All issues

To research dynamics of inhomogeneous polynucleotide DNA chain the Y-model with no dissipation term was used. Basing on this model using numerical methods calculations were carried out, which have shown the behaviour of nonlinear conformational excitation (kink), spreading along the inhomogeneous polynucleotide chain, consisting of two different homogeneous nucleotide sequences. As numerical analysis shows there are three ways of behaviour of the nonlinear kink excitation spreading along the DNA chain. After reaching the interface between two homogeneous sequences consisting of different types of bases kink can a) reflect, b) pass the interface with acceleration (increase its velocity), c) pass the interface with deceleration (decrease its velocity).

The article covered results of three-dimensional modeling of ecologic situation of shallow water on the example of the Azov Sea with using schemes of increased order of accuracy on multiprocessor computer system of Southern Federal University. Discrete analogs of convective and diffusive transfer operators of the fourth order of accuracy in the case of partial occupancy of cells were constructed and studied. The developed scheme of the high (fourth) order of accuracy were used for solving problems of aquatic ecology and modeling spatial distribution of polluting nutrients, which caused growth of phytoplankton, many species of which are toxic and harmful. The use of schemes of the high order of accuracy are improved the quality of input data and decreased the error in solutions of model tasks of aquatic ecology. Numerical experiments were conducted for the problem of transportation of substances on the basis of the schemes of the second and fourth orders of accuracy. They’re showed that the accuracy was increased in 48.7 times for diffusion-convection problem. The mathematical algorithm was proposed and numerically implemented, which designed to restore the bottom topography of shallow water on the basis of hydrographic data (water depth at individual points or contour level). The map of bottom relief of the Azov Sea was generated with using this algorithm. It’s used to build fields of currents calculated on the basis of hydrodynamic model. The fields of water flow currents were used as input data of the aquatic ecology models. The library of double-layered iterative methods was developed for solving of nine-diagonal difference equations. It occurs in discretization of model tasks of challenges of pollutants concentration, plankton and fish on multiprocessor computer system. It improved the precision of the calculated data and gave the possibility to obtain operational forecasts of changes in ecologic situation of shallow water in short time intervals.

The Lipschitz continuous property has been used for a long time to solve the global optimization problem and continues to be used. Here we can mention the work of Piyavskii, Yevtushenko, Strongin, Shubert, Sergeyev, Kvasov and others. Most papers assume a priori knowledge of the Lipschitz constant, but the derivation of this constant is a separate problem. Further still, we must prove that an objective function is really Lipschitz, and it is a complicated problem too. In the case where the Lipschitz continuity is established, Strongin proposed an algorithm for global optimization of a satisfying Lipschitz condition on a compact interval function without any a priori knowledge of the Lipschitz estimate. The algorithm not only finds a global extremum, but it determines the Lipschitz estimate too. It is known that every function that satisfies the Lipchitz condition on a compact convex set is uniformly continuous, but the reverse is not always true. However, there exist models (Arutyunova, Dulliev, Zabotin) whose study requires a minimization of the continuous but definitely not Lipschitz function. One of the algorithms for solving such a problem was proposed by R. J. Vanderbei. In his work he introduced some generalization of the Lipchitz property named $\varepsilon$-Lipchitz and proved that a function defined on a compact convex set is uniformly continuous if and only if it satisfies the $\varepsilon$-Lipchitz condition. The above-mentioned property allowed him to extend Piyavskii’s method. However, Vanderbei assumed that for a given value of $\varepsilon$ it is possible to obtain an associate Lipschitz $\varepsilon$-constant, which is a very difficult problem. Thus, there is a need to construct, for a function continuous on a compact convex domain, a global optimization algorithm which works in some way like Strongin’s algorithm, i.e., without any a priori knowledge of the Lipschitz $\varepsilon$-constant. In this paper we propose an extension of Strongin’s global optimization algorithm to a function continuous on a compact interval using the $\varepsilon$-Lipchitz conception, prove its convergence and solve some numerical examples using the software that implements the developed method.

