Aleš Jäger

Crystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographers

The CrysTBox software for electron diffraction analysis and visualization is presented. Among others, the software offers an automated zone axis determination using selected area diffraction, convergent beam diffraction and nanodiffraction patterns, ring diffraction evaluation, and interactive crystal visualization in both direct and reciprocal space.

Double twinning in magnesium

It is demonstrated that metalworking processes performed at different temperatures can lead to the - double twinning. This twinning mode has been observed during direct extrusion of the coarse-grained Mg-0.3at.%Al alloy at 433 K and analysed in detail on room-temperature rolled magnesium single crystal with the c-axis parallel to transverse direction and the a-axis parallel to rolling direction. The - double twins originated during initial stage of the formation on coarse-grained and single-crystalline structure.

The interplay between biological and physical scenarios of bacterial death induced by non-thermal plasma.

Direct interactions of plasma matter with living cells and tissues can dramatically affect their functionality, initiating many important effects from cancer elimination to bacteria deactivation. However, the physical mechanisms and biochemical pathways underlying the effects of non-thermal plasma on bacteria and cell fate have still not been fully explored. Here, we report on the molecular mechanisms of non-thermal plasma-induced bacteria inactivation in both Gram-positive and Gram-negative strains. We demonstrate that depending on the exposure time plasma induces either direct physical destruction of bacteria or triggers programmed cell death (PCD) that exhibits characteristic features of apoptosis. The interplay between physical disruption and PCD is on the one hand driven by physical plasma parameters, and on the other hand by biological and physical properties of bacteria. The explored possibilities of the tuneable bacteria deactivation provide a basis for the development of advanced plasma-based therapies. To a great extent, our study opens new possibilities for controlled non-thermal plasma interactions with living systems.

Non-thermal plasma mills bacteria: Scanning electron microscopy observations

Non-thermal plasmas hold great promise for a variety of biomedical applications. To ensure safe clinical application of plasma, a rigorous analysis of plasma-induced effects on cell functions is required. Yet mechanisms of bacteria deactivation by non-thermal plasma remain largely unknown. We therefore analyzed the influence of low-temperature atmospheric plasma on Gram-positive and Gram-negative bacteria. Using scanning electron microscopy, we demonstrate that both Gram-positive and Gram-negative bacteria strains in a minute were completely destroyed by helium plasma. In contrast, mesenchymal stem cells (MSCs) were not affected by the same treatment. Furthermore, histopathological analysis of hematoxylin and eosin–stained rat skin sections from plasma–treated animals did not reveal any abnormalities in comparison to control ones. We discuss possible physical mechanisms leading to the shred of bacteria under non-thermal plasma irradiation. Our findings disclose how helium plasma destroys bacteria and demo...

Atomic Layer Deposition Al2O3 Coatings Significantly Improve Thermal, Chemical, and Mechanical Stability of Anodic TiO2 Nanotube Layers

We report on a very significant enhancement of the thermal, chemical, and mechanical stability of self-organized TiO2 nanotubes layers, provided by thin Al2O3 coatings of different thicknesses prepared by atomic layer deposition (ALD). TiO2 nanotube layers coated with Al2O3 coatings exhibit significantly improved thermal stability as illustrated by the preservation of the nanotubular structure upon annealing treatment at high temperatures (870 °C). In addition, a high anatase content is preserved in the nanotube layers against expectation of the total rutile conversion at such a high temperature. Hardness of the resulting nanotube layers is investigated by nanoindentation measurements and shows strongly improved values compared to uncoated counterparts. Finally, it is demonstrated that Al2O3 coatings guarantee unprecedented chemical stability of TiO2 nanotube layers in harsh environments of concentrated H3PO4 solutions.

Automated CBED processing: sample thickness estimation based on analysis of zone-axis CBED pattern.

