bluuebunny/crossref_metadata_2025 huggingface dataset:
FEATURES OF THE APPLICATION OF MATHEMATICAL OPTIMIZATION METHODS FOR THE STUDY OF NANOSTRUCTURES BASED ON X-RAY DIFFRACTION DATA
Authors: Astaf’ev S. B. , Yanusova L. G.
Published: April 2024

The features of mathematical optimization methods are considered and algorithms for their use are proposed to increase the efficiency of finding extreme values in solving optimization problems. The proposed algorithms are universal in nature, which allows them to be applied in various fields of computational mathematics. As an illustration, the solution of the inverse problem of reflectometry in the framework of a box model of an electron density profile for a liquid crystal film of a block dendrimer is given. The structure of the thin-film layer on the aqueous subphase was also determined from the grazing-incidence diffraction data. The proposed algorithms of optimization methods are implemented within the analytical software package BARD (Basic Analisys of xRay Diffraction).
Dissolution Energies of Impurities and Their Clusters in Powellite CaMoO4
Authors: Dudnikova V. B. , Eremin N. N.
Published: April 2024

The impurity defects in CaMoO4 are simulated by the method of interatomic potentials. The dissolution energies of monovalent, divalent, and trivalent impurities are calculated, their comparative analysis is performed, and the main patterns of change are presented. The most probable localization of defects is determined. In the case of heterovalent impurities, the most energetically favorable mechanism for their charge compensation has been found, both due to intrinsic crystal defects and under conjugate isomorphism. It is shown that the formation of impurity clusters with intrinsic crystal defects and (to a greater extent) the formation of clusters of different-valence impurities may significantly reduce the dissolution energy of impurities. The formation of neutral clusters of univalent impurities with oxygen vacancies not only makes it possible to increase the solubility of impurities but also reduces the probability of the formation of color centers.
A New Method for Determining the Size of a Synchrotron Radiation Beam in the Focus of a Compound Refractive Lens
Authors: Folomeshkin M. S. , Kohn V. G. , Seregin A. Yu. , Volkovsky Yu. A. , Prosekov P. A. , Yunkin V. A. , Zverev D. A. , Barannikov A. A. , Snigirev A. A. , Pisarevsky Yu. V. , Blagov A. E. , Kovalchuk M. V.
Published: April 2024

A new method is proposed for determining experimentally the size of a synchrotron radiation beam in the focus of planar compound refractive lenses. The method consists in measuring the angular divergence of radiation after the focus using Bragg diffraction in a perfect crystal during its rotation. This method determines the beam size, which depends only on the focusing properties of the lenses in use, in contrast to other currently applied methods. The efficiency of the proposed approach has been experimentally demonstrated using nanofocusing planar silicon lenses as an example.
EXTRACTION, PURIFICATION, AND SMALL-ANGLE X-RAY SCATTERING ANALYSIS OF THE YSXC GTPASE OF STAPHYLOCOCCUS AUREUS
Authors: Biktimirov A. D. , Islamov D. R. , Validov S. Z. , Peter's G. S. , Khaliullina A. V. , Yusupov M. M. , Usachev K. S.
Published: April 2024

Study of the structures of various biological macromolecules is one of the main directions that are intensively developed using physical methods. Since proteins are an elementary unit of the structural and functional organization of a cell, the strategies for combating pathogenic microorganisms include the analysis of the bacterial protein synthesis apparatus and related systems. The extraction, purification, and small-angle X-ray scattering analysis of the structure of YsxC protein from the Staphylococcus aureus pathogenic bacterium are reported. This protein is involved in the cell growth and division processes, serves an energy-dependent factor, and participates in the assembly of large ribosome subunit. The structural study of this protein opens up a possibility of searching for small molecules capable of inhibiting its function. Since the structural variability of protein factors is higher than that of the conservative ribosome sites, their inhibition makes it possible to selectively affect a pathogenic microorganism.
HIGH-CAPACITY CALCIUM CARBONATE PARTICLES AS PH-SENSITIVE CONTAINERS FOR DOXORUBICIN
Authors: Pallaeva T. N. , Mikheev A. V. , Khmelenin D. N. , Eurov D. A. , Kurdyukov D. A. , Popova V. K. , Dmitrienko E. V. , Trushina D. B.
Published: April 2024

Nanostructured submicron calcium carbonate particles with sizes of 500 ± 90 and 172 ± 75 nm have been synthesized by mass crystallization in aqueous solutions with addition of glycerol, as well as a mixture of polyethylene glycol, polysorbate, and a cellular medium. CaCO3 : Si : Fe nanoparticles 65 ± 15 nm in size have been obtained by template synthesis in pores of silica particles. The crystal structure and polymorphism of these particles are studied, and the influence of the size and structure of particles on the efficiency of their loading with a chemotherapy agent , as well as its release under model conditions at different рН, is determined.
CRYSTAL AND MOLECULAR STRUCTURE OF THE ISLAND TETRANUCLEAR DIOXOMOLYBDENUM(VI) COMPLEX [MoO2(L1)]4 (H2L1 IS ACETYLACETONE ISONICOTINOYLHYDRAZONE) WITH LARGE INTRA- AND INTERMOLECULAR CHANNELS
Authors: Sergienko V. S. , Abramenko V. L. , Churakov A. V.
Published: April 2024

