Computer research and modeling
“Computer Research and Modeling” is a peer-reviewed Russian journal publishing original research papers and review articles in the field of computer research and mathematical modeling in physics, engineering, biology, ecology, economics, psychology etc.
The journal is edited and published in the Institute of Computer Science jointly with the Department of Biophysics at the Biological Faculty of Lomonosov Moscow State University.
Frequency: 6 issues per year.
ISSN: 2076-7633 (Print), 2077-6853 (Online).
Co-Editors-in-Chief
G.Yu. Riznichenko, A.I. Lobanov
Editorial Board
M. Anand, J. Awrejcewicz, N. V. Belotelov, A. N. Beznosikov, I. V. Bruttan, B. N. Chetverushkin, E. Ya. Frisman, P. V. Fursova — managing editor, A. V. Gasnikov, R. Hildebrand, G. R. Ivanitskiy, Ya. A. Kholodov, S. S. Khruschev — managing editor, A. A. Kilin, V. M. Komarov, A. V. Maloletov, I. S. Mamaev, A. B. Medvinsky, N. A. Mitin, S. C. Muller, A. V. Olchev, I. B. Petrov, T. Yu. Plyusnina, A. A. Polezhaev — associate editor, A. B. Rubin, P. E. Ryabov, A. V. Shapovalov, F. S. Stonyakin, A. E. Varshavskiy, E. V. Vetchanin, V. V. Voevodin, V. A. Volpert, L. V. Yakushevich, V. I. Zalyapin.
Founders of the journal
Innopolis University
Izhevsk Institute of Computer Science
Publisher
Institute of Computer Science
Edição corrente
Volume 16, Nº 4 (2024)
Editor’s note



MATHEMATICAL MODELING AND NUMERICAL SIMULATION
Optimization of geometric analysis strategy in CAD-systems
Resumo
Computer-aided assembly planning for complex products is an important engineering and scientific problem. The assembly sequence and content of assembly operations largely depend on the mechanical structure and geometric properties of a product. An overview of geometric modeling methods that are used in modern computer-aided design systems is provided. Modeling geometric obstacles in assembly using collision detection, motion planning, and virtual reality is very computationally intensive. Combinatorial methods provide only weak necessary conditions for geometric reasoning. The important problem of minimizing the number of geometric tests during the synthesis of assembly operations and processes is considered. A formalization of this problem is based on a hypergraph model of the mechanical structure of the product. This model provides a correct mathematical description of coherent and sequential assembly operations. The key concept of the geometric situation is introduced. This is a configuration of product parts that requires analysis for freedom from obstacles and this analysis gives interpretable results. A mathematical description of geometric heredity during the assembly of complex products is proposed. Two axioms of heredity allow us to extend the results of testing one geometric situation to many other situations. The problem of minimizing the number of geometric tests is posed as a non-antagonistic game between decision maker and nature, in which it is required to color the vertices of an ordered set in two colors. The vertices represent geometric situations, and the color is a metaphor for the result of a collision-free test. The decision maker’s move is to select an uncolored vertex; nature’s answer is its color. The game requires you to color an ordered set in a minimum number of moves by decision maker. The project situation in which the decision maker makes a decision under risk conditions is discussed. A method for calculating the probabilities of coloring the vertices of an ordered set is proposed. The basic pure strategies of rational behavior in this game are described. An original synthetic criterion for making rational decisions under risk conditions has been developed. Two heuristics are proposed that can be used to color ordered sets of high cardinality and complex structure.



