Rhenium-doped silicon samples had been synthesized by means of re-pulsed ion implantation (fluences 2.5 × 10
17
cm
−2
, 1 × 10
17
cm
−2
and 5 × 10
16
cm
−2
) and then stored under natural ...air-media conditions 5 years. The electronic structure of these samples was studied using combined XPS-and-DFT method. It was confidently established and demonstrated by means of XPS electronic structure mapping (core levels, valence band) that weak acidification occurs. The influence of air media leads to O…Si–O…Re
0
and …Re–Si–O… bonding appearance in the structure of 5-year aged samples rather than to normal rhenium oxidation. No any traces of Re
x
O
y
sub-oxide fractures were neither found experimentally nor predicted theoretically. DFT-derived acidification scenario points out energetically preferable Re atoms pairing when low concentrations ion-doping regime is applied and metallic Re clusterization in the high concentrations ion-doping regime. Experimentally established essential transformation of initial vicinity states in the top of valence bands by means of Re 5
d
doping is in a good agreement with DFT calculations of electronic structure and formation energy values of acidification process.
Optically transparent MgAl2O4 ceramics was functionalized by Cu2+-ions employing various implantation fluences. Depending on ion beam exposure, both radiation stimulated annealing and formations of ...intrinsic defects occur in the cation-anion sublattices of the used host-matrix. The surface plasmon resonance (SPR) phenomena were observed in optical absorption and Raman spectra of the samples irradiated with 5 × 1016 cm−2 implantation fluences and above. These phenomena were associated with formation of copper nanoparticles on the surface and near surface layers. An oxidation of copper with an increase of irradiation fluence was established. An effect of Raman modes enhancing was found and associated with oxidized copper particles upon excitation near absorption edge of surface plasmon. It is supposed that this effect is linked with the formation of a metal-oxide like “core-shell” structure of synthesized nanoparticles.
•Copper nanoparticles were synthesized in the surface layer of MgAl2O4 transparent ceramics as a result of ion implantation.•After ceramic implantation with copper ions, a surface plasmon resonance with a maximum energy of 2 eV was detected.•The effect of amplification of the Raman modes of oxidized copper upon excitation of surface plasmon resonance was observed.•Effect of amplification of the Raman modes is explained by the presence of “core-shell” structures in copper nanoparticles.
Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a ...riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
The electron-optical characteristics of transparent aluminum-magnesium spinel ceramics doped with various copper fluences are studied. As a result of the ion-beam modification, the formation of new ...optically active centers, caused by intrinsic defects of the matrix and impurity copper ions, occurs. At implantation doses of 1 × 10
17
cm
−2
, metallic copper nanoparticles are formed in the matrix, which are characterized by the absorption of electromagnetic radiation with an energy of 2 eV due to the effect of plasmon resonance.
The results of measurements of X‐ray photoelectron spectra (XPS) of a‐SiO2 host material after pulsed implantation with Mn+ and Co+, Mn+ ions as well as DFT‐calculations are presented. The low‐energy ...shift is found in XPS Si 2p and O 1s core‐levels of single Mn+ and dual Co+, Mn+ pulsed ion‐implanted a‐SiO2 (E = 30 keV, D = 2×1017 cm−2) with respect to those of untreated a‐SiO2. Similar changes are found in XPS Si 2p and O 1s of stishovite compared to those of quartz. This means that the pulsed ion implantation induces the local high pressure effect that leads to the appearance of SiO6‐structural units in a‐SiO2 host, forming “stishovite‐like” local atomic structure. This process can be described within an electronic bonding transition from the fourfold “quartz‐like” to sixfold “stishovite‐like” high‐pressure phase in the SiO2 host matrix. It is found that such octahedral conversion depends on the fluence and starts with doses higher than D = 3×1016 cm−2.
Experimental studies of aluminum-magnesium spinel modified by Cu2+ ions as a result of pulsed ion bombardment were carried out. The analysis of the modified samples with X-ray photoelectron ...spectroscopy (XPS) revealed the presence of metallic copper (Cu0) along with a small amount of oxidized copper at implantation doses of F = 5 × 1016 cm−2. It has been found with optical spectroscopy methods that, intrinsic (F, F+, anti-site) and impurity (Cu-related) optically active centers are formed in the matrix under the action of a beam of accelerated ions, and a complex dependence of the optical absorption intensity of these centers is observed with the increase of the annealing temperature. Experimental data allows us to conclude that the synthesis and evolution of metal nanoparticles formed in the surface layer of transparent ceramics MgAl2O4 showed a number of paradoxical properties, to interpret which a number of new physics of solid state concepts turned out to be adequate: the intermittency concept, which found its implementation in the Mott-Gurney kinetics, and the hierarchy of defective structure, which was realized in the trophic chains of defects.
