) to determine their orientations. On side view of the nucleosomes, we measured the distance between the DNA gyres around the particle (pitch P of the DNA superhelix). This reveals that both
in vitro
in solution and
in situ
in interphase nuclei, the nucleosome conformation is not unique, but fluctuates. In concentrated solution, both the supramolecular order (5) and the conformation depend on the ionic environment. In particular, the nucleosome is on average more “open” at low added salt concentration (with P = 30.5Å), than at high salt, where its conformation resembles that found in crystals formed by reconstituted recombinant particles (P = 28 Å). Surprisingly,
in situ
, the conformation of the nucleosome is also more “open” (31Å), matching the results found
in vitro
at low salt concentration.
Temporally and spatially resolved local strain tracking microscopy
Authors: Bayraktar Halil , Aydin Onur , Aksoy Bekir , Akalin Ozge Begum , Alaca B. Erdem
Published: December 2016

Cell‐stretching is a key method to regulate deformation magnitude, cyclic strain levels, and frequencies, therefore elucidating the biological processes involved in activation of mechanosensitive pathways, cell patterning and morphological changes at physiologically relevant mechanical loads. Although several approaches and methods such as uniaxial or biaxial devices have been demonstrated to deform cells and usually compute ration cross‐head displacement to original length of sample as an indicator of percentage stretch, however in‐plane strain components may have a non‐uniform spatial distribution due to heterogeneous extracellular matrix of connective tissue around cells. Therefore, the average value of the applied cross‐head strain is expected to be different than local strain in the vicinity of cells. This limitation has prompted us to develop an alternative approaches.

Here, we present a novel uniaxial cell‐stretching device integrated into inverted fluorescence microscope that provides a high spatial resolution to determine the local strain changes around fluorescent and non‐fluorescent cells (RSI, 2016, 87, 023905). Transparent and biocompatible polydimethylsiloxane PDMS elastomer modified with small fluorescent beads are used to deliver uniform strain at the physiologically relevant magnitude and cycles. The design of our device for acquisition of real‐time spatiotemporal data and single‐particle tracking methods to determine bead positions that was used for computation of strain fields at various sample geometries will be described (Fig. 1). Briefly, trajectory of beads is computed by comparing each registered location in consecutive frames and minimizing the square displacement of centroids. Displacement vector is obtained from displacements and later used to calculate longitudinal normal, traverse normal and shear components of strain with relevant deformation tensor (Fig. 2). Lastly, we will discuss that HeLa S3 cells adhered to biocompatible and flexible collagen coated surface are stretched to determine simultaneously detection of morphological changes and local strains around the cells by tracking embedded fluorescent beads (Fig. 3). The method enables to measure local strain field and image adherent cells simultaneously, therefore provides accurate and time‐resolved correlation between applied mechanical deformation and cell response.
Seeing nanostructures from a new angle ‐ tomography in a transmission electron microscope
Authors: O'Connell Eoghan , Guo Yina , Young Robert , Winkler Florian , Kardynal Beata , Bangert Ursel
Published: December 2016

Research interest in low dimensional materials has expanded immensely in the last decade. The fascinating properties of nanotubes, graphene and transition metal dichalcogenides (TMDCs) has pushed this research toward applications in composites, (opto)‐electronics and photovoltaics.

Seeing and understanding the physical and chemical structure of these nanostructures is a vital aspect of this growing research area. Using rotational tomography on low dimensional TMDCs, we reveal additional points of view that are not routine in transmission electron microscopy (TEM). Bright field TEM highlights the non‐uniformity of tungsten disulphide (WS
2
) nanotube tips, as well as revealing structural deformities in the nanotubes as a whole. Complimentary to this, we present high‐angle annular dark field (HAADF) scanning TEM tomography, which provides clearer structural interpretation through fewer Bragg scattering events being detected. 2D nanosheets are also characterised via high resolution TEM tomography, allowing for a three dimensional view of a 2D object. As the sample is rotated, further lattice and thickness information is acquired.

Having these complimentary tomographic methods available for nanomaterial characterisation will help to improve the accuracy of interpretation and results. Often, 2D TEM images lead to assumptions about the nature of these materials. Tomography at high resolution will reveal more information on the shape and structure of the studied nanomaterials (e.g., ripples) in 3D.
Cryo‐EMStructural characterization of the M. tuberculosisESX‐1 secreted virulence factorEspB
Authors: Tria Giancarlo , Siroy Axel , Delei Chen , Iakobachvili Nino , Furusho Hirotoshi , López‐Iglesias Carmen , Ravelli Raimond B. G. , Peters Peter J.
Published: December 2016

Mycobacterium tuberculosis(Mtb) is the top infectious disease killer worldwide. The threat posed by this bacterium is higher than ever, with the recent discovery of multi and extended‐drug resistant (MDR, XDR) strains with improved virulence.

Virulent mycobacteria infect their host cells through a Trojan Horse strategy: they get ingested by the normal phagocytosis route but instead of being digested through acidification and maturation of the phagosome to phagolysosome, these bacteria enter the host's cell cytosol where they replicate freely. Controlled death of the host cell will allow the spreading of the descendants in the infected organism.

