bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and chemical characterisation of novel
FeS
nanostructures for energy storage synthesised using a single‐source precursor
Authors: Lozano Juan G , Dillon Frank , Naylor Andy , Lee Lok Yi , Lippard Chris , Johnstone Duncan , Bruce Peter G , Grobert Nicole 
Published: December 2016

Iron sulphide is an interesting material for a wide range of potential applications due to its number of possible phases, high abundance, low cost and non‐toxicity [1]. In particular, Fe‐S phases are capable of undergoing reversible electrochemical reactions with lithium‐ions making Fe‐S a potential material for anodes in lithium‐ion batteries [2]. Furthermore, by engineering the electrode materials to nanometre scale, there will be (a) a larger surface area of electrode material in contact with the electrolyte per unit mass, allowing a larger flux of Li‐ions between the two electrodes, resulting in faster charging and discharging of the battery; (b) shorter diffusion distances of Li‐ions which will result in a higher power density; (c) a better accommodation of strain following conversion reactions, thus resulting in longer cycling life. This advantages are even further strengthened if the nanostructures are synthesised in the two‐dimensional form, since then the accessible surface area of the materials is dramatically increased. Despite their superior properties, the scarce number of published reports on the synthesis on two‐dimensional FeS nanostructures is remarkable [3].
Here we report structural and chemical characterisation of iron sulphide nanoparticles and two‐dimensional nanosheets synthesised using a one‐pot, fast and facile single source precursor method. This synthesis method offers the possibility of tailoring the design of the nanostructures with slight variations of the synthesis conditions. Conventional transmission electron microscopy (TEM), high resolution TEM, and selected area electron diffraction patterns confirmed that the nanoparticles consisted of high‐crystalline quality troilite FeS; while the nanosheets are made of small crystallites with random rotations while still lying on their (0001) basal plane. Scanning‐transmission electron microscopy (STEM) and electron energy‐loss spectroscopy confirmed that the majority of the crystallites in the nanosheets are troilite FeS, with some residual pyrite also present; and no oxides were formed during synthesis. Electrochemical tests also indicate that the nanosheets show much larger capacities compared with the nanoparticles.
Visualization of Dengue virus like particles interacting with antibodies
Authors: Deliot Aurelie , Nicolai Marie‐Claire , Ronzon Frederic , Lecouturier Valerie , Nemecek Daniel 
Published: December 2016

Dengue virus (DENV) is one of the most important arthropod‐borne viruses that infect humans. Approximately 400 million people are infected annually in tropical and sub‐tropical regions worldwide [1]. In 2015, Sanofi Pasteur released the first commercialized and approved tetravalent vaccine that is protective against the four DENV serotypes [2].
In the context of developing a better understanding of the interaction of dengue antigen with the immune system, it is important to fully understand the structure and accessibility of specific epitopes. Particularly in the case of the dengue virus, viral capsids bud into the host endoplasmic reticulum and acquire structural proteins prM and E embedded in the membrane. The prM and E proteins are assembled as trimers as part of an immature icosahedral shell and undergo significant structural rearrangement during viral exit via the Golgi apparatus. In the Golgi, Host furin‐type proteases concomitantly cleave the pr peptide triggering rearrangement of the trimers into dimers, which is necessary for infectivity of the viral particle [3]. However, maturation of DENV virions is not efficient and partly immature particles are released during DENV infection as well. It has been hypothesized that these particles function as decoys to avoid neutralization of the infectious mature particles by the immune system [4].
Recombinant antigens in the form of virus‐like particles are attractive as reagents for understanding antigen‐antibody interactions. Here, we investigated the molecular architecture of virus like particles (VLPs) made of dengue structural subunits, which are produced by The Native Antigen Company (Oxfordshire, UK). We found by SDS‐PAGE and confirmed by Western blot that DENV‐2 and DENV‐3 VLPs contain a significant fraction of uncleaved prM subunits. To assess the molecular architecture and conformation of subunits in the VLP particles, we determined 3D structure of individual particles by cryo‐electron tomography. The particles have a spherical (DENV‐2 VLPs) or elongated (DENV‐3 VLPs) outer shell with short spikes and an internal cavity (Figure 1). The spikes exhibit the same morphology as the prM/E subunits in the immature dengue viral particles. We additionally imaged and reconstructed the 3D structure of VLP particles mixed with monoclonal antibodies specific to the mature conformation of DENV. We identified bound antibodies to individual particles in subtomograms after subtraction of the VLP shell (Figure 2). Binding of the antibodies to the VLP particles was subsequently confirmed by Western blot and immunogenicity assays suggesting that these VLPs could adopt a mixed conformation with mature dimers and immature trimers on the same particles, as previously described for DEN virions or adopt a specific new conformation of mature prME specific to VLPs.
This study was funded by Sanofi Pasteur using equipment installed at Sanofi Pasteur.
In‐situ propagation ofAlin germanium nanowires observed by transmission electron microscopy
Authors: El Hajraoui Khalil , Robin Eric , Lopez‐Haro Miguel , Zeiner Clemens , Brunbauer Florian , Kral Sébastian , Lugstein Alois , Rouvière Jean‐Luc , Hertog Martien Den 
Published: December 2016