The solvated complex [МоО2(L1)]4dimethylformamide (I) was synthesized. Its structure wasdetermined by X-ray diffraction analysis. The crystal structure is composed of the tetranuclear complexes [МоО2(L1)]4 (Ia) as the structural units lying on crystallographic twofold axes. Both crystallographically independent molybdenum atoms are in a distorted octahedral coordination environment formed by two cis-О(oxo) ligands, two N(L1) atoms of two molecules Ia in trans positions to the О(oxo) ligands, and two О(L1) atoms of one complex molecule in cis positions to О(oxo) and trans to each other. Each (L1)2– ligand is coordinated to two Мо atoms in a tetradentate tridentate-chelating (2О, N) bridging (N) mode. The average bond lengths in complex Iа are as follows: Мо–О(oxo), 1.701 Å; Мо–N(L1), 2.460 (b) and 2.214 Å (c); Мо–О(L1), 1.980 Å. The О(oxo)–МоО–(oxo) bond angle is 105.6°. The ordered dimethylformamide molecule is located in a narrow channel in the structure. The strongly disordered (non-located) solvent molecules (methanol/dimethylformamide/water) occupy wide channels in the structure of I.
Search for New Potential T-Cell and B-Cell Epitopes in the Spike Protein of SARS-CoV-2
Authors: Kolesnikov I. A. , Timofeev V. I. , Nikolenko M. V. , Ermakov A. V. , Ivanovsky A. S. , Dyakova Yu. A. , Pisarevsky Yu. V. , Kovalchuk M. V.
Published: April 2024

The current epidemiological situation, including the existence of new SARS-CoV-2 virus with a high mutagenicity, requires fundamentally new deadlines for the development of vaccines, which may be achieved only applying modern computing technologies and simulation. Epitopes have been found in the spike protein of the SARS-CoV-2 virus using immunoinformatics methods, and their allergenicity and immunogenecity was predicted. It is shown that a vaccine against SARS-CoV-2 can be designed based on these epitopes.
ROCKING CURVE OF A DOUBLE-CRYSTAL SPECTROMETER IN THE BRAGG-BRAGG GEOMETRY INCLUDING THE ABSORPTION COEFFICIENT DEPENDENCY FROM THE NEUTRON WAVELENGTH
Authors: Schmeissner J. , Tyulyusov A. N.
Published: April 2024

An analytical expression is obtained for the rocking curve of a double-crystal spectrometer, which does not require restrictions on the absorption cross section dependency on the wavelength. A modeled rocking curve (instrumental line) for the Bragg–Bragg spectrometric scheme is calculated using the example of an InSb crystal in the region of weak dependency between the absorption cross section and the wavelength and in the region of wavelengths close to the absorption resonance.
MICROSTRUCTURE OF A CrSi2 TRANSITION LAYER PRODUCED BY HOT PRESSING OF Cr AND Si
Authors: Lukasov M. S. , Arkharova N. A. , Orekhov A. S. , Rakova E. V. , Solomkin F. Yu. , Klechkovskaya V. V.
Published: April 2024

Hot pressing of a Si single crystal in the bulk of electrolytic Cr powder at 1213 K, with subsequent annealing in air, leads to the formation of an intermediate polycrystalline silicide layer at the interface between the initial components. The phase composition and microstructure of the transition layer and its vicinity were investigated by scanning electron microscopy, X-ray energy-dispersive microanalysis, and electron backscatter diffraction. The transition layer has a crystal structure of the hexagonal phase of chromium disilicide (sp. gr. P6222). An additional annealing up to 120 h leads to insignificant recrystallization of small grains into larger ones.
Preliminary X-ray Diffraction Analysis of Purine Nucleoside Phosphorylase from the Haloalkaliphilic Bacterium Halomonas chromatireducens
Authors: Safonova T. N. , Antipov A. N. , Veiko V. P. , Mordkovich N. N. , Okorokova N A. , Dorovatovskii P. V. , Polyakov K. M.
Published: April 2024

Crystals of the enzyme purine nucleoside phosphorylase from the extremophilic bacterium Halomonas Chromatireducens AGD 8-3, suitable for X-ray diffraction, were grown by the vapor-diffusion method. The X-ray diffraction data were collected from these crystals at the Belok beamline of the Kurchatov synchrotron radiation source (National Research Centre “Kurchatov Institute”) at 100 K to 1.80 Å resolution. The X-ray diffraction data were processed in the space groups P1, P2, P21, and P622. The structure was solved by the molecular replacement method taking into account the twinning in the space groups P21 and P1 with one and two hexamers of the enzyme per asymmetric unit, respectively.
Application of the Crystal Structure of the SARS-CoV-2 Spike Protein for the Development of a Peptide Vaccine against Virus
Authors: Ivanovsky A. S. , Kolesnikov I. A. , Kordonskaya Yu. V. , Ermakov A. V. , Marchenkova M. A. , Timofeev V. I. , Pisarevsky Yu. V. , Dyakova Yu. A. , Kovalchuk M. V.
Published: April 2024

Based on the spike protein of the SARS-CoV-2 virus, a protein capable of causing an immune answer has been predicted. The protein stability in solution is confirmed by the molecular dynamics simulation. Immunomodulation has shown that this protein causes an immune reaction and, correspondingly, may serve a vaccine prototype.
Calculation of the Phonon Spectrum of PbMnBO4 Crystal Using Density Functional Theory
Authors: Krylova S. N.
Published: April 2024

The phonon dispersion and Raman spectrum of the PbMnBO4 ferromagnetic crystal have been calculated within the density functional theory. Imaginary phonon branches have been observed at the points Y, Z, and Г and along the X–S direction of the Brillouin zone, which indicates structural instability and a possible phase transition with variation in external factors (temperature and pressure). The shapes of vibrations and symmetry types of the normal modes of the crystal at the center of the Brillouin zone have been determined. The calculation results are compared with the experimental and theoretical spectra from other studies. It is shown that the vibrational mode of highest intensity at 692.5 cm–1 in the spectrum and the mode at 272.3 cm–1, corresponding to the experimental modes at 690.5 and 224.7 cm–1, are bending vibrations of oxygen atoms in distorted MnO6 octahedra.
Structure, Microstructure, and Properties of Modified Ceramics (Na,Sr)0.5Bi0.5TiO3
Authors: Kaleva G. M. , Politova E. D. , Mosunov A. V. , Stefanovich S. Yu. , Ilina T. S. , Kiselev D. A. , Sadovskaya N. V.
Published: April 2024

