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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.

A cluster method of mathematical modeling of interval-stochastic thermal processes in complex electronic systems (ES), is developed. In the cluster method, the construction of a complex ES is represented in the form of a thermal model, which is a system of clusters, each of which contains a core that combines the heat-generating elements falling into a given cluster, the cluster shell and a medium flow through the cluster. The state of the thermal process in each cluster and every moment of time is characterized by three interval-stochastic state variables, namely, the temperatures of the core, shell, and medium flow. The elements of each cluster, namely, the core, shell, and medium flow, are in thermal interaction between themselves and elements of neighboring clusters. In contrast to existing methods, the cluster method allows you to simulate thermal processes in complex ESs, taking into account the uneven distribution of temperature in the medium flow pumped into the ES, the conjugate nature of heat exchange between the medium flow in the ES, core and shells of clusters, and the intervalstochastic nature of thermal processes in the ES, caused by statistical technological variation in the manufacture and installation of electronic elements in ES and random fluctuations in the thermal parameters of the environment. The mathematical model describing the state of thermal processes in a cluster thermal model is a system of interval-stochastic matrix-block equations with matrix and vector blocks corresponding to the clusters of the thermal model. The solution to the interval-stochastic equations are statistical measures of the state variables of thermal processes in clusters - mathematical expectations, covariances between state variables and variance. The methodology for applying the cluster method is shown on the example of a real ES.

The article deals with the problem of a distributed system operation reliability. The system core is an open integration platform that provides interaction of varied software for modeling gas transportation. Some of them provide an access through thin clients on the cloud technology “software as a service”. Mathematical models of operation, transmission and computing are to ensure the operation of an automated dispatching system for oil and gas transportation. The paper presents a system solution based on the theory of Markov random processes and considers the stable operation stage. The stationary operation mode of the Markov chain with continuous time and discrete states is described by a system of Chapman–Kolmogorov equations with respect to the average numbers (mathematical expectations) of the objects in certain states. The objects of research are both system elements that are present in a large number – thin clients and computing modules, and individual ones – a server, a network manager (message broker). Together, they are interacting Markov random processes. The interaction is determined by the fact that the transition probabilities in one group of elements depend on the average numbers of other elements groups.

The authors propose a multi-criteria dispersion model of risk assessment for such systems (both in the broad and narrow sense, in accordance with the IEC standard). The risk is the standard deviation of estimated object parameter from its average value. The dispersion risk model makes possible to define optimality criteria and whole system functioning risks. In particular, for a thin client, the following is calculated: the loss profit risk, the total risk of losses due to non-productive element states, and the total risk of all system states losses.

Finally the paper proposes compromise schemes for solving the multi-criteria problem of choosing the optimal operation strategy based on the selected set of compromise criteria.

The paper considers the process of flow formation in an outflow of a binary gas mixture through a thin slit into vacuum. An approach to modeling the flows of rarefied gas mixtures in the transient regime is proposed based on the direct solution of the Boltzmann kinetic equation, in which the conservative projection method is used to calculate the collision integrals. Calculation formulas are provided; the calculation procedure is described in detail in relation to the flow of a binary gas mixture. The Lennard–Jones potential is used as an interaction potential of molecules. A software modeling environment has been developed that makes it possible to study the flows of gas mixtures in a transitional regime on systems of cluster architecture. Due to the use of code parallelization technologies, an acceleration of calculations by 50–100 times was obtained. Numerical simulation of a two-dimensional outflow of a binary argon-neon gas mixture from a vessel into vacuum through a thin slit is carried out for various values of the Knudsen number. The graphs of the dependence of gas mixture components output flow on time in the process of establishing the flow are obtained. Non-stationary regions of strong separation of gas mixture components, in which the molecular densities ratio reaches 10 or more, were discovered. The discovered effect can have applications in the problem of gas mixtures separation.

