bluuebunny/crossref_metadata_2025_split huggingface dataset:
3‐D areal functional parameters extracted from
AFM
data of polished dental tooth‐restorative nanocomposites
Authors: Lainović Tijana , Ţălu Ştefan , Stach Sebastian , Vilotić Marko , Blažić Larisa 
Published: December 2016

The analysis of contemporary areal functional surface parameters of functional parts in any system of elements, that are in contact with each other, is essential for the understanding of their frictional behaviour. Oral environment is a specific tribological system where a tooth or a tooth‐restoration is exposed to the cyclic mechanical, thermal, and pH changes. 3‐D areal texture parameters of tooth replacing materials are of a great importance for prediction and understanding of the materials' tribological properties during their functional use.
The aim of this study was to conduct a detailed AFM morphological analysis of contemporary dental nanocomposites and to calculate specific 3‐D surface texture parameters, after four dental polishing protocols.

Two representative materials were chosen for testing: nanohybrid (Filtek Z550, 3M ESPE ‐ FZ550) and nanofilled (Filtek Ultimate Body, 3M ESPE ‐ FUB). The polymerized composite samples were polished by four different dental polishing procedures: multi‐step (MSP), single‐step (SSP), multi‐step followed by diamond paste (MSP+D), and single‐step followed by diamond paste (SSP+D). For the texture analysis the atomic force microscopy was used (Veeco di CP‐II). Using the software packages: Mountains Map
®
7 (Digital Surf, Besançon, France, available from:
http://www.digitalsurf.fr
) and Gwyddion 2.28 (available from:
http://gwyddion.net/
), the depth histograms, volume surface parameters, peak count histograms, watershed segmentation algorithms, average power spectral density were calculated to describe the 3‐D surface properties of tested specimens.

These parameters offered the possibility of a more profound understanding of the structure‐related functional properties of the surfaces of tested materials. The MSP created a more favourable surface texture on both tested materials. It had narrower height distribution and volume surface parameters which indicated the lower wear probability of materials polished by MSP than the SSP. The number of motifs after the watershed segmentation was the highest on the samples polished by MSP, due to the presence of fine surface irregularities. SSP created lower number of motifs, by cutting the surface details and creating deep and wide grooves, plane aspects of dales or hills. MSP or MSP+D mostly created more isotropic surface texture, which indicates that the MSP can be considered as a reliable method for dental composites polishing in comparison with the SSP or SSP+D.
Recognition and measurements of nanoparticles in
TEM
/
STEM
images by fitting the model grayscale distribution to the real one: new approach for automated statistical analysis
Authors: Shvedchenko Dmitry , Suvorova Elena 
Published: December 2016

The main challenge to manufacture nanoparticles for applications in catalysis, medicine and pharmaceuticals is a mass production of stable nanoparticles with a narrow size distribution to target and control specific effects. Therefore reliable and fast statistical analysis of (nano)particles is of great interest especially for the particle size less than 10 nm due to strong chemical and biological activity associated with high penetrating capabilities through cell membranes. We would like to see these particles, to know their structure and composition, and to measure sizes. The intelligent, fast and reliable program can be a very useful tool for image analysis of “small” nanoparticles in TEM/STEM images.
In our work, we show that fitting of the calculated grayscale distribution to the real distribution in (S)TEM images is able to provide the maximum accuracy in measurements of the particle diameters in opposite to algorithms based on image binarization.