A key step in the infectious life cycle of the virulent mycobacteria is their escape from the phagosome compartment [1]. This phenomenon is mediated by the release of different proteins (EsxA, EsxB, EspB) with cytolytic activities, that will perforate the phagosome membrane. These factors are secreted by the specialized machinery ESX‐1 of the recently discovered Type 7 Secretion System family [2].

The ESX‐1 machinery is a multi‐protein complex thought to span the entire mycobacterial cell envelope. It is constituted by a core of structural proteins (EccACabBDE1) and the assembly and/or functioning of the machinery seems to require the recruitment of additional proteins, including substrates.

Among the different ESX‐1 substrates, the 48 kDa protein EspB seems to carry multiple roles: this secreted protein carries cytolytic activity on its own; it is co‐secreted with EsxA (the main virulence factor) and this secretion is mutually dependent; EspB may also play a structural role suggested by its ability to oligomerize as well as its proteolytic maturation by MycP1during the translocation process.

Recently, the structure of the N‐terminus of EspB was published [3] showing the N‐terminal be composed of a bundle of α‐helices, similar to other ESX substrates; the C‐terminal is predicted to be unfolded. A heptameric structure was modelled computationally based on the monomeric X‐ray data in combination with negative‐stain electron microscopy 2D classes.

Here, we report structural characterization of EspB using transmission electron microscopy data. We determined the structure of the N‐terminal helix bundle, the mature form as well as the pre‐protein EspB at sub‐nanometer resolution. Moreover, we were able to identify several discrete oligomeric states of the proteins that were not previously observed: these data will aid to a better understanding of ESX‐specific substrates.
Low energy electron beam induced cleaning of graphene layers in
SEM
s
Authors: Mikmekova Eliska , Frank Ludek , Mullerova Ilona , Sluyterman Seyno
Published: December 2016

In order to examine mutually overlapped flakes of two‐dimensional crystals such as graphene with an electron microscope we need to obtain a contrast contribution from a single layer of carbon atoms. This task requires increasing the scattering rate of incident electrons by means of a drastic lowering of their energy to hundreds of eV or less.

The effect of airborne contaminants, mainly hydrocarbons, on graphene layers distinguishing in low energy S(T)EMs can be significant and due to their removing from the surface by appropriate in‐situ methods is very important from practical point of view. During the scanning of the surfaces by electrons, the image usually gradually darkens because the hydrocarbon layer is deposited on the top. This effect can be described as an electron stimulated deposition, the thermal diffusion of organic molecules around the irradiated area is use as a source of building atoms, precursor. On the other hand, the effect of electron stimulated desorption occurred at the same time, especially at low observation energies, and then depends which process, deposition or desorption, is dominated. Our experiments have showed the fact that prolonged bombardment with electrons in a range of hundreds or even tens eV gradually increases the transmissivity (and decreases the reflectivity) of graphene due to the removal of adsorbed gas molecules providing an ultimate cleaning procedure evidently leading to an atomically clean surface. A sample such as graphene enables one to distinguish this kind of cleaning from radial damage, so this result opens up new possibilities for certain surface studies performed without ultrahigh vacuum.

Experiments have been performed in a FEI SEM/STEM microscope equipped by beam deceleration mode on free standing graphene (Ted Pella
®
) and the effects of landing electron energy, samples biasing, electron dose, heating, etc. on the cleaning efficiency of electrons was studied in details. Moreover, the structural damage of the graphene after extremely high electron doses was observed, and the critical values for selected impacted energies were also calculated.
10 bar nanoreactors for in situ transmission electron microscopy
Authors: Pandraud Gregory , Morana Bruno , Wei Jia , Juffermans Casper
Published: December 2016

Environmental transmission electron microscopy (ETEM) is becoming an increasingly important field of study as it is possible to investigate the material‐environment interactions on a nanoscale, the scale at which most of these interactions initiate. In a TEM, this can be achieved by one of the following approaches: the opened type, using a differentially pumped vacuum system where the reactive gases are spread around the specimen area of the TEM; and the closed type, using a windowed environmental cell. In the first case the maximum achievable pressure around 1 bar [1] but it is limited to flat samples and for the second type (where two chips are often put on top of each to obtain a closed cell) the maximum pressure rarely exceeds 4 bars [2]. However the last configuration is much closer to what happens in industrial applications.

We present in this paper, a new MEMS nanoreactor fully integrated on a single die. It enables atomic‐scale imaging of nanostructured materials under the high pressures and temperatures that are typical for many industrial applications (10 bar and 650°C). The reactor can therefore be used to study the behavior of e.g. catalysts in a transmission electron microscope (TEM). It has a channel of 5 µm (allowing therefore an efficient loading of the samples to study), which is made with surface micromachining techniques and contains pillars that prevent bulging. The channel high can be adjusted by adjusting the right layers in the devices processing. Integrated with the device are 22 very thin windows (20 nm) and a resistive heater. The material chosen for the heater is Molybdenum. It offers a very high stability at 650 C for up to 10 h. The reactor is very transparent and clean (the windows being etched in a such way that contamination/residues are prevented) enabling the imaging of atomic lattice fringes with a spacing down to at least 0.15 nm. The maximum working pressure measured over 50 devices is above 9 bars in 90% of the cases.