Single-phase ceramic samples of new compositions (Na1 – хSrх)0.5Bi0.5TiO3 (x = 0–0.5), including those modified by additives of SiO2 and ZnO oxides, have been obtained by solid-phase synthesis. The crystal structure and microstructure of these samples, as well as their dielectric, nonlinear optical, and local piezoelectric properties, have been studied. The formation of a perovskite-type phase with a pseudocubic unit cell in all synthesized samples and an increase in the cell volume as a result of partial substitution of perovskite structure cations are established. A decrease in the temperature of ferroelectric phase transitions (confirmed by the methods of dielectric spectroscopy and laser second-harmonic generation) to the tetragonal paraelectric phase is revealed. Remanent piezoelectric hysteresis loops are obtained for the synthesized samples in the polarization switching mode; this result confirms the occurrence of ferroelectric polarization switching.
The Role of Chemical Pressure in the Formation of the Structure and Barocaloric Properties of Complex Fluorides and Oxyfluorides
Authors: Flerov I. N. , Gorev M. V. , Bogdanov E. V. , Laptash N. M.
Published: April 2024

The role of chemical pressure as an effective tool in the processes of formation of initial and distorted (as a result of structural transformations) phases, thermodynamic properties, and direct and inverse barocaloric effects in some complex oxyfluorides and fluorides with octahedral, tetrahedral, and spherical anion and cation groups in the structure has been studied. It is found that, due to the small temperature hysteresis and high baric sensitivity of materials, the maximum values of absolute and integral barocaloric characteristics can be implemented at low pressures. Correspondingly, the temperature range of reversibility of thermodynamic cycles based on fluorides/oxyfluorides as solid-state coolants can be expanded.
Acousto-Optic Interaction in Biaxial Crystals
Authors: Molchanov V. Ya. , Kupreyichik M. I. , Naumenko N F. , Chizhikov A. I. , Yushkov K. B. , Chizhikov S. I.
Published: April 2024

Acousto-optic (AO) interaction in optically biaxial crystals is of great interest due to the variety of phase matching geometries caused by the low symmetry of the acoustic, optical, and photoelastic properties. The current state of the research in the field of acousto-optics of biaxial crystals is presented. Some promising biaxial crystals of the orthorhombic and monoclinic systems, which are of practical interest as materials for AO devices, are considered. The unique geometries of isotropic and anisotropic diffraction that exist in only biaxial crystals are analyzed, and the AO devices based on these crystals are briefly reviewed.
Spatial Spin-Modulated Structure of Bi1 – xSrxFeO3 – y (x = 0, 0.05, and 0.10) Multiferroics
Authors: Pokatilov V. S. , Rusakov V. S. , Gapochka A. M. , Sigov A. S.
Published: April 2024

The room-temperature X-ray and Mössbauer data on the BiFeO3, Bi0.95Sr0.05FeO3 – y, and Bi0.90Sr0.10FeO3 – y multiferroics obtained by solid-phase synthesis are presented. The samples have a rhombohedral crystal structure with the sp. gr. R3c. The lattice parameter ah is invariable, while the parameter ch decreases with increasing strontium content. The 57Fe Mössbauer spectra recorded at a temperature of 295 K have been interpreted within the cycloid spatial spin-modulated structure model. It has been established that the easy-axis magnetic anisotropy is implemented in the investigated multiferroics. The anharmonicity parameter m of the spin-modulated structure has been measured. Upon replacement of trivalent Bi3+ ions in small amounts (x = 0–0.10) with divalent Sr2+ ions, the parameter m increases by a factor of more than 3: from 0.10(4) at x = 0.00 to 0.36(10) at x = 0.10.
Effect of Reversion Back to Cys11 on the Structure and Function of S11C Cys-free Nt.BspD6I
Authors: Artyukh R. I. , Fatkhullin B. F. , Antipova V. N. , Perevyazova T. A. , Kachalova G. S. , Yunusova A. K.
Published: April 2024

The three-dimensional structure of recombinant nicking endonuclease S11C Cys-free Nt.BspD6I was determined at 1.85 Å resolution. Nickase S11C Cys-free Nt.BspD6I was produced by the reversion back to Cys11 in Cys-free Nt.BspD6I using site-directed mutagenesis. An analysis of the crystal structure of nickase S11C Cys-free Nt.BspD6I demonstrated that the reversion back to Cys11 induces significant conformational changes in the recognition domain of nickase, which are accompanied by changes in its functions, such as a decrease in the affinity to DNA, the loss of the ability to undergo oligomerization, and high activity of restriction endonuclease S11C Cys-free R.BspD6I.
Preparation and Crystallographic Analysis of a Complex of SARS-CoV-2 S-Protein Receptor-Binding Domain with a Virus-Neutralizing Nanoantibody
Authors: Boyko K. M. , Varfolomeeva L. A. , Egorkin N. A. , Minyaev M. E. , Alekseeva I. A. , Favorskaya I. A. , Ryabova E. I. , Prokofiev V. V. , Esmagambetov I. B. , Shcheblyakov D. V. , Logunov D. Yu. , Gintsburg A. L. , Popov V. O. , Sluchanko N. N.
Published: April 2024