We apply such fitting to the truth in the vicinity of a nanoparticle image revealing the mass‐thickness, diffraction, and Z‐contrast. In order to describe the dependence of grayscale from thickness of nanoparticles the polynomial g(t) = g
0
+g
1
t+g
2
t
2
+… with sufficiently high power (≥2) and uncertain coefficients was chosen. The high‐degree polynomial is required to take into account the possible non‐monotonic dependence of the grayscale from particle thickness due to the presence of diffraction contrast (in opposite to pure mass‐thickness contrast). Monotonic dependence of the grayscales from specimen thickness is the characteristic of mass‐thickness contrast of particles (amorphous or crystalline particles positioned out of Bragg conditions) in TEM images and Z‐contrast in STEM images. The transfer function of CCD cameras determined the grayscale in the given point of the micrograph through the intensity of the incident wave has also monotonic character. Only the presence of diffraction contrast in the images breaks the monotonic dependence. Thickness of the spherical nanoparticle in a point having (x,y)‐coordinates can be expressed as t(x,y)=((d/2)
2
‐(x‐x
c
)
2
‐(y‐y
c
)
2
)^(1/2). During fitting, the uncertain coefficients g
i
, coordinates of the particle center (x
c
,y
c
), and the particle diameter d are computing. Our algorithm for particle recognition and measuring sizes is proposed and realized in the program ANN (Automatic Nanoparticle Numerator).

Our algorithm for particle recognition and measuring sizes out of thresholding approach is proposed and realized in the program ANN (Automatic Nanoparticle Numerator). The comparative study of distributions of silver nanoparticle synthesized in different polymer‐water solutions determined manually (about 1000 particles), using ImageJ and ANN was performed (Fig.1 and Fig.2). It shoved a good agreement between results obtained manually and with ANN.
Experiment design for quantitative dark field imaging and spectroscopy of catalyst nanoparticles using Scanning Transmission Electron Microscopy (
STEM
)
Authors: Varambhia Aakash , Jones Lewys , De Backer Annick , Fauske Vidar , Van Aert Sandra , Ozkaya Dogan , Lozano‐Perez Sergio , Nellist Peter 
Published: December 2016

The performance of catalyst nanoparticles is generally dependent on their size, shape, strain, composition and support. However, the relationship between these parameters and the catalyst performance is not well understood. In most instances, the catalyst design process involves several design and testing iterations until the desired performance is attained, and identifying the structure‐property relationships would enable rational catalyst design. In order to relate the nanoparticle properties to catalytic activity, it is necessary to characterise them at atomic resolution.
With aberration corrected STEM it is now possible to image and perform spectroscopy on nanocatalysts at high resolution to obtain detailed structural and compositional information. Here we show how experiment design including detailed calibration of imaging and spectroscopy parameters can reveal the required information, using Ru, Pt and alloyed Pt‐Co catalyst nanoparticles as examples.

As a first example, structural studies of Ru nanoparticles, using methods recently developed
[1]–[3]
, indicated the formation of thin Ru rafts (Figure 1). The formation of Ru rafts has been controversial since their hypothesis
[4]
. These results demonstrate how quantitative ADF imaging can be used to resolve this question.

Using a new detector mapping technique developed at Oxford University, a range of Pt nanoparticles were characterised for their three dimensional structure (Figure 2). The models, created using an energy minimisation approach previously described in ref [3], indicate a Wulff‐like structure. We will show how these models can be used as input for density functional theory simulations, thus unlocking the possibility to study the electronic structure of experimental catalyst nanoparticles.

It is important to increase analysis throughput by software automation
[3]
in order to gain statistically meaningful results. In Figure 3 a rapid particle size measuring algorithm was used to measure the size distribution of Pt and Pt‐alloy nanoparticle systems. The size distribution can then be used as a guide for the microscopist to selectively choose nanoparticles which represent the particle ensemble.