NUMERICAL METHODS AND THE BASIS FOR THEIR APPLICATION
Noise removal from images using the proposed three-term conjugate gradient algorithm
Resumo
Conjugate gradient algorithms represent an important class of unconstrained optimization algorithms with strong local and global convergence properties and simple memory requirements. These algorithms have advantages that place them between the steep regression method and Newton’s algorithm because they require calculating the first derivatives only and do not require calculating and storing the second derivatives that Newton’s algorithm needs. They are also faster than the steep descent algorithm, meaning that they have overcome the slow convergence of this algorithm, and it does not need to calculate the Hessian matrix or any of its approximations, so it is widely used in optimization applications. This study proposes a novel method for image restoration by fusing the convex combination method with the hybrid (CG) method to create a hybrid three-term (CG) algorithm. Combining the features of both the Fletcher and Revees (FR) conjugate parameter and the hybrid Fletcher and Revees (FR), we get the search direction conjugate parameter. The search direction is the result of concatenating the gradient direction, the previous search direction, and the gradient from the previous iteration. We have shown that the new algorithm possesses the properties of global convergence and descent when using an inexact search line, relying on the standard Wolfe conditions, and using some assumptions. To guarantee the effectiveness of the suggested algorithm and processing image restoration problems. The numerical results of the new algorithm show high efficiency and accuracy in image restoration and speed of convergence when used in image restoration problems compared to Fletcher and Revees (FR) and three-term Fletcher and Revees (TTFR).



MODELS IN PHYSICS AND TECHNOLOGY
Localized nonlinear waves of the sine-Gordon equation in a model with three extended impurities
Resumo
In this work, we use analytical and numerical methods to consider the problem of the structure and dynamics of coupled localized nonlinear waves in the sine-Gordon model with three identical attractive extended “impurities”, which are modeled by spatial inhomogeneity of the periodic potential. Two possible types of coupled nonlinear localized waves are found: breather and soliton. The influence of system parameters and initial conditions on the structure, amplitude, and frequency of localized waves was analyzed. Associated oscillations of localized waves of the breather type as in the case of point impurities, are the sum of three harmonic oscillations: in-phase, in-phase-antiphase and antiphase type. Frequency analysis of impurity-localized waves that were obtained during a numerical experiment was performed using discrete Fourier transform. To analyze localized breather-type waves, the numerical finite difference method was used. To carry out a qualitative analysis of the obtained numerical results, the problem was solved analytically for the case of small amplitudes of oscillations localized on impurities. It is shown that, for certain impurity parameters (depth and width), it is possible to obtain localized solitontype waves. The ranges of values of the system parameters in which localized waves of a certain type exist, as well as the region of transition from breather to soliton types of oscillations, have been found. The values of the depth and width of the impurity at which a transition from the breather to the soliton type of localized oscillations is observed were determined. Various scenarios of soliton-type oscillations with negative and positive amplitude values for all three impurities, as well as mixed cases, were obtained and considered. It is shown that in the case when the distance between impurities much less than one, there is no transition region where which the nascent breather, after losing energy through radiation, transforms into a soliton. It is shown that the considered model can be used, for example, to describe the dynamics of magnetization waves in multilayer magnets.



The influence of tail fins on the speed of an aquatic robot driven by internal moving masses
Resumo
This paper describes the design of an aquatic robot moving on the surface of a fluid and driven by two internal moving masses. The body of the aquatic robot in cross section has the shape of a symmetrical airfoil with a sharp edge. In this prototype, two internal masses move in circles and are rotated by a single DC motor and a gear mechanism that transmits torque from the motor to each mass. Angular velocities of moving masses are used as a control action, and the developed kinematic scheme for transmitting rotation from the motor to the moving masses allows the rotation of two masses with equal angular velocities in magnitude, but with a different direction of rotation. It is also possible to install additional tail fins of various shapes and sizes on the body of this robot. Also in the work for this object, the equations of motion are presented, written in the form of Kirchhoff equations for the motion of a solid body in an ideal fluid, which are supplemented by terms of viscous resistance. A mathematical description of the additional forces acting on the flexible tail fin is presented. Experimental studies on the influence of various tail fins on the speed of motion in the fluid were carried out with the developed prototype of the robot. In this work, tail fins of the same shape and size were installed on the robot, while having different stiffness. The experiments were carried out in a pool with water, over which a camera was installed, on which video recordings of all the experiments were obtained. Next processing of the video recordings made it possible to obtain the object’s movements coordinates, as well as its linear and angular velocities. The paper shows the difference in the velocities developed by the robot when moving without a tail fin, as well as with tail fins having different stiffness. The comparison of the velocities developed by the robot, obtained in experimental studies, with the results of mathematical modeling of the system is given.



