bluuebunny/crossref_metadata_2025 huggingface dataset:
First woven covalent organic framework solved using electron crystallography
Authors: Liu Yuzhong , Ma Yanhang , Zhao Yingbo , Oleynikov Peter , Terasaki Osamu , Yaghi Omar
Published: December 2016

Making fabric by weaving is known as one of the oldest and most enduring methods. Nevertheless such an important design concept still needs to be emulated in extended chemical structures. Linking molecules into weaving structures would be of a great help to create materials with exceptional mechanical properties and dynamics. For this purpose a woven covalent organic framework‐505 (COF‐505) has been synthesized using a designed strategy [1]. However, COF‐505 is not well crystallized, which gives rise to a poorly resolved PXRD pattern. Therefore, approaches based on electron crystallography methods have been used. The structure of this COF has been solved by a combination of 3D electron diffraction tomography (3D EDT, [2]), high‐resolution TEM imaging and structure modeling.

3D EDT dataset was collected from a single sub‐micron crystal in a tilting range of –41.3° to +69.1°. The reconstructed 3D reciprocal lattice was identified as a
C
‐centered orthorhombic Bravais lattice with the unit cell parameters of
a
= 18.9 Å,
b
= 21.3 Å,
c
= 30.8 Å, and
V
= 12399 Å
3
, which have been used to index reflections observed in both PXRD pattern and Fourier diffractograms of HRTEM images. The derived reflection conditions were summarized as
hkl
:
h
+
k
= 2n;
hk
0:
h
,
k
= 2n;
h
0
l
:
h
= 2n and 0
kl
:
k
= 2n, leading to five possible space groups (s.g.):
Cm
2
a
(39),
Cc
2
a
(41),
Cmca
(64),
Cmma
(67) and
Ccca
(68).
Cm
2
a
,
Cmma
and
Ccca
were excluded because their projected plane group symmetries along [1‐10] do not coincide with those of the experimental HRTEM images (
pgg
). Furthermore, by performing Fourier analysis of the HRTEM images and imposing symmetry to the reflections, Cu(I) positions were determined from the reconstructed 3D potential map (Fig. 1). The structure of COF‐505 was built in Materials Studio by putting Cu(PDB)
2
units at copper positions and connecting them through biphenyl (reacted BZ) molecules. The chemical composition was determined by the elemental analysis, which indicated that the unit‐cell framework is constructed by 8 Cu(PDB)
2
and 16 biphenyl units (Fig. 2). However, symmetry operations of the s.g.
Cmca
require two PDB units connected to one copper onto a mirror plane perpendicular to the
a
–axis that is not the energetically favorable geometry. The final s.g. determined as
Cc
2
a
and was used to build and optimize a structure model. The PXRD pattern calculated from the model is consistent with the experimental pattern of activated COF‐505.
Tripartite assembly of
RND
multidrug efflux pumps in nanodisc and amphipol
Authors: Salvador Dimitri , Glavier Marie , Garnier Cyril , Picard Martin , Broutin Isabelle , Taveau Jean‐Christophe , Daury Laetitia , Lambert Olivier
Published: December 2016

*Two first authors equally contributed to this work

Tripartite multidrug efflux systems of Gram‐negative bacteria export a large variety of antimicrobial compounds at the expense of ATP or the proton motive force, thereby conferring resistance to a wide variety of antibiotics.
Pseudomonas aeruginosa
MexAB‐OprM and
Escherichia coli
AcrAB‐TolC, are prototypic proton motive force‐driven efflux systems from Resistance Nodulation and cell Division (RND) family. These efflux systems, composed of an inner membrane transporter, an outer membrane channel and a periplasmic adaptor protein, are assumed to form ducts inside the periplasm, facilitating drug exit across the outer membrane. Using lipid nanodisc system, we recently reported the reconstitution of native MexAB‐OprM tripartite system. Single particle analysis by electron microscopy revealed the lipid nanodisc‐embedded inner and outer membrane protein components linked together via the MexA periplasmic adaptor protein [1].

Recently the replacement of detergent by specially designed amphiphilic molecules such as amphipol or styrene–maleic acid copolymers is an alternative option to stabilize the membrane proteins in a free‐lipid environment. To further investigate key parameters controlling the formation of the tripartite system, we focus our study on MexA that in its mature form is anchored to the inner membrane via its palmitoyl moiety. To assess whether the lipid anchor is required for the reconstitution, we report here on the reconstitution of OprM and MexB in amphipol and compare with our previous results obtained with nanodiscs.
Monochromated Low‐Voltage
EELS
of Optical Resonances in Quantum Materials
Authors: Bell David , VonCube Felix , Rez Peter , Aoki Toshihiro
Published: December 2016