Finally, experiment design and preliminary EDX and EELS results at high resolution will be presented. This approach aims to decouple composition and thickness effects in order to obtain structural information of alloyed nanoparticles.
Microscopic approach to reveal nanoparticles effects in fish
Authors: Perrier Fanny , Mesmer‐Dudons Nathalie , Mornet Stéphane , Baudrimont Magalie , Simon Olivier , Feurtet‐Mazel Agnès 
Published: December 2016

According to the US National Nanotechnology Initiative, nanoparticles are a set of solid particles with a diameter ranged from 1 to 100 nm. Numerous domains employ nanoparticles (such as industry, cosmetic, construction, medicine…) due to their specific properties.
The significant arise of nanomaterials application leads to a boost of environmental discharges and especially in aquatic systems which represent an important pollutants receptacles. Nevertheless, the lack of knowledge about the toxicity of nanomaterials can be detrimental for the aquatic ecosystems sustainability. Trophic transfer is often referred as an important pathway of nanoparticles contamination in aquatic systems being reportedly the main exposure route to organisms. Among their great variety of nature and characteristics, gold nanoparticles (AuNPs, PEG coating, diameter 10nm) have been chosen as model contaminant due to their high stability in solution.

This work aims to characterize: (i) AuNPs transfer within food chain and (ii) a histological study of AuNPs damages in fish. Thereby natural river biofilms contaminated in laboratory for 48h at environmental AuNPs' concentrations were grazed by the fish
Hypostomus plecostomus
during a 21‐days laboratory experiment. Gold analyses (by atomic absorption spectroscopy) revealed that biofilms presented a high AuNPs retention capacity. Secondly, results point out that AuNPs were effectively transferred from natural biofilms to the grazer fish showing their ability to enter the food chain. Regarding AuNP fish distribution, organs involved in metabolism and excretion (
i.e
. liver and kidney) presented a significant bioaccumulation. Moreover, transmission electron microscopy observations showed tissue alterations indicating inflammatory responses for all organs studied. AuNPs appeared to be: (a) distributed by the circulatory system into fish organs without entering the erythrocytes and (b) not degraded once internalized by the fish.
Calculation of phase contrast in
Cc/Cs
‐corrected
STEM
Authors: Lee Zhongbo , Kaiser Ute , Rose Harald 
Published: December 2016

For STEM imaging, the pattern on the detector is a result of interference between elastically scattered wave and the incident wave. By recording the constructive interference and destructive interference with separate detectors, as well as by subtracting the two parts of intensity from each other, one can remove the background intensity as well as nonlinear information. As result, the remaining signal is enhanced phase contrast [1]. A recent experimental demonstration of differential contrast in STEM achieved by matching the detector geometry and the physical phase plates in STEM mode has been reported in [2].
On an aberration‐corrected STEM, an optimized differential phase contrast can be obtained by well designing the PCTF of the objective lens, and detector geometry accordant with the designed phase plate. The integrated spatial frequencies corresponding to positive contrast transfer is equal to those corresponding to negative contrast transfer. This ensures that nonlinear information cancels when the two parts of detector signals subtract each other.
Our calculation in Fig. 1 for Cc/Cs‐corrected STEM without damping factors illustrates the advantage of differential contrast compared with the conventional bright‐field imaging in STEM. The differential contrasts of single‐layer graphene are dominantly stronger than the contrasts achieved in STEM‐BF mode equipped with the same corrector. The differential contrast can reach 12, 18 and 26 times of the bright‐field contrast at 20kV, 50kV and 80kV, respectively! This demonstrates that in STEM mode equipped with an aberration corrector and a detector, matching the geometry of the phase plate, phase objects can be imaged with descent contrast.

With further improvement of the corrected state of the microscope, our calculation show that phase contrast imaging in STEM offers even more exciting possibilities. When the 5th‐order spherical aberration is corrected, the illumination angle dependent on the largest usable aperture, also increases, resulting in a shallow depth of field. This allows accurate focus at certain thickness of the sample, as shown in Fig. 2. At the 8
th
layer of a total 16‐layer (28nm) thick sample of Si, one silicon atom is replaced by a Germanium atom. A focal series through the sample shows that the layer marked by a substituted Ge atom is in focus at △f=‐12Å.