The article is devoted to the application of various methods of mathematical analysis, search for patterns and studying the composition of nucleotides in DNA sequences at the genomic level. New methods of mathematical biology that made it possible to detect and visualize the hidden ordering of genetic nucleotide sequences located in the chromosomes of cells of living organisms described. The research was based on the work on algebraic biology of the doctor of physical and mathematical sciences S. V. Petukhov, who first introduced and justified new algebras and hypercomplex numerical systems describing genetic phenomena. This paper describes a new phase in the development of matrix methods in genetics for studying the properties of nucleotide sequences (and their physicochemical parameters), built on the principles of finite geometry. The aim of the study is to demonstrate the capabilities of new algorithms and discuss the discovered properties of genetic DNA and RNA molecules. The study includes three stages: parameterization, scaling, and visualization. Parametrization is the determination of the parameters taken into account, which are based on the structural and physicochemical properties of nucleotides as elementary components of the genome. Scaling plays the role of “focusing” and allows you to explore genetic structures at various scales. Visualization includes the selection of the axes of the coordinate system and the method of visual display. The algorithms presented in this work are put forward as a new toolkit for the development of research software for the analysis of long nucleotide sequences with the ability to display genomes in parametric spaces of various dimensions. One of the significant results of the study is that new criteria were obtained for the classification of the genomes of various living organisms to identify interspecific relationships. The new concept allows visually and numerically assessing the variability of the physicochemical parameters of nucleotide sequences. This concept also allows one to substantiate the relationship between the parameters of DNA and RNA molecules with fractal geometric mosaics, reveals the ordering and symmetry of polynucleotides, as well as their noise immunity. The results obtained justified the introduction of new terms: “genometry” as a methodology of computational strategies and “genometrica” as specific parameters of a particular genome or nucleotide sequence. In connection with the results obtained, biosemiotics and hierarchical levels of organization of living matter are raised.

In this paper we consider mathematical model to control water quality. We study a system with two-level hierarchy: one environmental organization (supervisor) at the top level and a few industrial enterprises (agents) at the lower level. The main goal of the supervisor is to keep water pollution level below certain value, while enterprises pollute water, as a side effect of the manufacturing process. Supervisor achieves its goal by charging a penalty for enterprises. On the other hand, enterprises choose how much to purify their wastewater to maximize their income.The fee increases the budget of the supervisor. Moreover, effulent fees are charged for the quantity and/or quality of the discharged pollution. Unfortunately, in practice, such charges are ineffective due to the insufficient tax size. The article solves the problem of determining the optimal size of the charge for pollution discharge, which allows maintaining the quality of river water in the rear range.

We describe system members goals with target functionals, and describe water pollution level and enterprises state as system of ordinary differential equations. We consider the problem from both supervisor and enterprises sides. From agents’ point a normal-form game arises, where we search for Nash equilibrium and for the supervisor, we search for Stackelberg equilibrium. We propose numerical algorithms for finding both Nash and Stackelberg equilibrium. When we construct Nash equilibrium, we solve optimal control problem using Pontryagin’s maximum principle. We construct Hamilton’s function and solve corresponding system of partial differential equations with shooting method and finite difference method. Numerical calculations show that the low penalty for enterprises results in increasing pollution level, when relatively high penalty can result in enterprises bankruptcy. This leads to the problem of choosing optimal penalty, which requires considering problem from the supervisor point. In that case we use the method of qualitatively representative scenarios for supervisor and Pontryagin’s maximum principle for agents to find optimal control for the system. At last, we compute system consistency ratio and test algorithms for different data. The results show that a hierarchical control is required to provide system stability.