The study of the Volterra model describing the competition of three types is carried out. The corresponding system of first-order differential equations with a quadratic right-hand side, after a change of variables, reduces to a system with eight parameters. Two of them characterize the growth rates of populations; for the first species, this parameter is taken equal to one. The remaining six coefficients define the species interaction matrix. Previously, in the analytical study of the so-called symmetric model [May, Leonard, 1975] and the asymmetric model [Chi, Wu, Hsu, 1998] with growth factors equal to unity, relations were established for the interaction coefficients, under which the system has a one-parameter family of limit cycles. In this paper, we carried out a numerical-analytical study of the complete system based on a cosymmetric approach, which made it possible to determine the ratios for the parameters that correspond to families of equilibria. Various variants of oneparameter families are obtained and it is shown that they can consist of both stable and unstable equilibria. In the case of an interaction matrix with unit coefficients, a multicosymmetry of the system and a two-parameter family of equilibria are found that exist for any growth coefficients. For various interaction coefficients, the values of growth parameters are found at which periodic regimes are realized. Their belonging to the family of limit cycles is confirmed by the calculation of multipliers. In a wide range of values that violate the relationships under which the existence of cycles is ensured, a slow oscillatory establishment, typical of the destruction of cosymmetry, is obtained. Examples are given where a fixed value of one growth parameter corresponds to two values of another parameter, so that there are different families of periodic regimes. Thus, the variability of scenarios for the development of a three-species system has been established.

By numerical simulation methods the interaction processes of oscillating soliton (breather) with a 180-degree Neel domain wall in the framework of a (2 + 1)-dimensional supersymmetric O(3) nonlinear sigma model is studied. The purpose of this paper is to investigate nonlinear evolution and stability of a system of interacting localized dynamic and topological solutions. To construct the interaction models, were used a stationary breather and domain wall solutions, where obtained in the framework of the two-dimensional sine-Gordon equation by adding specially selected perturbations to the A3-field vector in the isotopic space of the Bloch sphere. In the absence of an external magnetic field, nonlinear sigma models have formal Lorentz invariance, which allows constructing, in particular, moving solutions and analyses the experimental data of the nonlinear dynamics of an interacting solitons system. In this paper, based on the obtained moving localized solutions, models for incident and head-on collisions of breathers with a domain wall are constructed, where, depending on the dynamic parameters of the system, are observed the collisions and reflections of solitons from each other, a long-range interactions and also the decay of an oscillating soliton into linear perturbation waves. In contrast to the breather solution that has the dynamics of the internal degree of freedom, the energy integral of a topologically stable soliton in the all experiments the preserved with high accuracy. For each type of interaction, the range of values of the velocity of the colliding dynamic and topological solitons is determined as a function of the rotation frequency of the A3-field vector in the isotopic space. Numerical models are constructed on the basis of methods of the theory of finite difference schemes, using the properties of stereographic projection, taking into account the group-theoretical features of constructions of the O(N) class of nonlinear sigma models of field theory. On the perimeter of the two-dimensional modeling area, specially developed boundary conditions are established that absorb linear perturbation waves radiated by interacting soliton fields. Thus, the simulation of the interaction processes of localized solutions in an infinite two-dimensional phase space is carried out. A software module has been developed that allows to carry out a complex analysis of the evolution of interacting solutions of nonlinear sigma models of field theory, taking into account it’s group properties in a two-dimensional pseudo-Euclidean space. The analysis of isospin dynamics, as well the energy density and energy integral of a system of interacting dynamic and topological solitons is carried out.

The paper proposes a mathematical model for the therapy of glioma, taking into account the blood-brain barrier, radiotherapy and antibody therapy. The parameters were estimated from experimental data and the evaluation of the effect of parameter values on the effectiveness of treatment and the prognosis of the disease were obtained. The possible variants of sequential use of radiotherapy and the effect of antibodies have been explored. The combined use of radiotherapy with intravenous administration of $mab$ $Cx43$ leads to a potentiation of the therapeutic effect in glioma.

