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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.

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.

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.

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.

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.

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.

This article reviews both historical achievements and modern results in the field of Markov Decision Process (MDP) and convex optimization. This review is the first attempt to cover the field of reinforcement learning in Russian in the context of convex optimization. The fundamental Bellman equation and the criteria of optimality of policy — strategies based on it, which make decisions based on the known state of the environment at the moment, are considered. The main iterative algorithms of policy optimization based on the solution of the Bellman equations are also considered. An important section of this article was the consideration of an alternative to the $Q$-learning approach — the method of direct maximization of the agent’s average reward for the chosen strategy from interaction with the environment. Thus, the solution of this convex optimization problem can be represented as a linear programming problem. The paper demonstrates how the convex optimization apparatus is used to solve the problem of Reinforcement Learning (RL). In particular, it is shown how the concept of strong duality allows us to naturally modify the formulation of the RL problem, showing the equivalence between maximizing the agent’s reward and finding his optimal strategy. The paper also discusses the complexity of MDP optimization with respect to the number of state–action–reward triples obtained as a result of interaction with the environment. The optimal limits of the MDP solution complexity are presented in the case of an ergodic process with an infinite horizon, as well as in the case of a non-stationary process with a finite horizon, which can be restarted several times in a row or immediately run in parallel in several threads. The review also reviews the latest results on reducing the gap between the lower and upper estimates of the complexity of MDP optimization with average remuneration (Averaged MDP, AMDP). In conclusion, the real-valued parametrization of agent policy and a class of gradient optimization methods through maximizing the $Q$-function of value are considered. In particular, a special class of MDPs with restrictions on the value of policy (Constrained Markov Decision Process, CMDP) is presented, for which a general direct-dual approach to optimization with strong duality is proposed.