Coronavirus SARS-CoV-2 was the cause of global pandemic COVID-19 that has claimed millions of lives around the world. One of the approaches to the therapy of severe forms of COVID-19 is based on the use of virus-neutralizing antibodies against the receptor-binding domain (RBD) of the virus spike glycoprotein (S). Detailed structural data on particular epitopes recognized by these virus-neutralizing antibodies is an important aspect of the improvement of available antibodies in order to extend the range of recognized virus strains. A stoichiometric complex of the virus-neutralizing single-domain antibody P2C5 and the glycosylated form of SARS-CoV-2 S protein RBD was obtained. Despite numerous conditions in which the crystal growth of the complex was observed, these crystals showed poor diffraction, apparently because of heterogeneity associated with the glycosylation of RBD. With the aim of improving the crystal quality, deglycosylase PNGase F was produced in a bacterial expression system and deglycosylation of RBD was performed. Despite low solubility of the deglycosylated form of RBD, it retains the ability to bind to the nanoantibody P2C5, resulting in the formation of a stable heterodimeric complex during gel filtration. The crystals of this complex were obtained. They showed diffraction to a similar resolution of ~4 Å on a laboratory X-ray diffractometer and at a synchrotron radiation source. The symmetry space group, the unit cell parameters of the crystal, and its protein composition were determined.
DETERMINATION OF THE ABSOLUTE CONFIGURATION OF MONOATOMIC CHIRAL CRYSTALS USING THREE-WAVE X-RAY DIFFRACTION
Authors: Kozlovskaya K. A. , Ovchinnikova E. N. , Ustyugov A. M. , Dmitrienko V. E. , Oreshko A. P.
Published: April 2024

Many molecules and crystals are chiral, i.e., can exist as right- and left-handed mirror isomers. It is shown that the absolute configuration of monoatomic chiral crystals, including selenium, tellurium, and b-manganese, can be determined using multi-wavelength diffraction of circularly polarized X-ray radiation.
SHIFTS OF THE KIESSIG OSCILLATIONS AND FARADAY ROTATION FOR X-RAY REFLECTIVITY FROM A MAGNETIZED FILM
Authors: Andreeva M. A. , Baulin R. A.
Published: April 2024

Appearance of the refraction effects and Faraday rotation of the plane of polarization of linearly polarized X rays has been analyzed for transmission and reflection at grazing incidence angles for a resonant film with allowance for the X-ray magnetic or Mössbauer scattering. It is shown that, when the magnetization is oriented along the radiation beam direction, magnetic additives to the susceptibility do not affect the phase shifts between the waves reflected from the surface and the substrate; however, they induce “orthogonal polarization” in the reflected beam, which corresponds to rotation of the plane of polarization. Rotation of the plane of polarization is maximum for the critical angle of total external reflection; it is characterized by an oscillating dependence on the grazing angle, which can be used in future to vary the polarization state of X-ray beams.
STATISTICAL THEORY OF X-RAY DIFFRACTION PHASE CONTRAST FORMATION
Authors: Bushuev V. A.
Published: April 2024

A successive consideration of the formation of X-ray diffraction phase contrast of weakly absorbing noncrystalline objects with statistically distributed small-scale density inhomogeneities has been performed. It was assumed that the incident X-ray beam has an arbitrary degree of spatial coherence, and the changes in the statistical characteristics of this radiation during Bragg diffraction reflection from the monochromator and analyzer were taken into account. The phenomena of the increase and/or decrease in the phase contrast from regions with randomly distributed microcalcifications, in dependence of their rms sizes, relative refractive index decrement, and the lengths of spatial coherence of radiation and phase correlation as a result of diffraction-enhanced diffuse scattering are explained.
THE ROLE OF MAGNETIC INTERFACES IN THE FORMATION OF FORBIDDEN REFLECTIONS
Authors: Baulin R. A. , Andreeva M. A.
Published: April 2024

The possibility of the existence of forbidden Bragg reflections in Mössbauer reflectivity, which are caused by the influence of interfaces on the mirror reflection, is demonstrated. The calculations show that the measurement of Mössbauer spectra using forbidden reflections provides a fundamental opportunity to study interfaces selectively.
THE ROLE OF SELFACCOMMODATION COMPLEXES IN THE CRYSTALLOGRAPHIC REVERSIBILITY OF NONTHERMOELASTIC MARTENSITE TRANSFORMATIONS AND CONJUGATION OF ANISOTROPIC STRUCTURES
Authors: Khundjua A. G. , Brovkina E. A.
Published: April 2024

The possible structure of self-accommodation complexes of martensite crystals in alloys based on g-Mn and titanium nickelide has been analyzed. The analysis is based on the calculation of shape deformation, averaged over an ensemble of domains (equivalent versions of orientation relationships); for complete self-accommodation this deformation should be described by a unit matrix. In this case the compensation of the shape variation and minimization of elastic energy occur on the microscopic level of individual complexes of twinned martensite crystals. It is shown that complete self-accommodation of rhombohedral martensite R, as well as tetragonal and orthorhombic martensites in alloys based on y-Mn is implemented only in the complexes containing either all crystallographically equivalent versions of orientation relationships or their doubled number
DEPARTMENT OF SOLID STATE PHYSICS OF THE FACULTY OF PHYSICS OF LOMONOSOV MOSCOW STATE UNIVERSITY
Authors: Oreshko A. P.
Published: April 2024

An essay on the 100-year history of the formation and development of the Department of X-ray Diffraction Analysis, subsequently transformed into the Department of Solid State Physics of the Faculty of Physics of Lomonosov Moscow State University, is presented.
CRYSTALLOCHEMICAL FEATURES OF Ti- AND Sb-RICH NEZILOVITE
Authors: Rastsvetaeva R. K. , Gridchina V. M. , Varlamov D. A. , Jancev S.
Published: April 2024