Radiotherapy must precede chemotherapy, as radio exposure reduces the barrier function of endothelial cells. Endothelial cells of the brain vessels fit tightly to each other. Between their walls are formed so-called tight contacts, whose role in the provision of BBB is that they prevent the penetration into the brain tissue of various undesirable substances from the bloodstream. Dense contacts between endothelial cells block the intercellular passive transport.

The mathematical model consists of a continuous part and a discrete one. Experimental data on the volume of glioma show the following interesting dynamics: after cessation of radio exposure, tumor growth does not resume immediately, but there is some time interval during which glioma does not grow. Glioma cells are divided into two groups. The first group is living cells that divide as fast as possible. The second group is cells affected by radiation. As a measure of the health of the blood-brain barrier system, the ratios of the number of BBB cells at the current moment to the number of cells at rest, that is, on average healthy state, are chosen.

The continuous part of the model includes a description of the division of both types of glioma cells, the recovery of BBB cells, and the dynamics of the drug. Reducing the number of well-functioning BBB cells facilitates the penetration of the drug to brain cells, that is, enhances the action of the drug. At the same time, the rate of division of glioma cells does not increase, since it is limited not by the deficiency of nutrients available to cells, but by the internal mechanisms of the cell. The discrete part of the mathematical model includes the operator of radio interaction, which is applied to the indicator of BBB and to glial cells.

Within the framework of the mathematical model of treatment of a cancer tumor (glioma), the problem of optimal control with phase constraints is solved. The patient’s condition is described by two variables: the volume of the tumor and the condition of the BBB. The phase constraints delineate a certain area in the space of these indicators, which we call the survival area. Our task is to find such treatment strategies that minimize the time of treatment, maximize the patient’s rest time, and at the same time allow state indicators not to exceed the permitted limits. Since the task of survival is to maximize the patient’s lifespan, it is precisely such treatment strategies that return the indicators to their original position (and we see periodic trajectories on the graphs). Periodic trajectories indicate that the deadly disease is translated into a chronic one.

The biological structure is considered as an open nonequilibrium system which properties can be described on the basis of kinetic equations. New problems with nonequilibrium boundary conditions are introduced. The nonequilibrium distribution tends gradually to an equilibrium state. The region of spatial inhomogeneity has a scale depending on the rate of mass transfer in the open system and the characteristic time of metabolism. In the proposed approximation, the internal energy of the motion of molecules is much less than the energy of translational motion. Or in other terms we can state that the kinetic energy of the average blood velocity is substantially higher than the energy of chaotic motion of the same particles. We state that the relaxation problem models a living system. The flow of entropy to the system decreases in downstream, this corresponds to Shrödinger’s general ideas that the living system “feeds on” negentropy. We introduce a quantity that determines the complexity of the biosystem, more precisely, this is the difference between the nonequilibrium kinetic entropy and the equilibrium entropy at each spatial point integrated over the entire spatial region. Solutions to the problems of spatial relaxation allow us to estimate the size of biosystems as regions of nonequilibrium. The results are compared with empirical data, in particular, for mammals we conclude that the larger the size of animals, the smaller the specific energy of metabolism. This feature is reproduced in our model since the span of the nonequilibrium region is larger in the system where the reaction rate is shorter, or in terms of the kinetic approach, the longer the relaxation time of the interaction between the molecules. The approach is also used for estimation of a part of a living system, namely a green leaf. The problems of aging as degradation of an open nonequilibrium system are considered. The analogy is related to the structure, namely, for a closed system, the equilibrium of the structure is attained for the same molecules while in the open system, a transition occurs to the equilibrium of different particles, which change due to metabolism. Two essentially different time scales are distinguished, the ratio of which is approximately constant for various animal species. Under the assumption of the existence of these two time scales the kinetic equation splits in two equations, describing the metabolic (stationary) and “degradative” (nonstationary) parts of the process.