We have imaged and produced EELS spectra of Vacancy (NV) centers in diamond with our Zeiss Libra TEM [1] with a monochromated electron source and in‐column energy filter, Fig. 1. With monochromated electron energy loss spectroscopy (EELS) we measure the amount of energy loss that an electron undergoes; this includes optical resonances and inter and intra band transitions but also of course the Cherenkov radiation background. The low acceleration voltage of 40 kV directly reduces the background noise of the Cherenkov radiation. According to the photoluminescence spectra, we find a resonance at 1.9 eV (corresponding to 638 nm wavelength). We have also demonstrated an unexpectedly strong surface‐plasmonic absorption at the interface of silver and high‐index dielectrics based on electron and photon spectroscopy [2]. The measured bandwidth and intensity of absorption deviate significantly from the classical theory. Our density‐functional calculation well predicts the occurrence of this phenomenon. It reveals that due to the low metal‐to‐dielectric work function at such interfaces, conduction electrons can display a drastic quantum spillover, causing the interfacial electron‐hole pair production to dominate the decay of surface plasmons. This finding can be of fundamental importance in understanding and designing quantum nanoplasmonic devices that utilize noble metals and high‐index dielectrics.

Depending on the composition, Quantum Materials may act as conductors, insulators, semiconductors or even as superconductors. Combinations of different quantum materials are of high interest to explore new phenomena and act as the foundation for future electronic devices at the nanometer scale. Our quantum materials research is widely spread, reaching from defect formation in graphene to the characterization of hybrid quantum materials. We present our work utilizing Low‐Voltage Monochromated EELS and Low‐Voltage High‐Resolution Electron Microscopy (LV HREM). Together, these often improve the contrast to damage ratio obtained on a large class of samples, such as Quantum Materials.

Fe
3
Sn
2
is a rare metallic Kagome ferromagnet, which synthesis as a single crystal has not previously been reported (Fig. 2). We study this single crystal as well as other topological insulators with the particular interest in the correlated behavior in topologically non‐trivial materials. The (S)TEM images mapped with low voltage EELS show the atomic structure of the layered material(Fig. 2), and the magnetic force microscopy measurements reveal the magnetic anisotropy of the crystal on the surface. Monochromated EELS is the key to all this work, due to increased signal to noise and background and/or ZLP reduction.
The Influence of Gold on Corrosion Resistance of
P
t
C
u3/
C
Nanoparticles Composite
Authors: Ruiz‐Zepeda Francisco , Gatalo Matija , Jovanovič Primož , Bele Marjan , Dražić Goran , Gaberšček Miran
Published: December 2016

One of the applications of Pt‐based nanoparticles on high surface area carbon (HSAC) support composites is as a catalyst in polymer electrolyte membrane fuel cells (PEMFC) [1]. Yet the full commercial implementation of the technology has been hindered by the composite cathode which exhibits a low catalytic activity for oxygen reduction reaction (ORR), a poor stability in electrochemical environment and is expensive due to use of Pt. One solution to those issues is to alloy Pt with other transitional metals, which will not only reduce the composite costs, but also increase the catalytic activity for ORR [2]. Chemical ordering of the Pt‐M/HSAC (M=Metal) composite has shown to improve the stability of the nanoparticles, as well as to enhance the catalytic activity for ORR. [3]. Recent work has shown that adding a small amount of gold can improve the durability of Pt and Pt‐based nanoparticles [4,5], as well as inhibit the oxidation of HSAC support [5].

We have used Aberration Corrected Scanning Transmission Electron Microscopy (AC‐STEM) to study the effect of gold on the Pt‐skin partially ordered intermetallic PtCu
3
/HSAC composite. Au doped PtCu
3
/C and PtCu
3
/C composites were compared side to side, before and after an electrochemical cycling treatment. Fig. 1 shows scanning transmission electron microscopy annular dark filed images and energy dispersive x‐rays maps of the two composites after 200 cycles of electrochemical activation (EA, 0.05 – 1.35 V
RHE
, 300 mVs
‐1
). Less porous nanoparticles and lower Cu dissolution are observed in the Au doped PtCu
3
/C composite. Surface modifications were also observed in non‐porous nanoparticles after performing 10 000 cycles of severe degradation (0.4 – 1.4 V, 1 Vs
‐1
): (1) thickening of the Pt skin, (2) faceting and (3) surface dislocations (Fig. 2). These surface modifications may have influence on stress and nanoparticle stability. Overall, the Au doped PtCu
3
/C composite exhibited higher Cu retention and better durability compared to its binary analogue.
STEM
‐
EELS
investigation of planar defects in olivine
Authors: Marinova Maya , Cuvillier Priscille , Gloter Alexandre , Jacob Damien , Leroux Hugues
Published: December 2016

Iron is an abundant element in meteorites, where it is contained in various forms such as metal, oxides, silicates or sulfides. In these materials, investigation of the oxidation state of transition metal elements and Fe in particular is an indicator of the environmental conditions during the meteorite formation and evolution. The detailed quantification of the element distribution, concentration variation and the structure of defects are important for understanding the formation and transformation stages. Therefore the correlative investigation of defects structure and oxidation state variation within a meteoritic material at the atomic level can be essential to the understanding of the distinct formation mechanisms.