A variety of the mineral nezilovite, containing antimony and an elevated amount of titanium, has been studied using microprobe and X-ray diffraction analysis. The diffraction experiment was performed on a crystal presenting an aggregate of nezilovite and högbomite with close unit-cell parameters. The parameters of the hexagonal cell of the nezilovite studied are a = 5.8855(2) Å, c = 23.092(1) Å, V = 692.73 (4) Å3,sp. gr. P63/mmc. The structural model is refined using a limited number of unique reflections 231F 4σ(F) to R = 0.08. The crystallochemical formula is (Z = 2) PbZn2(Ti0.9Al0.1)(Al0.6Sb )Mn Fe O18.5(O,OH)0.5. The distribution of cations of this composition over structure sites is established. A basis of the mineral structure is a set of spinel layers, consisting of edge-sharing Fe3+ octahedra. They alternate with two heteropolyhedral layers: Zn tetrahedra combine (Al,Sb) octahedra in one layer, and five-vertex Ti polyhedra combine dimers of Mn3+ octahedra in the other layer.
Varieties of Fossil Resins of the West Central Asia and Features of Their Molecular Structure
Authors: Martirosyan О. V. , Bogdasarov M. A.
Published: April 2024

This article provides the first modern overview of fossil resin finds in West Central Asia – far beyond the traditional resin-bearing areas, both in Russia and in northern Western Europe. Based on little-known facts and random references scattered in the geological literature, the main locations of fossil resins have been revisited and described, and the level of their study has been assessed. Peculiarities of molecular structure of fossil resins of Priaralie using IR spectroscopy has been studied for the first time. It is shown that the resins of this region, previously described as amber (in modern understanding – succinite), are not such, but are represented by exclusively fragile varieties – retinite, gedanite and do not represent practical interest as jeweller raw material.
Seismogenic Structures in Sediments of Different Lithological Composition and their Position in Mesozoic–Cenozoic Sections of the Northern Caucasus
Authors: Gavrilov Yu. O. , Gatatdinova Yu. R.
Published: April 2024

A comparative analysis of the morphological features of rock horizons affected by paleoearthquakes showed that seismites from lithologically different deposits differ significantly. Powerful earthquakes determine not only the destruction of the sedimentary structure of near-surface deposits and their chaotic mixing, but also actively affect the underlying layers to a depth of several tens of meters; since the degree of diagenetic lithification of rocks in different horizons varies with depth, the nature of their seismogenic changes also changes. It was found that major seismic events were associated with the time intervals of tectonic and paleogeographic restructuring of sedimentation basins, which consisted in the intensification of the process of bowing of the reservoir bed, changes in the material composition of sediments accumulated in the paleobasin. A special type of seismites was formed during the impact of earthquakes on siliceous deposits, in which the processes of diagenetic redistribution of authigenic mineral matter, which passed through the gel stage during diagenesis, actively proceeded.
Sources of Hydrocarbon Gases in the Mud Volcano Kedr, Southern Basin of Lake Baikal: Results of Experimental Investigations
Authors: Krylov A. A. , Khlystov O. M. , Semenov P. B. , Sagidullin A. K. , Malyshev S. A. , Bukin S. V. , Vidischeva O. N. , Manakov A. Yu. , Ismagilov Z. R.
Published: April 2024

Outcrops of the Oligocene-Pliocene coal-bearing Tankhoi suite are traced along the southern shore of Lake Baikal and submerge under its Southern Basin, in which several hydrate-bearing zones of focused discharge of hydrocarbon fluids have been found. To test the hypothesis that coals of the Tankhoi Suite can be sources of hydrocarbon gases in these zones, we collected coal samples from the Shakhterskaya Gorka outcrop. The experiment on gas generation from the selected samples was carried out in a special autoclave at a temperature of 90°C for eight months. This paper presents the results of this study, which confirm the important role of gas generation processes from coals in the formation of fluids in the Kedr mud volcano. Further migration of gases was accompanied by biodegradation and the formation of secondary microbial methane due to CO2 reduction. This was one of the reasons for the observed carbon isotopic pattern in methane (heavier than ‒50‰ VPDB) and carbon dioxide (positive values) taken from near-surface sediments and hydrates of the Kedr mud volcano, as well as for the significant enrichment of authigenic siderites in the heavy 13C isotope.
Microbial Destruction of Polypropylene and Polyvinylchloride Samples under the Anaerobic Conditions
Authors: Malakhova D. V. , Egorova M. A. , Leontieva M. R. , Elcheninov A. G. , Panova T. V. , Aleksandrov Yu. D. , Tsavkelova Е. А.
Published: April 2024

Abstract—The most advantageous characteristic of the materials made of synthetic polymers, such as their resistance to biodegradation, is simultaneously the reason for their accumulation and environmental pollution. Nevertheless, some type of plastics under aerobic conditions undergo slow microbial degradation, however, there is lack of information on the anaerobic degradation of plastics. In this work, we studied the growth of anaerobic moderately thermophilic (55°C) consortiums in the presence of samples made of polypropylene (PP) and polyvinyl chloride (PVC). It was shown that the microbial biomass increased compared to the control, as well as anaerobic decomposition products (CO2, H2, and H2S) were detected, and the total weight of the plastics decreased by 4.4% (PP) and 6.5% (PVC) compared to the control. Bacterial cells adhere and form colonies and biofilms on the surface of the plastic materials. An analysis of the composition of microbial communities showed an increased number of anaerobic hydrolytics of the genus Tepidimicrobium, potential syntrophic bacteria of the genus Tepidanaerobacter, and especially sulfate-reducing bacteria (Desulfohalotomaculum). With help of differential scanning calorimetry and Fourier spectroscopy it was revealed that the decrease in the mass of plastic mainly occurred due to the hydrolysis of additives (plasticizers). The role of such microbial communities in the aquatic environment and anaerobic layers of the municipal solid waste landfills, where PP and PVC plastics can be destructed under the elevated temperatures of anaerobic conditions, is discussed.
Molecular Genetic and Functional Analysis of the Genes Encoding Alkane 1‑Monoozygenase Synthesis in Members of the Genus Rhodococcus
Authors: Bulyarevich A. A. , Gurinovich A. S. , Filonov A. E. , Titok M. A.
Published: April 2024