•As a result of ion implantation of MgAl2O4 transparent ceramics by copper ions, the synthesis of copper metal nanoparticles occurs.•After the thermal treatment of the spinel implanted with copper ions, the concentration of copper nanoparticles changes.•A conceptual model of the growth of copper nanoparticles as a result of ion implantation is proposed.•The complex nature of the dependence of the concentration of nanoparticles on temperature is explained.
Telomeres are special DNA-protein structures that are located at the ends of linear eukaryotic chromosomes. The telomere length determines the proliferation potential of cells. Telomerase is a key ...component of the telomere length maintenance system. While telomerase is inactive in the majority of somatic cells, its activity determines the clonogenic potential of stem cells as a resource for tissue and organism regeneration. Reactivation of telomerase occurs during the process of immortalization in the majority of cancer cells. Telomerase is a ribonucleoprotein that contains telomerase reverse transcriptase and telomerase RNA components. The RNA processing mechanism of telomerase involves exosome trimming or degradation of the primary precursor. Recent data provide evidence that the competition between the processing and decay of telomerase RNA may regulate the amount of RNA at the physiological level. We show that termination of human telomerase RNA transcription is dependent on its promoter, which engages with the multisubunit complex Integrator to interact with RNA polymerase II and terminate transcription of the human telomerase RNA gene followed by further processing.
Optically transparent Mg1−xMnxAl2O4 (x = 0.005; 0.00005) nanoceramics were obtained by thermobaric synthesis. Varying the parameters of thermobaric synthesis leads to a controlled modification of ...crystallographic parameters, such as the lattice constant, the region of coherent scattering, and residual strain. It is shown that as a result of thermobaric pressing, intrinsic and impurity structural defects are formed, the concentration of which depends on the P-T parameters. Two stages of thermobaric synthesis were found, differing by both crystallographic and optical parameters. In optically transparent nanoceramics, a correlation between the residual strain and a scattering coefficient associated with localization of impurity manganese ions in anti-site positions of spinel was found. Thermobaric synthesis of optical nanoceramics can be used as a method of compressing nanosized objects in an optical spinel matrix while maintaining such objects in a metastable state.
•The thermobaric synthesis was used to obtain transparent MgAl2O4:Mn nanoceramics characterized by the presence of strain.•Manganese ions are localized in both normal and anti-site positions, thus stimulating a strain change in the spinel matrix.•Directed redistribution of impurity centers over positions makes it possible to control the optical properties of ceramics.
The effect of trivalent Eu impurity occupying a position with the S6 site symmetry in cubic Gd2O3 on the latter's structure and phonon spectrum is investigated. This study was performed by means of ...computer modeling within a shell model. The equilibrium structures and phonon local symmetrized densities of states were calculated. In addition, frequencies of localized vibrations induced by Eu ion were determined. The calculated results were compared with the available experimental data in literature.
Solid-phase synthesis of optical ceramics MgAl2O4 with various concentrations of iron as an impurity element was carried out without using sintering additives. Ceramics were characterized by intense ...absorption in the UV spectral region due to both intrinsic F-type defects and intrinsic iron ions. The effect of nonradiative energy transfer from optically active centers of the F-type to the impurity Fe3+ ion was observed. In ceramic samples with an iron concentration more than 0.4 mol%, the decrease in the intensity of the Fe3+ luminescent signal (coordination number, Z = 6) is due to the effect of concentration quenching, as well as the conversion of Fe3+ → Fe2+ ions. It was shown that, as a result of high-temperature synthesis, optically active centers of Fe3+ and Fe2+ are formed, which are localized in regular (octahedral and tetrahedral) lattice sites and defect anti-sites. According to the data of optical absorption spectroscopy, as the content of iron ions increases, the concentration of Fe2+ (Z = 6) increases. A new luminescence band with a maximum at 2.3 eV was detected by photoluminescence spectroscopy, presumably associated with the luminescence of Fe3+ in tetrahedral lattice sites (Z = 4).
•Optical ceramics MgAl2O4:Fe were synthesized without any plasticizing additives.•As a result of synthesis, iron ions enter the lattice in both 2 and 3 valence states.•Iron ions in Fe2+ state is partially localized in the octahedral site.•The luminescence of Fe3+ with a coordination number of 4 was detected.•Fe3+ ions can localize in defect sites with anomalous spectroscopic parameters.
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