In this context, the current study focusses on the detailed investigation by STEM‐EELS coupled to HAADF imaging of planar defects in Fe‐rich olivine (Mg,Fe)
2
SiO
4
, present in the Allende meteorite [1]. The nature of the planar defects in olivine is still controversial in the literature: it can be associated to a deformation mechanism [2] or can be due to an aqueous alteration episode [3]. HAADF images of two types of planar defects, present in the Allende meteorite are given in Fig. 1 (a) and (b). Both planar defects are parallel to (100) planes of the olivine. The thicker ones, Fig. 1(a), are Cr‐rich as seen on the EELS spectra given in Fig. 2. STEM‐EELS mapping reveals an enrichment of Fe at the interface between the thick Cr‐rich defects and olivine. The Fe‐L
3,2
ELNES structures do not seem to indicate any change of the oxidation state in this Cr‐rich defect. The thinner (100) defects, Fig. 1(b), are associated to considerable Fe enrichment and Mg depletion over 2 to 4 atomic planes. Even though these thinner defects are often linked to the Cr‐rich defects, they do not contain Cr. The analysis of the atomically resolved Fe‐L
3,2
fine structure reveals the appearance in certain cases of a change of oxidation state of iron and partial Fe
3+
state within the thin Fe‐rich planar defects. This study gives an important insight on the structure of planar defects in the olivine and the associated change of the Fe oxidation state. Based on this fine structure analysis, a possible formation mechanism constraining the evolution of the environment redox condition will be proposed.
Structure of an elongation factor G‐ribosome complex captured in the absence of any inhibitor
Authors: Mace Kevin , Chat Sophie , Thomas Daniel , Giudice Emmanuel , Gillet Reynald
Published: December 2016

The ribosome is a large molecular machine performing protein synthesis (translation) in all living cells. During the elongation cycle of protein synthesis, new amino acids are iteratively delivered to the ribosome by aminoacylated transfer RNAs (tRNAs) and incorporated into a growing polypeptide chain, directed by the decoding of mRNA codons. In prokaryotes, this process is catalyzed by the two universal GTPase elongation factors EF‐Tu and EF‐G. EF‐G is a large GTPase protein made of five domains. It is structurally similar to the ternary complex made by EF‐Tu in complex with the incoming tRNA and GTP, with its fourth domain mimicking the anticodon stem‐loop of the tRNA recognizing the codon into the ribosomal A‐site. Several structures of ribosome complexes with EF‐G were recently determined by X‐ray or cryo‐electron microscopy (cryo‐EM), allowing for an accurate understanding of EF‐G interactions and conformational changes during translocation. However, all the reported structures were obtained by trapping EF‐G into the ribosome, using non hydrolyzable guanosine 5'‐triphosphate (GTP) analogs, specific inhibitors (
eg
fusidic acid, thiostrepton, viomycin or dithyromycin) or a mutated form of EF‐G. How EF‐G binds to the ribosome in the absence of any inhibitor is still elusive. To obtain insights into the engagement of EF‐G into the ribosome in a pre‐translocation state, we performed cryo‐electron microscopy experiments in the presence of GTP. To avoid extensive release of EF‐G from the ribosome we increased the EF‐G/ribosome molecular ratio and used a non‐productive translation complex (NTC) stalled on a truncated mRNA and therefore unable to trigger GTP hydrolysis. We report a new high resolution structure of the ribosome complexes wtih EF‐G, providing new insights into the way EF‐G interacts with the decoding center.
Plasmonic Resonance in Metallic Nanoparticles
Authors: Campos Alfredo , Nicolas Troc , Weissker Hans‐Christian , Stéphan Odile , Hillenkamp Matthias , Kociak Mathieu
Published: December 2016

The optical properties of noble metal nanoparticles are dominated by the surface plasmons (SP), which are collective oscillations of the free electrons confined at the surface. Surface plasmons in noble‐metal nanoparticles have received considerable attention for the wide range of applications, ranging from surface‐enhanced Raman spectroscopy (SERS), biomolecule sensing, labeling of biomolecules, cancer therapy, plasmonic absorption enhancement in solar cells to nanophotonics.

Influence of particle size on the surface plasmons is of great interest. For large particles (> 10 nm), pure classical effects related to confinement of classical electromagnetic waves at the surface of the objects are well‐known. For smaller sizes, the major effects are related to quantum physics. Optical techniques have been employed to study the optical properties of sub‐10 nm nanoparticles
1
. However in these techniques the measurements are made for a set of particles. This implies an inhomogeneous broadening of the surface plasmon resonance which largely prevents observing the influence of quantum phenomena. In order to overcome these challenges, single particles measurements have been made in the past years by electron energy loss spectroscopy (EELS) in combination with a scanning transmission electron microscope (STEM). STEM‐EELS measurements allow the study of individual particles on the atomic scale and with high spectral resolution
2
.

