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Protein-protein interactions are of central importance for virtually every process in living matter. Modeling the dynamics of protein association is crucial for understanding their functionality. This paper proposes novel simulation software ProKSim (Protein Kinetics Simulator) for modeling of protein interactions by means of the multi-particle Brownian Dynamics. Effect of long-range electrostatic interactions on the process of transient encounter complex formation is numerically estimated. Investigation of transient encounter complex formation was performed for three pairs of proteins: ferredoxin and ferredoxin:NADP⁺-redustase, plastocyanin and cytochrome f, barnase and barstar.

The results of verification carried out for investigations of hydrodynamic effect on reentry conicalsegmental space vehicle are presented in the paper. The program complex Flow Vision is used for this analysis. The purpose of the study is verification of using Flow Vision program complex for problem solving mentioned above on the base of comparison between calculated and experimental data, obtained on the Apollo landing models and new development reentry spacecraft of manned transporting spaceship designed by RSC Energia. The comparison was carried out through the data of pressure values on spacecraft model surfaces during its water landing and inertia center motion parameters.

The results of study show good agreement between experimental and calculated data of force effects on vehicle construction during water landing and its motion parameters in the water medium. Computer simulation sufficiently well reproduces influence of initial velocities & water entry angles variations on water landing process.

Using of computer simulation provides simultaneous acquisition of all data information needed for investigation of water landing peculiarities during construction design, notably, hydrodynamic effects for structural strength calculations, parameters and dynamics of center mass motion and vehicle revolution around center mass for estimation water landing conditions, as well as vehicle stability after landing.

Obtained results confirm suitability of using Flow Vision program complex for water landing vehicle investigations and investigations of influence of different landing regimes through wide initial condition change range, that permits considerably decrease extent of expensive experimental tests and realize landing conditions which are sufficiently complicated for realizing in model physical experiments.

In this paper, we introduce a new version of Gauss–Newton method for solving a system of nonlinear equations based on ideas of the residual upper bound for a system of nonlinear equations and a quadratic regularization term. The introduced Gauss–Newton method in practice virtually forms the whole parameterized family of the methods solving systems of nonlinear equations and regression problems. The developed family of Gauss–Newton methods completely consists of iterative methods with generalization for cases of non-euclidean normed spaces, including special forms of Levenberg–Marquardt algorithms. The developed methods use the local model based on a parameterized proximal mapping allowing us to use an inexact oracle of «black–box» form with restrictions for the computational precision and computational complexity. We perform an efficiency analysis including global and local convergence for the developed family of methods with an arbitrary oracle in terms of iteration complexity, precision and complexity of both local model and oracle, problem dimensionality. We present global sublinear convergence rates for methods of the proposed family for solving a system of nonlinear equations, consisting of Lipschitz smooth functions. We prove local superlinear convergence under extra natural non-degeneracy assumptions for system of nonlinear functions. We prove both local and global linear convergence for a system of nonlinear equations under Polyak–Lojasiewicz condition for proposed Gauss– Newton methods. Besides theoretical justifications of methods we also consider practical implementation issues. In particular, for conducted experiments we present effective computational schemes for the exact oracle regarding to the dimensionality of a problem. The proposed family of methods unites several existing and frequent in practice Gauss–Newton method modifications, allowing us to construct a flexible and convenient method implementable using standard convex optimization and computational linear algebra techniques.

A review of the problems of preparing accurate geometric models of steel ropes based on mathematical models without significant simplifications, taking into account the intended purpose of the model, is carried out. Possible approaches to the generation of precise geometric models of steel ropes that have no fundamental limitations on their integration in computational domains and the subsequent construction of finite element models based on them are shown. A generalized parameterized geometric model of single and double twist ropes and its algorithmic implementation using the OpenCASCADE Core Technology geometric modeling kernel in the Gmsh environment (open source software) is considered. The problems of using generic tabular data from steel rope assortment standards as initial data for constructing geometric models are considered. Methods of preliminary verification of collisions of a geometric model based on the initial data of a geometric model are given. Post-verification methods based on Boolean operations over rope wire bodies are given to identify incorrect results of generating models of wire bodies with curvilinear side surfaces based on the algorithm of sequential hierarchical construction of individual wires of single strand and sequential copying of it. Various methods of the process of constructing geometric models of rope wires by extrusion are shown: through a sequence of generatrix with the formation of a body limited by curvilinear surfaces, through a sequence of generatrix with the formation of a body limited by linearly approximated surfaces, and extrusion of one generatrix along a single guideline. The computational complexity of the geometric model generation and the required volume of RAM for the two most universal methods of creating a body of wire are investigated. A method for estimating the value of the step of the arrangement of the generatrix of a single wire is shown, and the influence of its value on the computational complexity of the procedure of wire construction is investigated. Recommendations are given for choosing the value of the radial gap between the layers of wires. An algorithmic implementation of the method for searching for collisions of a geometric model of a steel rope in a non-interactive mode is shown. Approaches to the formation of procedures for processing collisions are proposed. Approaches presented in the article can be implemented in the form of software modules for execution in the Gmsh environment, as well as for another environment using the OpenCascade Core Technology geometric modeling kernel. Such modules allow automation of the construction of accurate geometric models of steel ropes in any configuration without fundamental restrictions on subsequent use, both stand-alone and in the form of objects (primitives) suitable for integration in a third-party model.