Semiconductor nanowires (NWs) are promising candidates for many device applications ranging from electronics and optoelectronics to energy conversion and spintronics. However, typical NW devices are fabricated using electron beam lithography and therefore source, drain and channel length still depend on the spatial resolution of the lithography. In this work we show fabrication of NW devices in a transmission electron microscope (TEM) where we can obtain atomic resolution on the channel length using in‐situ propagation of a metallic phase in the semiconducting NW. The corresponding channel length is independent on the lithography resolution. We show results on semiconducting NW devices fabricated on two different electron transparent Si3N4membranes: a calibrated heater chip from DENs solution [1] and homemade membranes where the NW‐metal contact is locally heated by Joule heating [2]. We demonstrate a real‐time observation of the metal diffusion in the semiconducting NW. First we present results on in‐situ propagation of aluminum metal in Ge NWs while monitoring the system temperature [3] and by Joule heating while measuring the current through the device. We study the kinetics and rate limiting step by monitoring the position of the reaction front as a function of time. Second we will show characterization of the formed phase at atomic length scales with different (S)TEM techniques (energy dispersive X‐ray spectroscopy, HR(S)TEM) to understand how the metal atoms diffuse and incorporate into the Ge NW at the reaction front and how these parameters relate to the electrical properties of the same interface.Using EDX analysis and comparing with 3D NW model calculations we show that the reacted NW part is pure Al, with a shell of Al2O3with a low Ge content on both sides of the Al2O3shell see Fig.2. EDX analysis show that both Al and Ge are diffusing in opposite directions.
Laboratory diffraction contrast tomography ‐ applications and future directions
Authors: Lavery Leah , Holzner Christian , Bale Hrishikesh , Merkle Arno , McDonald Samuel , Withers Philip , Zhang Yubin , Jensen Dorte Juul , Reischig Peter , Lauridsen Erik 
Published: December 2016

Determining crystallographic microstructure of a given material in 2D can be challenging. Further extending such an investigation to 3D on meaningful volumes (and without sample sectioning) can be even more so. Yet reaching this insight holds tremendous value for 3D materials science since the properties and performance of materials are intricately linked to microstructural morphology including crystal orientation. Achieving direct visualization of 3D crystallographic structure is possible by diffraction contrast tomography (DCT), albeit only available at a limited number of synchrotron X‐ray facilities around the world. Recent developments, however, have made DCT possible on an X‐ray microscope with a laboratory source.
The introduction of diffraction contrast tomography as an additional imaging modality on the ZEISS Xradia 520 Versa laboratory X‐ray microscope has opened up a whole new range of possibilities for studies of the effect of 3D crystallography on materials performance. The capability to link directly the crystallographic and grain microstructure information with that obtained via conventional absorption or phase contrast imaging, non‐destructively in three‐dimensions and all in the laboratory, creates a powerful and easy to access tool. [1] Using a polychromatic X‐ray source, laboratory diffraction contrast tomography technique (LabDCT) takes advantage of the Laue focusing effect, improving diffraction signal detection and allows handling of many and closely spaced reflections. Additionally, LabDCT opens the way for routine, non‐destructive and time‐evolution studies of grain structure to complement destructive electron backscatter diffraction (EBSD) end‐point characterization. Combination of grain information with microstructural features such as cracks, porosity, and inclusions all derived non‐destructively in 3D presents new insights for materials characterization of damage, deformation and growth mechanisms. Furthermore, 3D grain orientation data is a valuable input into multi‐scale, multi‐layered modeling platforms that can virtually evaluate mechanical properties to produce high fidelity simulation results. Here, we introduce the LabDCT technique and demonstrate its unique capability through a selection of application examples for materials science as well as discuss innovative methods to extend the current capabilities of the technology for a better understanding of materials structure evolution in 3D.
Precision top‐down delayering of microelectronics devices using broad‐beam argon ion milling
Authors: Nowakowski Pawel , Olexa Kristin , Ray Mary , Fischione Paul 
Published: December 2016