Here we investigate the plasmonic response of individual silver and gold nanoparticles, ranging from 2 to 10 nm in diameter. We will first discuss the instrumental progresses made to improve signal to noise ratio allowing detection of surface plasmons in ultrasmall nanoparticles and data treatment to improve energy resolution. We will then illustrate how bulk and surface plasmons evolve as a function of particle size. Figure 1 shows plasmons resonances well defined for a 5 nm silver particle and weak plasmons resonances (but yet visibles after deconvolution treatment) in a 2 nm silver particle. Furthermore in this work different configurations of substrate‐matrix will be shown in order to understand their influence on the plasmonic response.
Structure and non‐stoichiometry in Ca3‐xFe15+xO27‐y Hexaferrite
Authors: MONNIER Laurine , Boullay Phillipe , PELLOQUIN Denis
Published: December 2016

Recent studies led in the system Ca‐Fe‐O, and especially by considering the formation of intergrowths (CaFe
2
O
4
)(FeO)n [1], put forward a strong dependence in temperature so much point of structural view as electronics of these complex oxides with mixed valence Fe
2+
/Fe
3+
. In particular, it was demonstrated that CaFe
5
O
7
ferrite
,
n = 3 member of the series, exhibits a structural monoclinic/orthorhombic reversible transition in 360K associated with a transition of charge order [2].

New crystal chemistry studies by playing on possible non stoichiometry, so anionic as cationic, around the composition CaFe
5
O
7
, revealed the existence of a new structure which the stacking mode is related to the large family of hexaferrite. The structural resolution of this compound was performed by combining electronic diffraction and X‐ray diffraction data on powder. In particular, a tomographic approach in precession electron mode was carried out and will be presented. This structure which is also described as a mechanism of intergrowths will be detailed and illustrated by the high‐resolution imaging (HREM, HAADF). The electronic properties will be also exposed. The latter put forward two magnetic transitions over the room temperature: the first one around 350K, sensitive to the actual stoichiometry of the sample, and the second one in 460K [3].
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 , Rouvière 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 × 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 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.
Exotic Electron topologies ‐ Knitting with electron vortices
Authors: Clark Laura , Verbeeck Jo
Published: December 2016

Electron vortex studies have proliferated in the last few years, with many examples of their production, measurement and some examples of application.

However, these studies focus on the more standard cylindrically‐symmetric ideal electron vortex beam. We have recently noted an abundance of exotic vortex behaviours, outwith cylindrical symmetry [1]. Vortex‐antivortex loops were formed and annihilated at many different positions within the beam, with varying sizes. Other studies have shown how a vortex core can wend its way through a crystal lattice, with the vortex always remaining conserved [2].

In the sister field of optical vortices, it has recently been discovered that it is possible, with simultaneous manipulation of holography and careful limiting apertures, to produce 'knots' with the vortex cores [3]. These knots are not knots as known to the layman, but specific forms of multiply interlinked loops. These knots are unusual, and robust topological structures, and take the form of knotted dark threads within the beam [4].

Here, we investigate the feasibility of producing these exotic structures in the rather more confined space of a modern TEM, with finite aperture positioning and strict paraxial limitations. Adjusting the phase hologram technique of Leach et al [3], we have produced a design for a TEM phase mask

(see figure 1 and 2). Such a design is more detailed and technologically challenging than those produced so far in the electron vortex research field [5], but may just be within reach to enable the study of these unusual topological electron structures for the first time.
The interior of the rotavirus capsid
Authors: Estrozi Leandro F.
Published: December 2016

Rotavirus and other double‐stranded RNA viruses confine and protect their genome inside the capsid even after cell entry, hiding viral ds‐RNA from the cellular immune system. Thus, Rotavirus must be able to perform transcription and replication of its packed genome within a virus core formed by viral proteins by using a complex composed by the viral ds‐RNA and the RNA‐dependent RNA polymerase. For transcription, the resulting mRNAs has to exit the virus through channels in the capsid protein shells. For replication, viral mRNAs must enter the newly formed particles to be used by the polymerases as templates for dsRNA synthesis.

The symmetry mismatch between the symmetric capsid and the asymmetric complex formed by the polymerase and the ds‐RNA was used to reconstruct in 3D the interior of the rotavirus capsid showing for the first time how the ds‐RNA is organized and how it interacts with the polymerase.

Rotavirus has eleven different ds‐RNA segments and 11 to 12 polymerases inside each viral particle. Each polymerase is located underneath each one of the 12 icosahedral vertices [ref1].

The 3D reconstruction with icosahedral symmetry imposed obtained from cryo‐EM images of rotavirus was used to calculate synthetic 2D projections which were subtracted from the corresponding experimental images. This allowed the in‐silico isolation of the asymmetric parts of the structure by signal subtraction (Fig.4). The geometrical relationship between symmetric and asymmetric parts is known (assuming stable relative positioning) and it was is used to convert each one of the views associated to the symmetric 3D reconstruction into 12 sets of 5 views corresponding to the isolated asymmetric parts (5 views per icosahedral vertex). These 5 views were tested by projection matching [ref2] against a low‐resoltuion initial model and only the view giving the highest correlation coefficient was used to reconstruct an asymmetric structure by using the sub‐images without imposing symmetry.
3D
Reconstruction of Crack Formation in Austempered Ductile Cast Iron after an In‐situ Tensile Test
Authors: Tesařová Hana , Dluhoš Jiří , Petrenec Martin , Polák Jaroslav , Krahula Karel
Published: December 2016

A 3D reconstruction has been performed on a flat specimen after an interrupted in‐situ tensile tests. The sample consisted of austempered ductile cast iron (ADI) alloyed with 2.75% nickel. The analysis was performed by using a dual beam system (FIB‐SEM).