An automated processing of convergent beam electron diffraction (CBED) patterns is presented. The proposed methods are used in an automated tool for estimating the thickness of transmission electron microscopy (TEM) samples by matching an experimental zone-axis CBED pattern with a series of patterns simulated for known thicknesses. The proposed tool detects CBED disks, localizes a pattern in detected disks and unifies the coordinate system of the experimental pattern with the simulated one. The experimental pattern is then compared disk-by-disk with a series of simulated patterns each corresponding to different known thicknesses. The thickness of the most similar simulated pattern is then taken as the thickness estimate. The tool was tested on [0 1 1] Si, [0 1 0] α-Ti and [0 1 1] α-Ti samples prepared using different techniques. Results of the presented approach were compared with thickness estimates based on analysis of CBED patterns in two beam conditions. The mean difference between these two methods was 4.1% for the FIB-prepared silicon samples, 5.2% for the electro-chemically polished titanium and 7.9% for Ar(+) ion-polished titanium. The proposed techniques can also be employed in other established CBED analyses. Apart from the thickness estimation, it can potentially be used to quantify lattice deformation, structure factors, symmetry, defects or extinction distance.

Visco-plastic self-consistent modelling of a grain boundary misorientation distribution after equal-channel angular pressing in an AZ31 magnesium alloy

This study applies a visco-plastic self-consistent (VPSC) model to an AZ31 alloy processed by equal-channel angular pressing. The study focuses on the possibility of reproducing a grain misorientation distribution and the distribution of coincident site lattice boundaries in the model framework. Co-rotation and a magnesium misorientation scheme are employed together with the conventional VPSC model to improve its predictions. The results of the model are then compared with experimental data.

Quantitative analysis of structural inhomogeneity in nanomaterials using transmission electron microscopy

A method for quantifying inhomogeneity of crystal structure at the nanoscale is suggested and experimentally verified. The method is based on digital processing of images obtained by high-resolution transmission electron microscopy. A series of images is acquired and each image is divided into several overlapping sliding windows. Interplanar distances are determined using a fast Fourier transform and the CrysTBox software. A spatial distribution of the estimated distances is obtained considering the size and position of the sliding window within the analysed sample. This approach provides for a picometric precision and accuracy if applied on ideal data. Although this accuracy was verified on experimental data, it can be worsened by errors specific to a particular application and data acquisition technique. The achieved spatial resolution ranges from a few to tens of nanometres. These levels of accuracy, precision and spatial resolution are reached without the need for aberration correction or for a reference lattice parameter, and using samples prepared by focused ion beam milling.

Multi-temperature equal channel angular pressing of Mg-3 wt%Al-1 wt%Zn alloy

Grain refinement of magnesium alloys at temperatures below 200 °C via deformation processes is a challenging task. Equal channel angular pressing is one of the severe plastic deformation techniques which can significantly refine grain size. Refined grains consequently improve mechanical properties of magnesium alloys. In this paper, Mg-3 wt%Al-1 wt%Zn magnesium alloy was processed by different multi-temperature equal channel angular pressing cycles without backpressure. The lowest finishing temperature of equal channel angular pressing was 150 °C leading to fine-grained microstructure with sporadically large elongated grains. Shear bands were observed after equal channel angular pressing finishing at temperatures of 175 and 150 °C. Electron backscattered diffraction revealed that grain boundary distribution is qualitatively the same for all equal channel angular pressing cycles. Crystallographic analyses of large elongated grains showed that {0 0 0 1} and { } planes in these grains tend to be aligned parallel to the shear plane. Microtexture measurements showed split of (0 0 0 2) poles. The shape of stress–strain curves and consequently yields tensile strength of Mg-3 wt%Al-1 wt%Zn alloy after multi-temperature equal channel angular pressing was influenced by final texture and twinning.

Towards the understanding of non-thermal air plasma action: effects on bacteria and fibroblasts

Non-thermal plasma research has put a growing focus on the bacteria inactivation problem. In this article we show how low temperature atmospheric plasma destroys Gram-positive and Gram-negative bacteria and discuss the mechanisms of plasma bactericidal effects and a discrepancy in the plasma-triggered effects and ozone (which is a component of air plasma gases). The proven safety of air plasma for fibroblasts is a key factor for the medical applications of plasma.