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The purpose of research was to develop a mathematical model for pulsating blood flow in the part of aorta with their branches. Since the deformation of this most solid part of the aorta is small during the passage of the pulse wave, the blood vessels were considered as non-deformable curved cylinders. The article describes the internal structure of blood and some internal structural effects. This analysis shows that the blood, which is essentially a suspension, can only be regarded as a non-Newtonian fluid. In addition, the blood can be considered as a liquid only in the blood vessels, diameter of which is much higher than the characteristic size of blood cells and their aggregate formations. As a non-Newtonian fluid the viscous liquid with the power law of the relationship of stress with shift velocity was chosen. This law can describe the behaviour not only of liquids but also dispersions. When setting the boundary conditions at the entrance into aorta, reflecting the pulsating nature of the flow of blood, it was decided not to restrict the assignment of the total blood flow, which makes no assumptions about the spatial velocity distribution in a cross section. In this regard, it was proposed to model the surface envelope of this spatial distribution by a part of a paraboloid of rotation with a fixed base radius and height, which varies in time from zero to maximum speed value. The special attention was paid to the interaction of blood with the walls of the vessels. Having regard to the nature of this interaction, the so-called semi-slip condition was formulated as the boundary condition. At the outer ends of the aorta and its branches the amounts of pressure were given. To perform calculations the tetrahedral computer network for geometric model of the aorta with branches has been built. The total number of meshes is 9810. The calculations were performed with use of the software package ABACUS, which has also powerful tools for creating geometry of the model and visualization of calculations. The result is a distribution of velocities and pressure at each time step. In areas of branching vessels was discovered temporary presence of eddies and reverse currents. They were born via 0.47 s from the beginning of the pulse cycle and disappeared after 0.14 s.

The work is devoted to the study of the theoretical value of destructive influence on normal tissues of an organism by infrared radiation that goes beyond the treated pathological focus. This situation is possible if the direct laser radiation on the tissues is extremely long-acting. The solution to this problem can be the uniform distribution of heat inside the volume through indirect heating of the liquid, which contributes to minimal damage to the perifocal structures. A non-stationary thermophysical model of the process of heat propagation in biological tissues is presented, allowing to carry out studies of energy transfer from internal liquid contents of Baker's cyst heated by infrared laser radiation of a given specific power through a certain thickness of its wall to surrounding biological tissues. Calculation of the spacetime temperature distribution in the cyst wall and surrounding fat tissue is carried out by the finite-difference method. The time of effective exposure to temperature on the entire thickness of the cyst wall was estimated to be 55 ° C on its outer surface. The safety procedure ensures the exposure duration of this value is not more than 10 seconds.

As a result of the calculations carried out, it is established that there are several operating modes of a surgical laser that meet all the safety requirements with a simultaneous effective procedure. Local one-sided hyperthermia of the synovial membrane and subsequent coagulation of the entire wall thickness due to heat transfer contributes to the elimination of the cavity neoplasm of the popliteal region. With a thickness of 3 mm, the heating mode is satisfactory, under which the exposure time lasts about 200 seconds, and the specific power of the laser radiation in the internal medium of the liquid contents of the Baker cyst is approximately 1.

The review and systematization of current papers on the mathematical modeling of population dynamics allow us to conclude the key interests of authors are two or three main research lines related to the description and analysis of the dynamics of both local structured populations and systems of interacting homogeneous populations as ecological community in physical space. The paper reviews and systematizes scientific studies and results obtained within the framework of dynamics of structured and interacting populations to date. The paper describes the scientific idea progress in the direction of complicating models from the classical Malthus model to the modern models with various factors affecting population dynamics in the issues dealing with modeling the local population size dynamics. In particular, they consider the dynamic effects that arise as a result of taking into account the environmental capacity, density-dependent regulation, the Allee effect, complexity of an age and a stage structures. Particular attention is paid to the multistability of population dynamics. In addition, studies analyzing harvest effect on structured population dynamics and an appearance of the hydra effect are presented. The studies dealing with an appearance and development of spatial dissipative structures in both spatially separated populations and communities with migrations are discussed. Here, special attention is also paid to the frequency and phase multistability of population dynamics, as well as to an appearance of spatial clusters. During the systematization and review of articles on modeling the interacting population dynamics, the focus is on the “prey–predator” community. The key idea and approaches used in current mathematical biology to model a “prey–predator” system with community structure and harvesting are presented. The problems of an appearance and stability of the mosaic structure in communities distributed spatially and coupled by migration are also briefly discussed.