The procedure of this analysis consisted in studying the elastic‐plastic behaviour along with the nucleation and the growing of cracks in ADI at room temperature. For this purpose, a field emission scanning electron microscope (FE‐SEM) equipped with a tensile stage was used.

A systematic observation at the same location on the sample surface was used to clarify the tensile curves which are in agreement with deformation mechanisms. During the testing, decohesion of graphite nodules from the matrix was observed. The cracks initiated mainly at the interface of graphite nodule and the austenitic matrix. The elastic‐plastic region is connected with the plastic deformation of the matrix, growth and linking of microscopic cracks which are connected and finally leading to fracture of the sample.
Imaging and characterization of
H
g
S
nanoclusters in natural organic matrix: challenges and results
Authors: GAILLOT Anne‐Claire , LEMOUCHI Cyprien , LANSON Martine , MANCEAU Alain , NAGY Kathryn L.
Published: December 2016

Methylmecury is the environmental form of neurotoxic mercury that is biomagnified in the food chain. Methylation rates are reduced when the metal is sequestered in crystalline mercury sulfides or bound to thiol groups in macromolecular natural organic matter. Mercury sulfide minerals are known to nucleate in anoxic zones, by reaction of the thiol‐bound mercury with biogenic sulfide, but not in oxic environments. However, recent work, using indirect characterization methods such as EXAFS spectroscopy, provided evidence that mercury sulfide forms from thiol‐bound mercury alone in aqueous dark systems in contact with air. To confirm such new result, proof of mercury sulfide precipitation using direct characterization methods was needed. Such direct imaging, using TEM techniques, was however challenging due to the scarce occurrence and tininess of mercury sulfide particles in heterogeneous an beam‐sensitive natural soil samples. First results of HRTEM imaging of HgS nanoclusters of particles in Hg‐contaminated humic acid from Elliott reference soil, combined with diffraction technique to assess the of HgS polymorph, will be presented. Specific challenges due to the nature of the samples will be discussed.
DPC measurements on annealed cobalt thin films
Authors: Beer Thomas , Schwarzhuber Felix , Zweck Josef
Published: December 2016

In this work we present the results of differential phase contrast (DPC) [1,2] measurements of micro magnetic field distributions in annealed cobalt thin films. The polycrystalline specimens with a thickness of about 50 nm were produced by thermal boat evaporation under high vacuum conditions. After annealing the average size of individual cobalt crystals is increased and their magnetic properties are changed as shown by G. Herzer in [3] and [4]. Our goal was to determine, if DPC is a suitable technique to investigate how these changes in the crystallographic structure effect the magnetic properties of our specimen. Therefore we performed single DPC measurements as well as DPC tilting series to investigate if and how the magnetic behaviour of the annealed cobalt films is changed.

We investigated 5 different samples. One being the untempered thin film and the others were annealed over one hour with increasing temperatures ranging from 520 K to 820 K. To investigate the magnetic properties we performed a DPC tilt series for each sample. By tilting the specimen relative to the magnetic field of the objective lens we change the effective external in plane field on our samples. This leads to a change of the in plane induction in our cobalt thin films. We started each tilting series at large angles of α=20°, to be sure that all magnetic moments in our specimen are aligned in one direction. Figure 1 shows a DPC measurement of such a saturated state. The homogeneous green colour of the measurement confirms that the magnetic induction is saturated along the direction indicated by the colourwheel. Figures 2‐4 show an excerpt of DPC measurements performed during the tilt series of the specimen annealed at 850 K. It can be seen, that the magnetic structure changes with decreasing α and it seems, that one of the magnetic ripples is pinned to the highlighted crystallites in the center of figures 2 and 3.

By calculating the average direction and strength of the beam deflection for each individual DPC measurement we get information about the dependency between the magnetic induction and the tilting angle respectively the external magnetic field applied. We will present the results of our measurements on the different annealed specimen showing hysteretic behaviour of the magnetic induction and discuss the differences between them.

During our experiments especially the tilt series, which take about 4 hours to obtain, we encountered some difficulties with the DPC technique. In this work we will present these shortcomings and show solutions to some of the problems occured.
Wet
STEM
in
SEM
for Morphological Characterization of Novel Bacterial Species: Vibrio galatheae and Photobacterium galatheae
Authors: Valentina Mateiu Ramona , Giubergia Sonia , Machado Henrique , Gram Lone , Wagner Jakob Birkedal
Published: December 2016

Scanning electron microscope (SEM) is increasingly used for morphology characterization in various research fields. The technique is appealing due to the fact that it has a fairly large field of view (µm to mm) with nm lateral resolution, which makes it suitable for characterization of micrometer scale objects, which have nm scale features, such as bacteria. The major limiting factors for SEM as a visualization tool of bacteria are the sample preparation, which is prone to artefacts, and the sample interaction volume, which limits the lateral resolution. Here, we present an approach for morphology characterization, which involves minimal sample preparation and maximized lateral resolution: the use of environmental SEM (E‐SEM) with a scanning transmission electron detector (STEM); wet STEM. We use wet STEM for morphological characterization (identification of cell shape, size and appendices) of two bacteria isolated from a mussel collected in the Solomon Sea (Solomon Islands) during the Danish research expedition Galathea 3:

Vibrio galatheae
1

and

Photobacterium galatheae
2

.