The semiconductor industry is a dynamic, rapidly growing manufacturing sector. In 2015, global sales of semiconductor products increased 9.9% and reached a record US $335.8 billion [1]. Constantly evolving microelectronic device designs continue to grow more complex, more compact, and smaller. For example, three‐dimensional (3D) NAND flash memory cells are layered vertically in three‐dimensional stacks, which provides much greater cell density and increases memory capacity [2]. Such design complexity makes maintaining manufacturing quality standards a consistent challenge for the industry and failure analysis plays a critical role in meeting that challenge. Failure analysis can determine the root cause of a defective device; it enables failure identification and characterization, as well as provides feedback for product and process improvement. Many failure analysis techniques, both nondestructive and destructive, have been developed in the past five decades [3, 4]:
· nondestructive techniques: electrical measurement and testing, infrared and X‐ray examination, and optical or electron microscopy evaluation
· destructive techniques: chemical etching, mechanical polishing, plasma etching, and delayering
Many techniques are untenable for multilayer devices. For example, Samsung found that etching agents are too aggressive and the company enumerated several major structural failures that can occur in NAND flash memory related to etching or particle contamination. Delayering is a popular choice because it allows top‐down, whole chip characterization. However, delayering 3D devices with multiple layers is difficult. The main challenge presented by a vertical stack is looking through a stack of many dissimilar layers. Instrumentation that employs low energy, broad beam, argon ion milling using a top‐down delayering technique can help to expose a defect region for further analysis [5]. The work presented is a new development in semiconductor device delayering for failure analysis using low energy, broad‐beam argon ion milling.
Random scanning mode for the spectroscopy of sensitive materials
Authors: Tararan Anna , Tencé Marcel , Brun Nathalie , Kociak Mathieu , Zobelli Alberto 
Published: December 2016