Ñhaotic flow evolution arising in a body force field
Resumo
This article presents the results of an analytical and computer study of the chaotic evolution of a regular velocity field generated by a large-scale harmonic forcing. The authors obtained an analytical solution for the flow stream function and its derivative quantities (velocity, vorticity, kinetic energy, enstrophy and palinstrophy). Numerical modeling of the flow evolution was carried out using the OpenFOAM software package based on incompressible model, as well as two inhouse implementations of CABARET and McCormack methods employing nearly incompressible formulation. Calculations were carried out on a sequence of nested meshes with $64^2, 128^2, 256^2, 512^2, 1024^2$ cells for two characteristic (asymptotic) Reynolds numbers characterizing laminar and turbulent evolution of the flow, respectively. Simulations show that blow-up of the analytical solution takes place in both cases. The energy characteristics of the flow are discussed relying upon the energy curves as well as the dissipation rates. For the fine mesh, this quantity turns out to be several orders of magnitude less than its hydrodynamic (viscous) counterpart. Destruction of the regular flow structure is observed for any of the numerical methods, including at the late stages of laminar evolution, when numerically obtained distributions are close to analytics. It can be assumed that the prerequisite for the development of instability is the error accumulated during the calculation process. This error leads to unevenness in the distribution of vorticity and, as a consequence, to the variance vortex intensity and finally leads to chaotization of the flow. To study the processes of vorticity production, we used two integral vorticity-based quantities — integral enstrophy ($\zeta$) and palinstrophy ($P$). The formulation of the problem with periodic boundary conditions allows us to establish a simple connection between these quantities. In addition, $\zeta$ can act as a measure of the eddy resolution of the numerical method, and palinstrophy determines the degree of production of small-scale vorticity.



Simulation of two-phase flow in porous media using an inhomogeneous network model
Resumo
We present an inhomogeneous two-dimensional network model of two-phase flow in porous media. The edges of the network are assumed to be capillary tubes of different radii. We propose a new algorithm for handling phase fluxes at the nodes of this network model. We perform two test problems and show that the two-phase flow in this inhomogeneous network model demonstrates properties that are analogous to those of real porous media: capillary imbibition, dependence of capillary pressure on saturation and effect of capillary forces in two-phase displacement. The two test problems are: the counter-current imbibition and the twophase displacement in a periodically inhomogeneous porous medium. In the former problem, we implement a network consisting of two regions: a region of low-permeability with thin capillaries surrounded by a region of high-permeability with thick capillaries, initially saturated with wetting and nonwetting incompressible fluids, respectively. Capillary equilibrium is established due to counter-current imbibition by a region. We examine the dependence: of saturation of the wetting fluid with respect to time in the regions, and of capillary pressure on the current saturation. We have obtained a qualitative agreement with the known experimental and theoretical results, which will further allow us to use this network model to verify homogenized models of capillary nonequilibrium. In the latter problem, we consider the two-phase displacement, where the network is initially saturated with nonwetting fluid. Then wetting fluid is injected through a boundary at a constant rate. We analyze the saturation with respect to the axis which is along the applied pressure gradient for various moments in time with various values of coefficients of surface tension. The results show that for lower values of coefficient of surface tension, the wetting fluid prefers to invade through the thicker tubes, and in the case of higher values, through thinner tubes.