The paper presents a review of recent developments of hybrid discrete-continuous models in cell population dynamics. Such models are widely used in the biological modelling. Cells are considered as individual objects which can divide, die by apoptosis, differentiate and move under external forces. In the simplest representation cells are considered as soft spheres, and their motion is described by Newton’s second law for their centers. In a more complete representation, cell geometry and structure can be taken into account. Cell fate is determined by concentrations of intra-cellular substances and by various substances in the extracellular matrix, such as nutrients, hormones, growth factors. Intra-cellular regulatory networks are described by ordinary differential equations while extracellular species by partial differential equations. We illustrate the application of this approach with some examples including bacteria filament and tumor growth. These examples are followed by more detailed studies of erythropoiesis and immune response. Erythrocytes are produced in the bone marrow in small cellular units called erythroblastic islands. Each island is formed by a central macrophage surrounded by erythroid progenitors in different stages of maturity. Their choice between self-renewal, differentiation and apoptosis is determined by the ERK/Fas regulation and by a growth factor produced by the macrophage. Normal functioning of erythropoiesis can be compromised by the development of multiple myeloma, a malignant blood disorder which leads to a destruction of erythroblastic islands and to sever anemia. The last part of the work is devoted to the applications of hybrid models to study immune response and the development of viral infection. A two-scale model describing processes in a lymph node and other organs including the blood compartment is presented.

The development of structured molecular systems based on a nucleic acid framework takes into account the ability of single-stranded DNA to form a stable double-stranded structure due to stacking interactions and hydrogen bonds of complementary pairs of nucleotides. To increase the stability of the DNA double helix and to expand the temperature range in the hybridization protocols, it was proposed to use more stable metal-mediated complexes of nucleotide pairs as an alternative to Watson-Crick hydrogen bonds. One of the most frequently considered options is the use of silver ions to stabilize a pair of cytosines from opposite DNA strands. Silver ions specifically bind to N3 cytosines along the helix axis to form, as is believed, a strong N3–Ag⁺–N3 bond, relative to which, two rotational isomers, the cis- and trans-configurations of C–Ag⁺–C can be formed. In present work, a theoretical study and a comparative analysis of the free energy profile of the dissociation of two С–Ag⁺–C isomers were carried out using the combined method of molecular mechanics and quantum chemistry (QM/MM). As a result, it was shown that the cis-configuration is more favorable in energy than the trans- for a single pair of cytosines, and the geometry of the global minimum at free energy profile for both isomers differs from the equilibrium geometries obtained previously by quantum chemistry methods. Apparently, the silver ion stabilization model of the DNA duplex should take into account not only the direct binding of silver ions to cytosines, but also the presence of related factors, such as stacking interaction in extended DNA, interplanar hydrogen bonds, and metallophilic interaction of neighboring silver ions.

In real problems of exploration seismology we deal with a heterogeneity of the nature of elastic waves interaction with the surface of a fracture by the propagation through it. The fracture is a complex heterogeneous structure. In some locations the surfaces of fractures are placed some distance apart and are separated by filling fluid or emptiness, in some places we can observe the gluing of surfaces, when under the action of pressure forces the fracture surfaces are closely adjoined to each other. In addition, fractures can be classified by the nature of saturation: fluid or gas. Obviously, for such a large variety in the structure of fractures, one cannot use only one model that satisfies all cases.

This article is concerned with description of developed mathematical fracture models which can be used for numerical solution of exploration seismology problems using the grid-characteristic method on unstructured triangular (in 2D-case) and tetrahedral (in 3D-case) meshes. The basis of the developed models is the concept of an infinitely thin fracture, whose aperture does not influence the wave processes in the fracture area. These fractures are represented by bound areas and contact boundaries with different conditions on contact and boundary surfaces. Such an approach significantly reduces the consumption of computer resources since there is no need to define the mesh inside the fracture. On the other side, it allows the fractures to be given discretely in the integration domain, therefore, one can observe qualitatively new effects, such as formation of diffractive waves and multiphase wave front due to multiple reflections between the surfaces of neighbor fractures, which cannot be observed by using effective fracture models actively used in computational seismology.

The computational modeling of seismic waves propagation through layers of mesofractures was produced using developed fracture models. The results were compared with the results of physical modeling in problems in the same statements.

The review is based on some of the authors ’early works of particular scientific, methodological and practical interest and the greatest attention is paid to recent works, where quite detailed numerical studies of not only single, but also double and multiple explosions in a wide range of heights and environmental conditions have been performed . Since the shock wave of a powerful explosion is one of the main damaging factors in the lower atmosphere, the review focuses on both the physical analysis of their propagation and their interaction. Using the three-dimensional algorithms developed by the authors, the effects of interference and diffraction of several shock waves, which are interesting from a physical point of view, in the absence and presence of an underlying surface of various structures are considered. Quantitative characteristics are determined in the region of their maximum values, which is of known practical interest. For explosions in a dense atmosphere, some new analytical solutions based on the small perturbation method have been found that are convenient for approximate calculations. For a number of conditions, the possibility of using the self-similar properties of equations of the first and second kind to solve problems on the development of an explosion has been shown.