Abstract—Organization and localization of the alkB genes and of alkane 1-monooxygenases they encode in members of the genus Rhodococcus was investigated. All members of a phylogenetic group were found to possess specific types of the alkB genes (alkB1-type in the operons containing rubredoxin-coding genes, rubredoxin reductase, and a regulatory protein and/or alkB2-type in the operons lacking the rubredoxin-reductase-coding gene, and supplementary, separately located determinants of the alkB3−alkB8 type). The alkB1-type genes were present in the chromosomes of bacteria of groups B1 (R. aetherivorans, R. ruber), С (R. opacus, R. jostii, R. wratislaviensis, R. koreensis), D (R. erythropolis, R. qingshengii), G (R. triatomae), and E (R. fascians). The alkB2-type genes occurred in strictly specified loci of the chromosomes of members of the phylogenetic groups А (R. hoagii/R. equi), В2 (R. coprophilus, R. pyridinivorans, R. rhodochrous), and D (R. erythropolis, R. qingshengii). The separately located alkB3−alkB5 were revealed in the chromosomes of members of the D group D (alkB5 was found only in R. qingshengii), the alkB6 genes occurred in members of the groups B1 and В2, and alkB7−alkB8 were present in members of group Е. The proteins coded by the genes alkB1 and alkB2 belonged to three phylogenetic groups. The first one comprised AlkB1-type proteins of members of groups В1 and С and the AlkB2-type proteins of members of groups D and A. The second one was represented by AlkB2-type proteins of bacteria of group В2. The third group comprised AlkB1-type proteins of members of groups G and D. Alkane 1-monooxygenases encoded by separately localized genes alkB3−alkB8 were represented by three phylogenetic lineages: AlkB3−AlkB5, AlkB6, and AlkB7 and AlkB8. In the genome of R. pyridinivorans 5Ар, the genes alkB2 and alkB6 characteristic of group В1 were revealed. This determinants were shown to be required for biosurfactant synthesis. Emulsifying activity of the mutant with impaired alkB2 gene at 28 and 42°С was 16 and 3 times lower, respectively, while the amount of trehalose-containing surfactants decreased 7 and 3 times, respectively. Independent on the cultivation temperature, the mutant with impaired alkB6 gene exhibited 1.2 times lower emulsifying activity and more than twofold lower decrease of the synthesis of trehalose-containing surfactants. These results indicated the key role of alkB2 in biosurfactant synthesis at different cultivation temperatures. The role of alkB6 increased at 42°С, probably due to its elevated transcriptional activity.
Microbial Processes of Methane Oxidation at the Kara Sea Sites of Gas Prospecting
Authors: Tikhonova E. N. , Rusanov I. I. , Kadnikov V. V. , Demkina E. V. , Toshchakov S. V. , Izotova A. O. , Pimenov N. V.
Published: April 2024

Abstract—Methane oxidation rates and diversity of methane-oxidizing microorganisms in the Kara Sea upper sediments at the sites of conserved gas prospecting wells were investigated. Analysis of the 16S rRNA gene sequences revealed members of the class Gammaproteobacteria, order Methylococcales. All samples exhibited similar diversity of the methane filter microorganisms, comprising mainly of methanotrophs related to the genus Methyloprofundus and of uncultured methanotrophic bacteria detected previously in the upper sediments of the Arctic seas. Molecular identification of methane-oxidizing bacteria of this community by high-throughput sequencing of the pmoA gene encoding particulate methane monooxygenase confirmed the similar structure of the methane filter in the upper sediments impaired by drilling and at the reference sites at significant distance from the wells. The sediments at the conserved well drilled less than two years earlier were shown to have the characteristics of a methane seep, i.e., elevated level of dissolved methane and high rates of microbial methane oxidation. No indication of methane seepage was observed for the wells conserved more than two years earlier; abundance of methane-oxidizing bacteria in their vicinity was below the detection threshold.
Glycoside Hydrolases of the Obligate Methanotroph Methyloferula stellata: an Unusual Evolutionary Strategy not Involving Distant Lateral Transfers
Authors: Naumoff D. G. , Dedysh S. N.
Published: April 2024

Abstract—The genome of the obligately methanotrophic bacterium Methyloferula stellata AR4 encodes thirty glycoside hydrolases. The closest homologues for most of these proteins belong to other members of the class Alphaproteobacteria. Two exceptions are represented by the genes encoding glycoside hydrolases of the families GH39 and GH65, which presumably appeared in M. stellata AR4 due to the lateral transfer from distantly related bacteria. This work was devoted to the study of the evolutionary history of these two genes. In the case of a member of the GH65 family of glycoside hydrolases, this scenario was not confirmed. Kojibiose phosphorylase encoded by this gene is common among Alphaproteobacteria. The suggested lateral transfer of the corresponding gene had an opposite direction, into one of the evolutionary lineages of the class Betaproteobacteria. The potential glycoside hydrolase of the GH39 family was shown to be the only one which gene is not of proteobacterial origin. The role of lateral transfers in the evolution of glycoside hydrolases and their homologues in methanotrophs and other bacteria is discussed.
Anaerobic Thermodesulfovibrio and Aerobic Meiothermus Coexist in Deep Thermal Water
Authors: Lukina A. P. , Kadniko V. V. , Rusanov I. I. , Avakyan M. R. , Beletsky A. V. , Mardanov A. V. , Pimenov N. V. , Ravin N. V. , Karnachuk O. V.
Published: April 2024