Electron Energy Loss Spectroscopy (EELS) and Cathodoluminescence (CL) in a STEM microscope allow to characterize chemical composition and optical properties down to a subatomic scale. Nevertheless, a high electron dose is conveyed onto limited regions of the specimen and generates strong radiation damages in fragile materials. Spectroscopy of individual molecular systems remains therefore still highly challenging. Here we demonstrate how this traditional limit can be largely overcome by acquiring hyperspectral images through a non‐standard random scanning mode. This is achieved by considering the pixels in the scanning array as a list that is shuffled and loaded into a dedicated scan generator. At the end of spectrum acquisition a signal from the detector triggers the next beam position.
The luminescence of high efficiency molecular dyes has been investigated through an original CL set up integrated within a STEM microscope, which allows a nanometric spatial resolution. Illumination damages have been reduced thanks to a liquid nitrogen cooling system at the sample stage and a 60 keV electron beam.
The dyes have been deposited at a very low concentration on hexagonal boron nitride (h‐BN) flakes. This one represents the ideal substrate for luminescence, being chemically inert and displaying a wide energy band gap. Furthermore, it can actively participate in the luminescence processes: electron induced excitations in the h‐BN substrate may recombine at the molecular sites. The luminescence of the molecules should appear therefore in CL‐hyperspectral images as isotropic emission spots some tens of nanometres wide, corresponding to the excitation diffusion length in h‐BN.
We show that a traditional sequential line‐by‐line scan leads to a rapid bleaching of the molecules, whose luminescence appears only in a short line of pixels. On the contrary, by using a random scan routine we were able to obtain the expected isotropic emission spots. Unlikely a sequential scan, in a random survey the energy deposited in an illuminated area can be evacuated before an adjacent pixel is illuminated. Even when the bleaching of the molecule cannot be avoided, this acquisition mode allows to collect a signal from a higher number of pixels with respect to the sequential scan.
Beside CL, EELS investigations could in principle derive great advantage from this random acquisition. More precisely, core EELS studies of fragile materials could benefit from a higher spatial resolution of the hyperspectra. Finally, the random scan opens also new perspectives in terms of compressed sensing techniques.
Fusion to a symmetric scaffold allows cryo‐
EM
analysis of a small monomeric protein
Authors: Coscia Francesca , Estrozi Leandro , Hans Fabienne , Malet Hélène , Noirclerc‐Savoye Marjolaine , Schoehn Guy , Petosa Carlo 
Published: December 2016

Single particle cryo‐electron microscopy (cryoEM) is a powerful method for determining the structures of large macromolecules and their complexes. Recent technical advances in direct electron detectors, phase plates and computational procedures for image processing have revolutionized the field, allowing 3D reconstructions to be obtained at near‐atomic resolution (<4 Å). However, most monomeric proteins of biomedical interest remain too small (<100 kDa) for cryo‐EM analysis. In this work we propose a new method to overcome this size limitation by fusing a monomeric protein (target) to a homo‐oligomeric scaffold protein, whose large size and symmetry facilitates cryoEM analysis. As proof‐of‐principle, we fused maltose‐binding protein (MBP), a 40 kDa monomer, to glutamine synthetase (GS), a dodecamer formed by two hexameric rings.
We designed an initial MBP‐GS construct with a linker sufficiently long to allow the fused moieties to fold properly without mutual steric hindrance. The junction was optimized by progressively deleting linker and/or flanking residues to reduce the spatial separation between the two fusion partners, thereby restricting the relative mobility of the target subunits (Figure A). We bacterially expressed 18 MBP‐GS constructs and used biophysical analysis (native poly‐acrylamide gel electrophoresis, size exclusion chromatography, dynamic light scattering and differential scanning fluorimetry) to screen for particle compactness and homogeneity. Negative stain EM analysis confirmed the trend observed by the biophysical assays, and both approaches identified the same construct as the most compact and conformationally homogeneous.
Cryo‐EM analysis of the most promising construct led to a reconstruction with an overall resolution of 4.2 Å (FSC=0.143 criterion) and a local resolution that varied from ~4 Å within the GS subunit to between 6 and 10 Å within the MBP subunit. Fitting the GS crystal structure into this map revealed an excellent fit, allowing all secondary structure elements and certain large side chains to be visualized. A good fit was also observed for MBP: the N‐ and C‐terminal lobes enclosing the active site were clearly defined, several helical elements were well resolved, and the bound maltose ligand was partly visible (Figure B). These findings illustrate the feasibility of using homo‐oligomeric scaffolds to enable cryo‐EM analysis of monomeric proteins, raising the prospect of applying this strategy to more challenging structures resistant to crystallographic and NMR analysis.
Probing the radiative and full electromagnetic local densities of states with electron energy loss spectroscopy and cathodoluminescence spectroscopy
Authors: Losquin Arthur , Kociak Mathieu 
Published: December 2016