Based on numerical analysis, a fundamental change in the structure of the development of the perturbed region with a change in the height of the explosion in the range of 100–120 km is shown. At altitudes of more than 120 km, the geomagnetic field begins to influence the development of the explosion; therefore, even for a single explosion, the picture of the plasma flow after a few seconds becomes substantially three-dimensional. For the calculation of explosions at altitudes of 120–1000 km under the guidance of academician A. Kholodov. A special three-dimensional numerical algorithm based on the MHD approximation was developed. Numerous calculations were performed and for the first time a quite detailed picture of the three-dimensional flow of the explosion plasma was obtained with the formation of an upward jet in 5–10 s directed in the meridional plane approximately along the geomagnetic field. After some modification, this algorithm was used to calculate double explosions in the ionosphere, spaced a certain distance. The interaction between them was carried out both by plasma flows and through a geomagnetic field. Some results are given in this review and are described in detail in the original articles.

This study is devoted to a comparative study of the conformational stability of the DNA aptamer to adenosine derivatives in a free state and in a complex with AMP and HMP molecules by use of molecular dynamics. It was shown that, in the free state, the structure of the inner loop of the DNA aptamer hairpin, due to the special packing of guanines, closes the cavity of the binding site from external ligands, and the condition for the specific selection of adenosine derivatives in comparison with guanine arises. New stabilization factors of the AMP and aptamer complex have been revealed — hydrogen bonds between the O3’ of the ribose atom of the ligands with the oxygen of the nearest phosphate group. It was also shown that guanines, which form hydrogen bonds with AMP within the binding site, are additionally stabilized by hydrogen bonds with phosphate groups opposing along the chain. The proposed scheme is in qualitative agreement with the experimental data, according to which the aptamer in solution acquires a hairpin conformation with the formation of a binding site, while the formed site exhibits high specificity when interacting only with adenosine derivatives.

The work is devoted to the study of the influence of nonlinear processes in the boundary layer on the general nature of gas flows in microchannels of technical systems. Such a study is actually concerned with nanotechnology problems. One of the important problems in this area is the analysis of gas flows in microchannels in the case of transient and supersonic flows. The results of this analysis are important for the gas-dynamic spraying techique and for the synthesis of new nanomaterials. Due to the complexity of the implementation of full-scale experiments on micro- and nanoscale, they are most often replaced by computer simulations. The efficiency of computer simulations is achieved by both the use of new multiscale models and the combination of mesh and particle methods. In this work, we use the molecular dynamics method. It is applied to study the establishment of a gas microflow in a metal channel. Nitrogen was chosen as the gaseous medium. The metal walls of the microchannels consisted of nickel atoms. In numerical experiments, the accommodation coefficients were calculated at the boundary between the gas flow and the metal wall. The study of the microsystem in the boundary layer made it possible to form a multicomponent macroscopic model of the boundary conditions. This model was integrated into the macroscopic description of the flow based on a system of quasi-gas-dynamic equations. On the basis of such a transformed gas-dynamic model, calculations of microflow in real microsystem were carried out. The results were compared with the classical calculation of the flow, which does not take into account nonlinear processes in the boundary layer. The comparison showed the need to use the developed model of boundary conditions and its integration with the classical gas-dynamic approach.

Actin is a conserved structural protein that is expressed in all eukaryotic cells. When polymerized, it forms long filaments of fibrillar actin, or F-actin, which are involved in the formation of the cytoskeleton, in muscle contraction and its regulation, and in many other processes. The dynamic and mechanical properties of actin are important for interaction with other proteins and the realization of its numerous functions in the cell. We performed 204.8 ns long molecular dynamics (MD) simulations of an actin filament segment consisting of 24 monomers in the absence and the presence of MgADP at 300 K in the presence of a solvent and at physiological ionic strength using the AMBER99SBILDN and CHARMM36 force fields in the GROMACS software environment, using modern structural models as the initial structure obtained by high-resolution cryoelectron microscopy. MD calculations have shown that the stationary regime of fluctuations in the structure of the F-actin long segment is developed 80–100 ns after the start of the MD trajectory. Based on the results of MD calculations, the main parameters of the actin helix and its bending, longitudinal, and torsional stiffness were estimated using a section of the calculation model that is far enough away from its ends. The estimated subunit axial (2.72–2.75 nm) and angular (165–168^◦) translation of the F-actin helix, its bending (2.8–4.7 · 10⁻²⁶ N·m²), longitudinal (36–47·10⁻⁹ N), and torsional (2.6–3.1·10⁻²⁶ N·m²) stiffness are in good agreement with the results of the most reliable experiments. The results of MD calculations have shown that modern structural models of F-actin make it possible to accurately describe its dynamics and mechanical properties, provided that computational models contain a sufficiently large number of monomers, modern force fields, and relatively long MD trajectories are used. The inclusion of actin partner proteins, in particular, tropomyosin and troponin, in the MD model can help to understand the molecular mechanisms of such important processes as the regulation of muscle contraction.