The bacteria were grown in marine broth in flask cultures. After 24h growth at 25°C the marine broth was washed with miliQ water and a 0.5 µL droplet placed on a plasma treated carbon film 200 mesh copper grid. The sample was negatively stained with 2 % uranyl acetate aqueous solution and imaged in an FEI Quanta 200 FEG E‐SEM with an electron beam with spot 3 accelerated to 15 keV. During electron microscopy the bacterial cells were kept fully hydrated by using water as auxiliary gas and continuously condensing water on the sample. The bacteria were imaged using the transmitted electrons and a STEM detector (a 2 quad, diode back scattered electron detector mounted below the sample).

The wet STEM micrographs revealed that the
Vibrio galatheae
, has Vibrio monotrichous cells, 1.482±0.365 µm long, 0.743±0.181 µm width and 3.625±0.639 µm long flagellum (Figure 1), and the
Photobacterium galatheae
has Bacillus monotrichous cells , 2.261±0.404 µm long, 0.985±0.128 µm wide and 4.306±1.094 µm long flagellum (Figure 2).
Crystal growth of bullet‐shaped magnetite in magnetotactic bacteria of the Nitrospirae phylum
Authors: Li Jinhua , Menguy Nicolas , Gatel Christophe , Boureau Victor , Snoeck Etienne , Leroy Eric , Patriarche Gilles
Published: December 2016

Magnetotactic bacteria (MTB) are known to produce single‐domain magnetite or greigite crystals within intracellular membrane organelles and to navigate along he Earth's magnetic field lines. MTB have been suggested as being one of the most ancient biomineralizing metabolisms on the Earth and they represent a fundamental model of intracellular biomineralization. Moreover, the determination of their specific structure and morphology is essential for paleoenvironmental studies. Yet, the mechanisms of MTB biomineralization remain poorly understood, although this process has been extensively studied in several cultured MTB strains in the Proteobacteria phylum. Here, we present a comprehensive TEM study of magnetic and structural properties down to atomic scales on bullet‐shaped magnetites produced by the uncultured strain MYR‐1 belonging to the Nitrospirae phylum, a deeply branching phylogenetic MTB group. HAADF‐STEM imaging and XEDS elemental mapping revealed a phenotypical heterogeneity among MYR‐1 cells, Phenotype III produces numerous sulfur‐rich globules (fig.1a‐c). Electron tomography (ET) demonstrated that the bullet‐shaped magnetosomes are organized into 3–5 bundles of chains (fig.1d,e). Off‐axis Electron Holography results show that each bundle of MYR‐1 chains appears to behave magnetically as a large uniaxial single domain (USD) magnet that maximizes the net magnetic moment of the cell (fig.1f).

We observed a multiple‐step crystal growth of MYR‐1 magnetite: initial growth forming cubo‐octahedral particles (fig.2), subsequent anisotropic growth and a systematic final elongation along [001] direction (fig. 3). During the crystal growth, one major {111} face is developed and preserved at the larger basal end of the crystal (fig. 4.a). The basal {111} face appears to be terminated by a tetrahedral–octahedral‐mixed iron surface, suggesting dimensional advantages for binding protein(s), which may template the crystallization of magnetite (fig. 4b,c). This study offers new insights for understanding magnetite biomineralization within the Nitrospirae phylum.
A
JEOL
‐based cooling holder with a low specimen drift allowing sub 1Å
STEM
imaging
Authors: Bell David , Zandbergen Henny
Published: December 2016

With the development of aberration corrected microscopy has come the necessity of more stable sample stages, one area that needs further refinement is cryogenic sample system, both for biological imaging and for sensitive materials samples that would benefit from cryo‐stability. The basic principles of the holder are given in Fig. 1. It shows the main components of the cooling holder, the main coldness losses and the measures taken to create a thermal equilibrium, such that the drift is minimized. This allows for drifts of less than 2 nm/min and sub 1 Å resolution. In the cross‐section of the holder, schematically given in Fig. 1, the outside tube contains a heater close to thermal isolator near the tip, such that the temperature of the outside tube can be regulated to the temperature of the goniometer (or any other temperature). This is done to minimize the drift related to thermal expansion and to prevent any cooling (from the tip of the holder) of parts of the goniometer.

The thermal expansion stability is important since the cooling of the goniometer parts can result in unpredictable (slow) changes in the specimen position, for instance in the electron beam direction resulting in a focus change. In case of the temperature difference between the holder and the goniometer, the heat transfer between the outside rod and the goniometer is uncertain because it depends on the mechanical contact (that can vary with tilt) and the effect of the thermal gradient on each of the relevant components in the goniometer. Likewise the “coldness” influx depends on quite a number of parameters, like the size of the beard, how deep it is in the liquid nitrogen, whether the dewar has a “good” cover to isolate and to prevent turbulence. For that reason we have an option of a heater close to the cryo‐beard. Fig. 2 shows the experimental setup of the JEOL ARM, the holder and the dewar.