A simplified implicit Euler method was analyzed as an alternative to the explicit Euler method, which is a commonly used method in numerical modeling in electrophysiology. The majority of electrophysiological models are quite stiff, since the dynamics they describe includes a wide spectrum of time scales: a fast depolarization, that lasts milliseconds, precedes a considerably slow repolarization, with both being the fractions of the action potential observed in excitable cells. In this work we estimate stiffness by a formula that does not require calculation of eigenvalues of the Jacobian matrix of the studied ODEs. The efficiency of the numerical methods was compared on the case of typical representatives of detailed and conceptual type models of excitable cells: Hodgkin–Huxley model of a neuron and Aliev–Panfilov model of a cardiomyocyte. The comparison of the efficiency of the numerical methods was carried out via norms that were widely used in biomedical applications. The stiffness ratio’s impact on the speedup of simplified implicit method was studied: a real gain in speed was obtained for the Hodgkin–Huxley model. The benefits of the usage of simple and high-order methods for electrophysiological models are discussed along with the discussion of one method’s stability issues. The reasons for using simplified instead of high-order methods during practical simulations were discussed in the corresponding section. We calculated higher order derivatives of the solutions of Hodgkin-Huxley model with various stiffness ratios; their maximum absolute values appeared to be quite large. A numerical method’s approximation constant’s formula contains the latter and hence ruins the effect of the other term (a small factor which depends on the order of approximation). This leads to the large value of global error. We committed a qualitative stability analysis of the explicit Euler method and were able to estimate the model’s parameters influence on the border of the region of absolute stability. The latter is used when setting the value of the timestep for simulations a priori.

One of problems in developing the gas condensate fields lies on the fact that the condensed hydrocarbons in the gas-bearing layer can get stuck in the pores of the formation and hence cannot be extracted. In this regard, research is underway to increase the recoverability of hydrocarbons in such fields. This research includes a wide range of studies on mathematical simulations of the passage of gas condensate mixtures through a porous medium under various conditions.

In the present work, within the classical approach based on the Darcy law and the law of continuity of flows, we formulate an initial-boundary value problem for a system of nonlinear differential equations that describes a depletion of a multicomponent gas-condensate mixture in porous reservoir. A computational scheme is developed on the basis of the finite-difference approximation and the fourth order Runge .Kutta method. The scheme can be used for simulations both in the spatially one-dimensional case, corresponding to the conditions of the laboratory experiment, and in the two-dimensional case, when it comes to modeling a flat gas-bearing formation with circular symmetry.

The computer implementation is based on the combination of C++ and Maple tools, using the MPI parallel programming technique to speed up the calculations. The calculations were performed on the HybriLIT cluster of the Multifunctional Information and Computing Complex of the Laboratory of Information Technologies of the Joint Institute for Nuclear Research.

Numerical results are compared with the experimental data on the pressure dependence of output of a ninecomponent hydrocarbon mixture obtained at a laboratory facility (VNIIGAZ, Ukhta). The calculations were performed for two types of porous filler in the laboratory model of the formation: terrigenous filler at 25 .„R and carbonate one at 60 .„R. It is shown that the approach developed ensures an agreement of the numerical results with experimental data. By fitting of numerical results to experimental data on the depletion of the laboratory reservoir, we obtained the values of the parameters that determine the inter-phase transition coefficient for the simulated system. Using the same parameters, a computer simulation of the depletion of a thin gas-bearing layer in the circular symmetry approximation was carried out.

Represented study considers numerical simulation of corium cooling driven by natural convection within a horizontal hemicylindrical cavity, boundaries of which are assumed isothermal. Corium is a melt of ceramic fuel of a nuclear reactor and oxides of construction materials.

Corium cooling is a process occurring during severe accident associated with core melt. According to invessel retention conception, the accident may be restrained and localized, if the corium is contained within the vessel, only if it is cooled externally. This conception has a clear advantage over the melt trap, it can be implemented at already operating nuclear power plants. Thereby proper numerical analysis of the corium cooling has become such a relevant area of studies.