Abstract—Research on the microorganisms inhabiting deep aquifers is based on sampling the water released from deep wells and is seldom concerned with the physicochemical processes of the water-rock system. The issue of metabolism of aerobic prokaryotes revealed in deep habitats by molecular techniques remains unclear. Cultivation is required for direct determination of relation of prokaryotes to oxygen. In the present work, aerobic and anaerobic bacteria, which were revealed in thermal radon baths of the Belokurikha resort by molecular techniques, were isolated. Profiling by the 16S rRNA gene revealed predominance of members of the Deionococcus-Thermus group belonging to the genus Meiothermus (17.6% reads) and considered strictly aerobic. Anaerobic sulfate-reducing Thermodesulfovibrio were also present in the sample. The habitat was characterized by reductive, alkaline conditions. Target-oriented cultivation revealed aerobically growing Meiothermus sp. 1165, which was closely related to Meiothermus cerbereus. An alkaliphilic anaerobic sulfate reducer Thermodesulfovibrio sp. 1176 was also isolated. The rate of sulfate reduction measured in the Belokurikha water using \({\text{Na}}_{{\text{2}}}^{{{\text{ 35}}}}{\text{S}}{{{\text{O}}}_{{\text{4}}}}\) yielded the value of 41.4 ± 1.06 µm Sred L–1 day–1, or 1.29 nmol S mL–1 day–1. Analysis of the genome of strain 1176 revealed the presence of various mechanisms responsible for its relative resistance to oxygen and oxidative stress, which included superoxide reductase, rubredoxin, a Fe-Mn family superoxide dismutase, a KatG catalase-peroxidase, and a cytochrome bd ubiquinol oxidase. The low redox potential and intense anaerobic sulfate reduction provide evidence for the generally reduced conditions in the Belokurikha deep horizons. Spatial separation of aerobes and anaerobes in the water-rock system, similar to the one occurring in the terrestrial microbial mats, may be hypothesized, as well as occurring of aerobic processes in microniches.
Collections of Microalgae and Cyanobacteria in Russia: Present State, Problems, and Prospects
Authors: Temraleeva A. D. , Sinetova M. A.
Published: April 2024

Abstract—Biological collections are systematic repositories of living cultures or fixed preparations and provide researchers with the material required both for basic and applied studies and for educational activities. A collection sample is the only reliable evidence of the existence of a living organism in time and space, whose multifunctionality allows it to be studied as a part of biodiversity and as a bioresource for the development of biotechnologies. Microalgae are an ancient ecological group of taxonomically diverse organisms (cyanobacteria, diatoms, charophytes, green and yellow-green algae, etc.), possessing unique physiology, broad ecological valency and plasticity, which results in their predominance in various habitats. This evolutionarily successful group is also in high demand for commercial applications in environmental monitoring, agriculture, bioenergetics, pharmacy, and the food industry. The analysis of data from an independent survey of 21 Russian collections of microalgae and cyanobacteria is provided. The survey included information on the main characteristics of the collections (funds, profile, methods, document management, etc.), emerging problems, and approaches to their solution.
Effect of the Extracts from Lichens and Lichenophilic Fungi on in vitro Growth of Clinically Significant Microorganisms
Authors: Pankratov T. A. , Shcherbatov R. E. , Del’tsov A. A.
Published: April 2024

Abstract—Activity of the ethanol extracts from lichens (LE), of the cultures of lichenophilic (endobiotic) fungi (LFE), and of ethanol extracts from these cultures was tested using the following test organisms: Escherichia coli, Salmonella typhimurium, Pseudomonas fluorescens, Staphylococcus aureus, Micrococcus luteus, Enterococcus faecium, Paenibacillus sp., and Candida parapsilosis. Selective activity of LE and LFE against yeasts and gram-positive and gram-negative bacteria was revealed. The extracts from Cladonia rangiferina exhibited no activity against any of the tested cultures. The previously reported locus effect on activity of metabolites of one lichen species was confirmed. Agar block technique was used to detect selective activity of 23 out of 61 analyzed fungal strains against gram-positive and gram-negative bacteria, and of 8 strains, against yeasts. Ethanol extracts of six cultures were shown to suppress growth of St. aureus, M. luteus, Paenibacillus sp., and E. coli. Strain NM10F28209 from the lichen Stereocaulon paschale, which exhibited inhibitory activity against Ca. parapsilosis was selected for priority development of an antifungal preparation.
Magnetic Force and Nonlinear Optical Microscopy of the Surface Domain Structure in an Epitaxial Iron Garnet Film
Authors: Mamonov E. A , Novikov V. B , Maydykovskiy A. I , Temiryazeva M. P , Temiryazev A. G , Fedorova A. A , Logunov M. V , Nikitov S. A , Murzina T. V
Published: April 2024

The magnetic properties of the surface layer of an epitaxial bismuth-doped iron garnet film with a weak uniaxial anisotropy are studied by magnetic force, optical, and nonlinear optical microscopy. A significant modulation of optical second harmonic generation intensity along stripe domains is detected near the free film surface. This modulation is caused by periodic distortions of the stripe domain structure near the film surface and the presence of surface closure domains detected by magnetic force microscopy (MFM). A series of MFM images of the film taken in an in-plane magnetic field varying from –400 to 400 Oe demonstrates quasi-static nucleation of closure domains periodically located along stripe domains.
Hysteresis of Magnetization and Electric Polarization in Magnetic Nanostructures with Dzyaloshinskii–Moriya Interaction
Authors: Gareeva Z. V , Shul'ga N. V , Sharafullin I. F , Doroshenko R. A , Zvezdin A. K
Published: April 2024