Our initial tests with the prototype sample holder on a sample of small gold particles on a thin C film show a resolution stability in HRTEM showing sub 1Å information transfer (Fig. 3). This stability is sufficient to operate the holder in STEM HAADF imaging conditions (Fig. 4) which was acquired at 2k resolution with 17.6 us pixel dwell time. Further work needs to be done to increase the operational duty cycle, however the basic configuration of the holder seems to provide a workable solution for high‐resolution cryo‐imaging.
Advances in
FIB
EDX
‐Nanotomography
Authors: Cantoni Marco , Nabiei Farhang , Burdet Pierre
Published: December 2016

FIB‐tomography is used in materials science for 3D‐analysis of nanostructured materials [1]and in life science for the analysis of complex structures like brain tissue [2]. This presentation summarizes recent technological improvements, which include advancements in detector technology for electron imaging and elemental analysis, scan generator technology for high throughput imaging, and automated drift correction for reliable 3D reconstruction. New in‐column detectors have a higher sensitivity for low energy electrons, which is the basis for a very high resolution down to a few nm voxel size. The low kV imaging can be combined with energy filtering in order to detect a pure signal of backscattered electrons (BSE), which improves the reliability of phase segmentation and quantitative analysis. The quality of the 3D reconstructions can also be improved with refined procedures for drift correction based on reference marks. In addition, with the new scan generators image acquisition and ion milling can be performed synchronously. In this way the acquisition speed increases further. Finally, spectral and elemental mapping (XEDS) based on Silicon Drift Detectors (SDD) with higher collection solid angles provides higher X‐ray count rates. These increased count rates open new possibilities in chemical analysis that provide larger data cubes with higher representativeness. As EDX Analysis requires higher beam energies in order to ionize the elements of interest the interaction volume increases and the resolution decreases. The latest development of acquisition software allows to switch high tensions in order to acquire data sets with small voxel sizes and high resolution using SE and BSE detectors with high efficiency at low voltages and to acquire a second data set under conditions that match the requirements for EDX Analysis (higher voltages and larger voxel sizes). The new possibilities of FIB EDX‐Tomography are illustrated with the following examples:

High throughput elemental analysis is performed of a NiTi stainless steel with a complicated multi‐phase microstructure [3]. The examples document the recent advancements in resolution, contrast, stability and throughput, which are necessary for reliable and representative 3D‐analysis. The segmentation of the different phases was done using the EDX‐maps and further refined with the SE‐images. Fig.1

Representation of the complex chemistry of a diamond‐anvil cell laser heated spot. The conditions used (50GPa, 4000K) resemble conditions at the earth core and reveal a complex microstructure with phases that are only formed under theses extreme conditions. Fig.2
High‐resolution
TEM
study of colloidal cesium lead bromide nanocrystals
Authors: Dang Zhiya , Brescia Rosaria , Akkerman Quinten , Shamsi Javad , Prato Mirko , Manna Liberato
Published: December 2016

Cesium lead halide perovskites, of the type CsPbX
3
(X=Cl, Br, I), are promising candidate materials for optoelectronics, solar devices and high‐energy radiation detection [1‐6]. Colloidal CsPbBr
3
nanocrystals with morphology of nanocubes [1], nanoplatelets [2‐3] and nanowires [4] have been successfully synthesized in the last few years. Orthorhombic, tetragonal, and cubic phases were reported for bulk CsPbBr
3
, the cubic phase being the high‐temperature one [6]. The majority of CsPbBr
3
nanocrystals were reported to have cubic phase, e.g. nanocubes [1] and nanoplatelets [2‐3]. On the other hand, nanowires [4] and also nanocubes [5] exhibited orthorhombic phase, the latter ones despite their cubic shape. Here a study of colloidally grown CsPbBr
3
nanocubes (NCs), with edge length of about 40 nm, and large nanosheets (NSs) using high‐resolution TEM (HRTEM) and selected area electron diffraction (SAED) shows that nanocrystals with both morphologies share the same orthorhombic phase (ICSD # 97851, see Figure 1). The observations were carried out by using an image Cs‐corrected JEOL JEM‐2200FS TEM (accelerating voltage = 200 kV). The lattice parameters,
a
',
b
',
c
'
,
recalculated with respect to the ideal perovskite(a/ , b/ , c/2) for bulk orthorhombic CsPbBr
3
are very similar at room temperature (298 K) and further decreasing of temperature below the transition temperature 361 K increases the discrepancy between them. Here we performed HRTEM and SAED study for CsPbBr
3
NCs at various lower temperatures (Figure 2). The results have shown that the spacing among closely spaced peaks (298 K) increases at low temperature (153 K), indicating a larger discrepancy among the lattice parametes (see the arrows labelled in Figure 2). The orthorhombic CsPbBr
3
NCs and NSs exhibit significantly different facetting: the NCs are enclosed by {1‐10}, {110} and {001} planes (Figure 3(a,b)). However, in the growth condition of NSs, the {001} planes are strongly passivated and the growth along [001] is inhibited. The growth in the plane of (001) leads to formation of large nanosheets confined in [001], and extended at the plane (001) and enclosed by {1‐10} and {110} (Figure 3(c,d)).
Low Voltage Imaging of Defects in
2D
‐Quantum Materials
Authors: Bell David , VonCube Felix
Published: December 2016