Electron Energy Loss Spectroscopy (EELS) and CathodoLuminescence spectroscopy (CL) map the surface plasmon modes of metallic nanoparticles at the nanometer scale [1]. Although they yield similar results, EELS and CL differ by nature. EELS measures the energy lost by fast electrons interacting with a sample whereas CL measures the energy of the light emitted from this interaction [2]. However, the consequence of this different nature has remained unexplored because combining EELS and CL on single nanoobjects could not be achieved.
We combined EELS and CL on single nanoobjects using a Scanning Transmission Electron Microscope (STEM) [3]. In a STEM, an electron beam is focused onto a nanometric probe that is scanned over the sample. At each point of the sample, the transmitted electrons are collected for EELS, while the emitted light is collected for CL; both a full EELS spectrum and a full CL spectrum are recorded. We studied small gold triangular nanoprisms as a model system (Fig. 1a). The combination of EELS and CL allows us to map the same surface plasmon modes using both techniques (Fig. 1b and c).
We showed that CL only probes the dipolar mode, contrary to EELS that probes both the dipolar and quadrupolar modes. Furthermore, the dipolar mode resonates at shifted resonances in EELS and CL for prisms with edge lengths larger than 100 nm relying on carbon substrate (Fig. 2a). The magnitude of the shift relates to the mode damping.
Having demonstrated that EELS and CL signals differ, we showed that the full and radiative ElectroMagnetic Local Densities Of States (EMLDOS) differ similarly (Fig. 2b) [4]. Whereas EELS measures a quantity close to the full EMLDOS projected along the electron direction [5], CL measures a quantity close to the radiative EMLDOS projected along the electron direction [4]. Contrary to EELS, CL probes only the radiative modes, which are not necessarily dipolar for object sizes beyond the quasistatic limit. The ratio of the CL resonance to the EELS resonance quantifies the radiative weight of the mode damping. If the modes are damped and induce interfering radiation, CL resonant line shapes are shifted and asymmetric compared to EELS.
This work demonstrates the great interest of combining EELS and CL for plasmonics [3, 4].
The research leading to these results has received funding from the European Union Seventh Framework Programme [No. FP7/2007‐2013] under Grant Agreement No. n312483 (ESTEEM2). We gratefully aknowledge the following collaborators who significantly contributed to this work : Luiz F. Zagonel, Viktor Myroshnychenko, Benito Rodríguez‐González, Marcel Tencé, Leonardo Scarabelli, Jens Förstner, Luis M. Liz‐Marzán, F. Javier García de Abajo and Odile Stéphan.
Effects of dose and image registration on exit wave reconstruction of low‐dose focal series
Authors: Huang Chen , Sawada Hidetaka , Kirkland Angus 
Published: December 2016

Dose effects are an important topic in electron microscopy (EM) due to the close connection to radiation damage and hence to quantitative image analysis [1]. Two main problems restricting the application of exit wave reconstruction to radiation‐sensitive materials are the high noise level in low‐dose images and the contrast reversals close to zero defocus. Both problems cause difficulty in correctly registering a focal series of images and a well‐aligned image series is a prerequisite for valid wave restoration [2].

In this work, a simulation‐assisted cross‐correlation function (SA‐XCF) registration scheme is proposed and tested with five focal series of the same cerium oxide (CeO
2
) nanoparticle taken under identical imaging conditions except for varying electron dose between different focal series. The registration results demonstrate the superiority of the new registration scheme over a simple neighboring‐reference cross‐correlation function (NR‐XCF) registration (Figure 1). The impact of registration quality on exit wave reconstruction is explored by the comparing the IQ factor, an image quality measurement calculated from the power spectrum of an image of the phase restored from the same focal series aligned by two different registration methods. Better phase restoration results are obtained with the focal series registered by SA‐XCF in comparison to NR‐XCF.

With improved image alignment exit waves reconstructed from focal series data at variable dose were compared. The comparison result confirms the natural hypothesis that higher electron dose series give improved restored exit waves than lower dose series. However, this improvement with increased dose appears to plateau beyond a certain dose threshold. Exit wave reconstruction from focal series at very low dose tends to preserve more noise from the images and leads to worse IQ factor values (Figure 2).
It has also been observed that the restored exit waves from focal series at very low dose can be unreliable for quantitative interpretation (Figure 3) where the phase shift is noticeably attenuated. This leads to the question of how a critical dose can be determined in order to obtain a quantitatively interpretable exit wave subject to the most efficient use of an allowed electron dose budget.