In the research, we assume the corium is contained within a horizontal semitube. The corium initially has temperature of the walls. In spite of reactor shutdown, the corium still generates heat owing to radioactive decays, and the amount of heat released decreases with time accordingly to Way–Wigner formula. The system of equations in Boussinesq approximation including momentum equation, continuity equation and energy equation, describes the natural convection within the cavity. Convective flows are taken to be laminar and two-dimensional.

The boundary-value problem of mathematical physics is formulated using the non-dimensional nonprimitive variables «stream function – vorticity». The obtained differential equations are solved numerically using the finite difference method and locally one-dimensional Samarskii scheme for the equations of parabolic type.

As a result of the present research, we have obtained the time behavior of mean Nusselt number at top and bottom walls for Rayleigh number ranged from 10³ to 10⁶. These mentioned dependences have been analyzed for various dimensionless operation periods before the accident. Investigations have been performed using streamlines and isotherms as well as time dependences for convective flow and heat transfer rates.

The article presents the numerical modeling and study of the kinetic model of propane pyrolysis. The study of the reaction kinetics is a necessary stage in modeling the dynamics of the gas flow in the reactor.

The kinetic model of propane pyrolysis is a nonlinear system of ordinary differential equations of the first order with parameters, the role of which is played by the reaction rate constants. Math modeling of processes is based on the use of the mass conservation law. To solve an initial (forward) problem, implicit methods for solving stiff ordinary differential equation systems are used. The model contains 60 input kinetic parameters and 17 output parameters corresponding to the reaction substances, of which only 9 are observable. In the process of solving the problem of estimating parameters (inverse problem), there is a question of non-uniqueness of the set of parameters that satisfy the experimental data. Therefore, before solving the inverse problem, the possibility of determining the parameters of the model is analyzed (analysis of identifiability).

To analyze identifiability, we use the orthogonal method, which has proven itself well for analyzing models with a large number of parameters. The algorithm is based on the analysis of the sensitivity matrix by the methods of differential and linear algebra, which shows the degree of dependence of the unknown parameters of the models on the given measurements. The analysis of sensitivity and identifiability showed that the parameters of the model are stably determined from a given set of experimental data. The article presents a list of model parameters from most to least identifiable. Taking into account the analysis of the identifiability of the mathematical model, restrictions were introduced on the search for less identifiable parameters when solving the inverse problem.

The inverse problem of estimating the parameters was solved using a genetic algorithm. The article presents the found optimal values of the kinetic parameters. A comparison of the experimental and calculated dependences of the concentrations of propane, main and by-products of the reaction on temperature for different flow rates of the mixture is presented. The conclusion about the adequacy of the constructed mathematical model is made on the basis of the correspondence of the results obtained to physicochemical laws and experimental data.

Social media is a crucial indicator of the position of assets in the financial market. The paper describes the rigid solution for the classification problem to determine the influence of social media activity on financial market movements. Reputable crypto traders influencers are selected. Twitter posts packages are used as data. The methods of text, which are characterized by the numerous use of slang words and abbreviations, and preprocessing consist in lemmatization of Stanza and the use of regular expressions. A word is considered as an element of a vector of a data unit in the course of solving the problem of binary classification. The best markup parameters for processing Binance candles are searched for. Methods of feature selection, which is necessary for a precise description of text data and the subsequent process of establishing dependence, are represented by machine learning and statistical analysis. First, the feature selection is used based on the information criterion. This approach is implemented in a random forest model and is relevant for the task of feature selection for splitting nodes in a decision tree. The second one is based on the rigid compilation of a binary vector during a rough check of the presence or absence of a word in the package and counting the sum of the elements of this vector. Then a decision is made depending on the superiority of this sum over the threshold value that is predetermined previously by analyzing the frequency distribution of mentions of the word. The algorithm used to solve the problem was named benchmark and analyzed as a tool. Similar algorithms are often used in automated trading strategies. In the course of the study, observations of the influence of frequently occurring words, which are used as a basis of dimension 2 and 3 in vectorization, are described as well.