The influence of the Dzyaloshinskii–Moriya interaction (DMI) on the formation of polar structures in nanoscale magnetoelectric films has been studied. The sequence of micromagnetic structures of different topology at magnetization and remagnetization of a film of limited size in a magnetic field oriented along the normal to the film surface is investigated. It is shown that the formation of polar structures is related to the existence of magnetic structures. Specific features of polar states in dependence of the DMI type and the interface symmetry is analyzed.
Laser-Controlled Spin-Wave Interference in an Irregular Magnonic Structure
Authors: Grachev A. A , Sadovnikov A. V
Published: April 2024

Using experimental and numerical investigation, we demonstrate laser-controlled propagation and interaction of spin waves in an irregular magnetic structure in the geometry of the Mach–Zehnder interferometer. It is shown that the use of laser radiation for heating one of the interferometer arms leads to controlled interference of a spin-wave signal in the output section. The yttrium–iron garnet film heating under the action of laser radiation is measured experimentally. Using micromagnetic modeling, the evolution of the spin-wave interference pattern under the action of laser heating of one of the interferometer arm is demonstrated. The results of this study ensure a simple solution for developing tunable spin-wave interferometers for the paradigm of the magnonic logics.
Luttinger Liquid with Attraction and One Impurity: Exact Solution
Authors: Afonin V. V
Published: April 2024

The exact solution to the problem of scattering of one-dimensional attracted fermions on a point impurity, which exists in the Kane–Fisher model is analyzed for a Luttinger parameter equal to 2. The expression obtained for the frequency dependence of the coefficient of fermion reflection from an impurity demonstrates impossibility of extrapolation of results for a relatively weak fermion–fermion interaction to the range of coupling constants on the order of unity.
Quasi-Isentropic Compression of Gaseous Helium and Deuterium in Spherical Structures at Terapascal Pressures
Authors: Zhernokletov M. V , Manachkin S. F , Davydov N. B , Raevskiy V. A , Blikov A. O , Panov K. N , Ryzhkov A. V , Arinin V. A , Tkachenko B. I
Published: April 2024

The results of four experiments on studying preliminarily statically compressed gaseous helium and deuterium during their subsequent compression in explosive spherical cascade structures providing quasi-isentropic gas compression are presented. For helium, the following parameters were achieved: in one experiment, the compression pressure is Pmean ≈ 4.9 TPa at a density ρmax ≈ 6.4 g/cm3 and the compression ratio is δ = ρ/ρ0 ≈ 320; in another experiment, Pmean ≈ 10.9 TPa, ρmax ≈ 10.3 g/cm3, and δ ≈ 470. For deuterium, these parameters are Pmean ≈ 3.4 TPa, ρmax ≈ 6.0 g/cm3, and δ ≈ 162 in one experiment and Pmean ≈ 13.3 TPa, ρmax ≈ 11.4 g/cm3, and δ ≈ 520 in another experiment. The gas density was determined by an X-ray method using the position of the boundaries of the steel shells compressing a gas. The experiments are simulated with a one-dimensional gasdynamic software package, in which the Kopyshev–Khrustalev equations of state are used for the gases under study. The pressures are determined using calculations, in which the dynamics of gas compression is satisfactorily simulated for the entire set of experiments.
Generation of Longitudinal Ultrasound by Shear Strain Pulses in the Spin–Phonon Echo Regime
Authors: Sazonov S. V
Published: April 2024

The possibility of generation of longitudinal ultrasonic pulses of gigahertz frequencies in the spin–phonon echo regime by acting on a magnetized isotropic paramagnet with nanosecond shear strain pulses is predicted. The frequency of generated longitudinal ultrasonic echo signals is twice as high as the frequency of pulses entered into the medium. This effect can be realized when the velocity of longitudinal ultrasound exceeds the velocity of shear strain waves by less than two times. This resonant mechanism of the pulsed regime of second harmonic generation, which is accompanied by a nonlinear transformation of transverse into longitudinal ultrasound, has no optical analog.
Synchronization of the Self-Oscillations of the Magnetic Vortices in Exchange-Coupled Ferromagnetic Disks
Authors: Tatarskiy D. A , Mironov V. L , Fraerman A. A
Published: April 2024

The low-frequency (gyrotropic) self-oscillations of the magnetic vortices in interacting ferromagnetic disks, which are caused by a spin-polarized current, are studied by numerical simulation. Various magnetization oscillation modes depending on the configuration of the magnetic state of the system are considered. The influence of the pumping current nonuniformity on the phase difference of the vortex gyration in neighboring disks is investigated. The overlap of the disks is shown to increase the interaction between the vortices and, hence, to decrease the dephasing of the vortex core oscillations. The prospects of using overlapping disks to ensure phase synchronization of arrays of spin-transfer vortex oscillators are discussed.
Mechanism of Transverse Charge Transfer in Thin Films of Hexagonal Boron Nitride
Authors: Islamov D. R , Perevalov T. V , Gismatulin A. A , Azarov I. A , Spesivtsev E. V , Gritsenko V. A
Published: April 2024

A mechanism of transverse charge transfer through hexagonal boron nitride (h-BN) in a MIS structure has been studied. Experimental data for charge transfer have been analyzed in terms of different models of charge transfer in insulators. It has been shown that charge transfer in h-BN is described by the model of phonon-assisted tunneling between neutral traps. The thermal and optical energies of phonon-coupled traps in h-BN have been determined. Based on charge transfer measurements, XPS spectra, and the ab initio electronic structure of intrinsic defects in h-BN it has been found that boron–nitrogen divacancies are most probably responsible for charge transfer in h-BN and transfer is provided by electrons.