As a summary, the method of obtaining differential contrast in an aberration‐corrected STEM can be powerful for investigating weak scattering objects. Under a further improved corrected state of the Cc/Cs corrector, the differential contrast realized with this technique is extremely thickness‐sensitive, and focussing through atomic planes may come into reach.
Picometre‐precision atomic structure of inversion domain boundaries in
GaN
Authors: Haas Benedikt , McLeod Robert A. , Auzelle Thomas , Daudin Bruno , Eymery Joël , Lançon Frédéric , Zuo Jian‐Min , Rouvière Jean‐Luc 
Published: December 2016

Here, we report on the precise analysis of the atomic structure of inversion domain boundaries (IDBs) in GaN by scanning transmission electron microscopy. IDBs are a common defect in GaN that traps carriers and leads to a slightly modified luminescence wavelength [1,2].
Our analysis of IDBs in MOCVD grown nanowires confirms recent coherent Bragg imaging (CBI) results [3] stating that the atomic structure of this IDB is different or slightly different from the one determined in 1996 by first‐principle calculations (IDB*) [4]. CBI experiments measured a 8 pm shift of the c‐planes of the two domains [3], whereas first‐principle calculations predicted no shift. A previous study by STEM [5] found a shift of “ca. 0.6 Å” (60pm), corresponding roughly to the switch of the Ga and N positions without any additional shift. Here in addition to a shift along c, we show that the interface configuration corresponds qualitatively to the IDB* model (cf. Fig. 1) and that there is a 10 pm dilatation perpendicular to the interface (shown in Fig. 3) in agreement with this model, while CBI did not find a dilatation.
To facilitate the measurement of atom positions across the IDB with picometre‐precision, we use HAADF‐STEM to avoid coherent effects leading to artefacts. Scanning and drift artefacts are being suppressed by acquiring series of rapid STEM images and aligning them using the newly developed Zorro code. This algorithm is based on calculating estimated drift positions by correlating every frame to multiple frames and minimizing the error of the overdetermined system to obtain a best estimate for the frame positions relative to each other. The sub‐pixel aligned frames are then averaged and the peak positions are determined via TeMA (template‐matching algorithm).
Our quantitative analysis of experimental and simulated STEM images shows that when atomic columns are very close to each other the measured distance can be slightly different from the real value. For instance, when the distance between atomic columns becomes smaller than 0.1 nm, the difference between the measured and real values can account for several picometres. This effect can be well observed when an IDB kinks perpendicular to the observation direction leading to closely projected columns in the overlap region of the two domains as seen in Fig. 2. Electron scattering simulations show that the apparently wider distance between atoms is a channeling effect.
These results have provided elements to revisit previous theoretical models of IDBs in GaN.
Dispersion, dose and stability of semiconductor quantum dot biomarkers
Authors: Brown Andy , Harvie Andrew , Critchley Kevin , Chantry Ruth , Kepaptsoglou Demie , Ramasse Quentin , Rees Paul , Brown M Rowan , Summers Huw , Brydson Rik , Hondow Nicole 
Published: December 2016