The discovery of extraordinary new quantum materials with striking properties has caused great excitement, and promises to transform signal processing and computation. We have performed integrated research on three materials (1) Graphene (G) ‐ electrons that move as massless particles at a constant speed; (2) Topological Insulators (TI) ‐ mobile surface electrons with spins fixed to the direction of motion; and (3) Nitrogen‐vacancy (NV) Centers in Diamond ‐ a single spin stores a bit of quantum information. Remarkably, the quantum phenomena displayed by these materials persists at room temperature, changing the rules for signal processing and computation and opening the way for quantum electronics.

Defects in materials effect the propagation of electrons and holes in graphene and topological insulators act in ways that are totally unlike carriers in conventional semiconductors ‐ they move like two‐dimensional (2D) massless, ultra‐relativistic electrons, except their speed is much less than the speed of light. Because there is no bandgap, an electron can pass through a potential barrier by temporarily turning into a hole, dramatically reducing scattering and improving coherence. In addition, for topological insulators the direction of the spin of a surface electron is tied to its direction of motion, providing an ideal means to transport spin information.

We have imaged and characterized high quality graphene‐like materials, such as hexagonal boron nitride (hBN) and hybrid graphene‐hBN structures (Fig. 1). Compared with mechanical exfoliation, CVD synthesis [1‐2] can provide larger areas, with wafer‐scale monolayer or multilayer graphene sheets. Aberration‐corrected electron microscopy has been used to characterize MBE‐grown films with high resolution at low beam voltages (40 & 80kV) to directly visualize structural defects and relate them to performance.

We use a Cs corrected Zeiss Libra TEM to investigate chemical vapor deposition (CVD) graphene with added copper and mercury defects. With TEM we address the question, where the Hg and Co atoms are placed on the graphene. At the same time, we observe the effect of the copper and mercury on the pi electrons in graphene with Raman spectroscopy. Furthermore, we are interested in graphene based hybrid structures, such as graphene oxide embedded in a vanadium pentoxide nanofiber matrix (Fig. 2). The graphene sheets and the nanofibers have approximately the same thickness, leading to a material with enhanced mechanical performance in comparison to pure vanadium pentoxide and pure graphene oxide sheets.

Application of Low‐Voltage Electron Microscopy and its development and future directions will be presented.
Separating Magnetic and Non‐magnetic Signals at the
Fe/MgO
Interface
Authors: Spiegelberg Jakob , Thersleff Thomas , Rusz Ján
Published: December 2016

Despite various efforts, it remains an experimentally challenging task to access magnetic properties at (sub) nanoscale. One route towards a direct measurement of magnetism is the measurement of electron magnetic circular dichroism (EMCD) [1]. Being based on the measurement of electron energy loss (EEL) spectra, EMCD can in principle be measured at atomic resolution and can open the door to study exciting new area of physics such as magnetism in the vicinity of defects or interfaces. However, in addition to general concerns of low signal to noise ratios of EMCD spectra measured at high resolutions calling for a statistical data treatment, there might be other, non‐magnetic contributions to the signal which cause a change in the white line ratio of the L3/L2 edge peak of the magnetic species. These white line changes might be related to the occurrence of a different chemical species of the same element, e.g., due to in situ oxidation of the sample, or also to position dependent changes of the electron wavefunction if the EMCD experiment is carried out at atomic resolution [2]. Such effects may render the correct interpretation of EMCD signals impossible if they can not be clearly separated from the true magnetic signal. The issue calls out for a statistical tool to separate the components.

We demonstrate how a canonical polyadic decomposition (CPD) [3],[4],[5] can be used to separate magnetic and non‐magnetic signals measured at the Fe/MgO interface. The system has recently received a lot of attention as a candidate for magnetic tunnel junctions due to its large tunneling magnetoresistance (e.g. [6],[7]), its magnetic properties, epecially at the interface are thus of interest. Through the additional explanatory power of CPD, insight is gained on a perceived increase of orbital to spin moment ratio at the interface [8]. Besides the spectral components and their spatial maps (Fig.1), CPD also returns a vector containing the weight of the respective component in the data sets measured with an aperture position such that the sign of the EMCD signal is positive, negative and such that the magnetic component vanishes (Fig.2). The components shown below indicate a significant non‐magnetic white line branching towards the Fe/MgO interface.

CPD can not only be used as a technique to extract EMCD from noisy data and separate it from potential non‐magnetic signals, targeting both the aforementioned problems, but it can be generalized to any problem of identifying different signal contributions in experiments where multiple data sets are measured on the same sample area, such as momentum resolved EELS. It possesses desirable features such as uniqueness while not constraining the components along either of the modes and comparatively low computational costs. The assumptions on the tensor's structure match the physical model and thus lead to directly interpretable components. Hence, CPD is a useful addition to the set of statistical tools for the analysis of microscopy data.