A method and a complex of computer programs are developed for the numerical simulation of the polaron states excitation process in condensed media. A numerical study of the polaron states formation in water under the action of the ultraviolet range laser irradiation is carried out. Our approach allows to reproduce the experimental data of the hydrated electrons formation. A numerical scheme is presented for the solution of the respective system of nonlinear partial differential equations. Parallel implementation is based on the MPI technique. The numerical results are given in comparison with the experimental data and theoretical estimations.

The article focuses on a nonlinear mathematical model that describes the interaction of the different age groups of the employed population. The interactions are treated by analogy with population relationship (competition, discrimination, assistance, oppression, etc). Under interaction of peoples we mean the generalized social and economic mechanisms that cause related changes in the number of employees of different age groups. Three age groups of the employed population are considered. It is young specialists (15–29 years), workers with experience (30–49 years), the employees of pre-retirement and retirement age (50 and older). The estimation of model’s parameters for the southern regions of the Far Eastern Federal District (FEFD) is executed by statistical data. Analysis of model scenarios allows us to conclude the observed number fluctuations of the different ages employees on the background of a stable total employed population may be a consequence of complex interactions between these groups of peoples. Computational experiments with the obtained values of the parameters allowed us to calculate the rate of decline and the aging of the working population and to determine the nature of the interaction between the age groups of employees that are not directly as reflected in the statistics. It was found that in FEFD the employed of 50 years and older are discriminated against by the young workers under 29, employed up to 29 and 30–49 years are in a partnership. It is shown in most developed regions (Primorsky and Khabarovsk Krai) there is “uniform” competition among different age groups of the employed population. For Primorsky Krai we were able to identify the mixing effect dynamics. It is a typical situation for systems in a state of structural adjustment. This effect is reflected in the fact the long cycles of employed population form with a significant decrease in migration inflows of employees 30–49 years. Besides, the change of migration is accompanied by a change of interaction type — from employment discrimination by the oldest of middle generation to discrimination by the middle of older generation. In less developed regions (Amur, Magadan and Jewish Autonomous Regions) there are lower values of migration balance of almost all age groups and discrimination by young workers up 29 years of other age groups and employment discrimination 30–49 years of the older generation.

One of the destroying natural processes is the initiation of the regional seismic activity. It leads to a large number of human deaths. Much effort has been made to develop precise and robust methods for the estimation of the seismic stability of buildings. One of the most common approaches is the natural frequency method. The obvious drawback of this approach is a low precision due to the model oversimplification. The other method is a detailed simulation of dynamic processes using the finite-element method. Unfortunately, the quality of simulations is not enough due to the difficulty of setting the correct free boundary condition. That is why the development of new numerical methods for seismic stability problems is a high priority nowadays.

The present work is devoted to the study of spatial dynamic processes occurring in geological medium during an earthquake. We describe a method for simulating seismic wave propagation from the hypocenter to the day surface. To describe physical processes, we use a system of partial differential equations for a linearly elastic body of the second order, which is solved numerically by a grid-characteristic method on parallelepiped meshes. The widely used geological hypocenter model, called the “double-couple” model, was incorporated into this numerical algorithm. In this case, any heterogeneities, such as geological layers with curvilinear boundaries, gas and fluid-filled cracks, fault planes, etc., may be explicitly taken into account.

In this paper, seismic waves emitted during the earthquake initiation process are numerically simulated. Two different models are used: the homogeneous half-space and the multilayered geological massif with the day surface. All of their parameters are set based on previously published scientific articles. The adequate coincidence of the simulation results is obtained. And discrepancies may be explained by differences in numerical methods used. The numerical approach described can be extended to more complex physical models of geological media.