Photoluminescent semiconductor nanoparticles or quantum dots have significant potential for medical imaging. For optimum performance however, the dispersion of the nanoparticulate material when suspended in delivery or incubation media, any transformation of the particles in the media, plus the nature and degree of uptake of the nanoparticles by a particular cell or organism all need to be understood. Analytical electron microscopy can play a vital role in assessing this complex inter‐relationship, and we discuss here specific methods developed for this type of analysis.
First, we will review the in vitro cellular uptake of commercially available CdSe/ZnS quantum dot nanoparticles with a coating specifically targeted for endocytic uptake (Invitrogen QTracker 705), dispersed in cell culture media and exposed to human osteosarcoma (U‐2 OS) cells. We have examined these nanoparticles as‐dispersed in cell culture media (t = 0 h), after 1 hour exposure to cells and after a round of cell division (t = 24 h). Transmission electron microscopy (TEM) has been used to assess the dispersion state of the nanoparticles in media after rapidly freezing suspensions to avoid drying artefacts [1], and in exposed cells which have been fixed and resin embedded [2]. The resin‐embedded cells have been further examined using serial block face scanning electron microscopy (SBF‐SEM), which enables quantification of nanoparticle loaded organelles in whole cell volumes for quantitative correlation to imaging flow cell cytometry [2]. From this we have measured probability densities for the number of quantum dots per agglomerate when in cell culture media and following uptake by cells in vitro [3, 4 and Figure 1 a‐d]. Thus, we will discuss the agglomeration processes that occur both in suspension and during endocytosis.
Second and looking forward, most commercially available semiconductor quantum dots currently contain cadmium although its health and environmental risks may limit exploitation. Thus, copper indium sulfide (CIS) quantum dots have been investigated as a potential replacement [5]. Aberration corrected STEM‐EELS has identified some elemental separation of Cu and In within individual quantum dots [Figure 1 e‐h], which may be the origin of an In‐Cu anti‐site defect state known to act as a donor in the radiative recombination pathway for chalcopyrite CIS quantum dots. We will report here on further analysis using a FEI Titan cubed Themis 300 G2 S/TEM to assess elemental distribution by STEM‐EDX. Such analysis will enable additional characterisation of core‐shell coatings (e.g. CIS/ZnS/ZnS:Al) designed to improve photo luminescent quantum yield while enhancing environmental stability of the particles.
Studies of the structure of spray pyrolysed bioactive glasses using electron diffraction and
DFT
simulations
Authors: Chou Yu‐Jen , Borisenko Konstantin , Shih Shao‐Ju , Kirkland Angus 
Published: December 2016

Bioactive glasses have received considerable attention during the past few decades. Recently, Shih et al. demonstrated that Si‐Ca‐P based glasses prepared by spray pyrolysis can have better bioactivity than glasses prepared by other methods [1]. To understand the reason behind these improved properties we have studied the structure of several Si‐Ca‐P glasses with different compositions.
In this study structural information from bioactive glass samples was obtained using electron diffraction. Compared to X‐ray and neutron diffraction electrons can be easily focused on specific nano volumes and used to probe nanoscale variations in structure. Using reduced density function (RDF) analysis local structural parameters of the materials can be extracted from experimental diffraction patterns with high precision [2]. However, experimental diffraction data alone is not sufficient to build reliable atomic models. Therefore, we used DFT molecular dynamics simulations of liquid‐quench to obtain atomic models of the materials, which serve as initial models for further structure refinements.

All experimental data presented here was collected using a JEOL JEM2100 transmission electron microscope (TEM) operating at 200kV. Electron diffraction patterns were recorded on a Gatan Orius CCD that eliminates charge overflow to the neighbouring pixels, even when saturated. Using a camera length of ~180mm and the central beam positioned at the edge of the detector, the usable range of scattering vectors,
q
extends to 18Å
‐1
, comparable with X‐ray experiments. Figure 1 (a‐d) shows typical TEM images and diffraction patterns of two specimens, with the corresponding RDF curves shown in Figure 1 (e).

DFT simulations were carried out on ARC supercomputer facilities at the University of Oxford. The CASTEP software [3] was used to perform molecular dynamics simulations of liquid quench from 3000K to 300K, with cooling rate of 2·10
14
K/s. Energy optimizations with a 300eV pseudo potential cut‐off were performed after quenching. Figure 2 (a) shows a model of 60%SiO
2
‐35%CaO‐5%P
2
O
5
glass simulated by Reverse Monte Carlo using only experimental diffraction data and the model after DFT simulation is presented in Figure 2 (b), indicating considerable structural changes. This model already demonstrates a good agreement with the experimental RDF curve (Figure 2 (c) and has been used for further RMC refinements.

We will discuss correlations between bioactivity and structural data in these materials.
Financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative (Ref 312483‐ESTEEM2) is gratefully acknowledged.