The article is devoted to the numerical study of shock-wave flows in inhomogeneous media–gas mixtures. In this work, a two-speed two-temperature model is used, in which the dispersed component of the mixture has its own speed and temperature. To describe the change in the concentration of the dispersed component, the equation of conservation of “average density” is solved. This study took into account interphase thermal interaction and interphase pulse exchange. The mathematical model allows the carrier component of the mixture to be described as a viscous, compressible and heat-conducting medium. The system of equations was solved using the explicit Mac-Cormack second-order finite-difference method. To obtain a monotone numerical solution, a nonlinear correction scheme was applied to the grid function. In the problem of shock-wave flow, the Dirichlet boundary conditions were specified for the velocity components, and the Neumann boundary conditions were specified for the other unknown functions. In numerical calculations, in order to reveal the dependence of the dynamics of the entire mixture on the properties of the solid component, various parameters of the dispersed phase were considered — the volume content as well as the linear size of the dispersed inclusions. The goal of the research was to determine how the properties of solid inclusions affect the parameters of the dynamics of the carrier medium — gas. The motion of an inhomogeneous medium in a shock duct divided into two parts was studied, the gas pressure in one of the channel compartments is more important than in the other. The article simulated the movement of a direct shock wave from a high-pressure chamber to a low–pressure chamber filled with a dusty medium and the subsequent reflection of a shock wave from a solid surface. An analysis of numerical calculations showed that a decrease in the linear particle size of the gas suspension and an increase in the physical density of the material from which the particles are composed leads to the formation of a more intense reflected shock wave with a higher temperature and gas density, as well as a lower speed of movement of the reflected disturbance reflected wave.

The paper analyzes the methods of studying the process of interaction of soil environments with the tillage tools of soil processing machines. The mathematical methods of numerical modeling are considered in detail, which make it possible to overcome the disadvantages of analytical and empirical approaches. A classification and overview of the possibilities the continuous (FEM — finite element method, CFD — computational fluid dynamics) and discrete (DEM — discrete element method, SPH — hydrodynamics of smoothed particles) numerical methods is presented. Based on the discrete element method, a mathematical model has been developed that represents the soil in the form of a set of interacting small spherical elements. The working surfaces of the tillage tool are presented in the framework of the finite element approximation in the form of a combination of many elementary triangles. The model calculates the movement of soil elements under the action of contact forces of soil elements with each other and with the working surfaces of the tillage tool (elastic forces, dry and viscous friction forces). This makes it possible to assess the influence of the geometric parameters of the tillage tools, technological parameters of the process and soil parameters on the geometric indicators of soil displacement, indicators of the self-installation of tools, power loads, quality indicators of loosening and spatial distribution of indicators. A total of 22 indicators were investigated (or the distribution of the indicator in space). This makes it possible to reproduce changes in the state of the system of elements of the soil (soil cultivation process) and determine the total mechanical effect of the elements on the moving tillage tools of the implement. A demonstration of the capabilities of the mathematical model is given by the example of a study of soil cultivation with a disk cultivator battery. In the computer experiment, a virtual soil channel of 5×1.4 m in size and a 3D model of a disk cultivator battery were used. The radius of the soil particles was taken to be 18 mm, the speed of the tillage tool was 1 m/s, the total simulation time was 5 s. The processing depth was 10 cm at angles of attack of 10, 15, 20, 25 and 30°. The verification of the reliability of the simulation results was carried out on a laboratory stand for volumetric dynamometry by examining a full-scale sample, made in full accordance with the investigated 3D-model. The control was carried out according to three components of the traction resistance vector: $F_x$, $F_y$ and $F_z$. Comparison of the data obtained experimentally with the simulation data showed that the discrepancy is not more than 22.2%, while in all cases the maximum discrepancy was observed at angles of attack of the disk battery of 30°. Good consistency of data on three key power parameters confirms the reliability of the whole complex of studied indicators.