The work is devoted to the construction of efficient and applicable to real tasks first-order methods of convex optimization, that is, using only values of the target function and its derivatives. Construction uses OGMG, fast gradient method which is optimal by complexity, but requires to know the Lipschitz constant for gradient and the strong convexity constant to determine the number of steps and step length. This requirement makes practical usage very hard. An adaptive on the constant for strong convexity algorithm ACGM is proposed, based on restarts of the OGM-G with update of the strong convexity constant estimate, and an adaptive on the Lipschitz constant for gradient ALGM, in which the use of OGM-G restarts is supplemented by the selection of the Lipschitz constant with verification of the smoothness conditions used in the universal gradient descent method. This eliminates the disadvantages of the original method associated with the need to know these constants, which makes practical usage possible. Optimality of estimates for the complexity of the constructed algorithms is proved. To verify the results obtained, experiments on model functions and real tasks from machine learning are carried out.

Buckling problems of thin elastic shells have become relevant again because of the discrepancies between the standards in many countries on how to estimate loads causing buckling of shallow shells and the results of the experiments on thinwalled aviation structures made of high-strength alloys. The main contradiction is as follows: the ultimate internal stresses at shell buckling (collapsing) turn out to be lower than the ones predicted by the adopted design theory used in the USA and European standards. The current regulations are based on the static theory of shallow shells that was put forward in the 1930s: within the nonlinear theory of elasticity for thin-walled structures there are stable solutions that significantly differ from the forms of equilibrium typical to small initial loads. The minimum load (the lowest critical load) when there is an alternative form of equilibrium was used as a maximum permissible one. In the 1970s it was recognized that this approach is unacceptable for complex loadings. Such cases were not practically relevant in the past while now they occur with thinner structures used under complex conditions. Therefore, the initial theory on bearing capacity assessments needs to be revised. The recent mathematical results that proved asymptotic proximity of the estimates based on two analyses (the three-dimensional dynamic theory of elasticity and the dynamic theory of shallow convex shells) could be used as a theory basis. This paper starts with the setting of the dynamic theory of shallow shells that comes down to one resolving integrodifferential equation (once the special Green function is constructed). It is shown that the obtained nonlinear equation allows for separation of variables and has numerous time-period solutions that meet the Duffing equation with “a soft spring”. This equation has been thoroughly studied; its numerical analysis enables finding an amplitude and an oscillation period depending on the properties of the Green function. If the shell is oscillated with the trial time-harmonic load, the movement of the surface points could be measured at the maximum amplitude. The study proposes an experimental set-up where resonance oscillations are generated with the trial load normal to the surface. The experimental measurements of the shell movements, the amplitude and the oscillation period make it possible to estimate the safety factor of the structure bearing capacity with non-destructive methods under operating conditions.

Dynamic game theoretic models of the corporative innovative development are investigated. The proposed models are based on concordance of private and public interests of agents. It is supposed that the structure of interests of each agent includes both private (personal interests) and public (interests of the whole company connected with its innovative development first) components. The agents allocate their personal resources between these two directions. The system dynamics is described by a difference (not differential) equation. The proposed model of innovative development is studied by simulation and the method of enumeration of the domains of feasible controls with a constant step. The main contribution of the paper consists in comparative analysis of efficiency of the methods of hierarchical control (compulsion or impulsion) for information structures of Stackelberg or Germeier (four structures) by means of the indices of system compatibility. The proposed model is a universal one and can be used for a scientifically grounded support of the programs of innovative development of any economic firm. The features of a specific company are considered in the process of model identification (a determination of the specific classes of model functions and numerical values of its parameters) which forms a separate complex problem and requires an analysis of the statistical data and expert estimations. The following assumptions about information rules of the hierarchical game are accepted: all players use open-loop strategies; the leader chooses and reports to the followers some values of administrative (compulsion) or economic (impulsion) control variables which can be only functions of time (Stackelberg games) or depend also on the followers’ controls (Germeier games); given the leader’s strategies all followers simultaneously and independently choose their strategies that gives a Nash equilibrium in the followers’ game. For a finite number of iterations the proposed algorithm of simulation modeling allows to build an approximate solution of the model or to conclude that it doesn’t exist. A reliability and efficiency of the proposed algorithm follow from the properties of the scenario method and the method of a direct ordered enumeration with a constant step. Some comprehensive conclusions about the comparative efficiency of methods of hierarchical control of innovations are received.