Image classification based on deep learning with automatic relevance determination and structured Bayesian pruning
Resumo
Deep learning’s power stems from complex architectures; however, these can lead to overfitting, where models memorize training data and fail to generalize to unseen examples. This paper proposes a novel probabilistic approach to mitigate this issue. We introduce two key elements: Truncated Log-Uniform Prior and Truncated Log-Normal Variational Approximation, and Automatic Relevance Determination (ARD) with Bayesian Deep Neural Networks (BDNNs). Within the probabilistic framework, we employ a specially designed truncated log-uniform prior for noise. This prior acts as a regularizer, guiding the learning process towards simpler solutions and reducing overfitting. Additionally, a truncated log-normal variational approximation is used for efficient handling of the complex probability distributions inherent in deep learning models. ARD automatically identifies and removes irrelevant features or weights within a model. By integrating ARD with BDNNs, where weights have a probability distribution, we achieve a variational bound similar to the popular variational dropout technique. Dropout randomly drops neurons during training, encouraging the model not to rely heavily on any single feature. Our approach with ARD achieves similar benefits without the randomness of dropout, potentially leading to more stable training.To evaluate our approach, we have tested the model on two datasets: the Canadian Institute For Advanced Research (CIFAR-10) for image classification and a dataset of Macroscopic Images of Wood, which is compiled from multiple macroscopic images of wood datasets. Our method is applied to established architectures like Visual Geometry Group (VGG) and Residual Network (ResNet). The results demonstrate significant improvements. The model reduced overfitting while maintaining, or even improving, the accuracy of the network’s predictions on classification tasks. This validates the effectiveness of our approach in enhancing the performance and generalization capabilities of deep learning models.



Analysis of predictive properties of ground tremor using Huang decomposition
Resumo
A method is proposed for analyzing the tremor of the earth’s surface, measured by means of space geodesy, in order to highlight the prognostic effects of seismicity activation. The method is illustrated by the example of a joint analysis of a set of synchronous time series of daily vertical displacements of the earth’s surface on the Japanese Islands for the time interval 2009–2023. The analysis is based on dividing the source data (1047 time series) into blocks (clusters of stations) and sequentially applying the principal component method. The station network is divided into clusters using the K-means method from the maximum pseudo-F-statistics criterion, and for Japan the optimal number of clusters was chosen to be 15. The Huang decomposition method into a sequence of independent empirical oscillation modes (EMD — Empirical Mode Decomposition) is applied to the time series of principal components from station blocks. To provide the stability of estimates of the waveforms of the EMD decomposition, averaging of 1000 independent additive realizations of white noise of limited amplitude was performed. Using the Cholesky decomposition of the covariance matrix of the waveforms of the first three EMD components in a sliding time window, indicators of abnormal tremor behavior were determined. By calculating the correlation function between the average indicators of anomalous behavior and the released seismic energy in the vicinity of the Japanese Islands, it was established that bursts in the measure of anomalous tremor behavior precede emissions of seismic energy. The purpose of the article is to clarify common hypotheses that movements of the earth’s crust recorded by space geodesy may contain predictive information. That displacements recorded by geodetic methods respond to the effects of earthquakes is widely known and has been demonstrated many times. But isolating geodetic effects that predict seismic events is much more challenging. In our paper, we propose one method for detecting predictive effects in space geodesy data.



ANALYSIS AND MODELING OF COMPLEX LIVING SYSTEMS
Stochastic transitions from order to chaos in a metapopulation model with migration
Resumo
This paper focuses on the problem of modeling and analyzing dynamic regimes, both regular and chaotic, in systems of coupled populations in the presence of random disturbances. The discrete Ricker model is used as the initial deterministic population model. The paper examines the dynamics of two populations coupled by migration. Migration is proportional to the difference between the densities of two populations with a coupling coefficient responsible for the strength of the migration flow. Isolated population subsystems, modeled by the Ricker map, exhibit various dynamic modes, including equilibrium, periodic, and chaotic ones. In this study, the coupling coefficient is treated as a bifurcation parameter and the parameters of natural population growth rate remain fixed. Under these conditions, one subsystem is in the equilibrium mode, while the other exhibits chaotic behavior. The coupling of two populations through migration creates new dynamic regimes, which were not observed in the isolated model. This article aims to analyze the dynamics of corporate systems with variations in the flow intensity between population subsystems. The article presents a bifurcation analysis of the attractors in a deterministic model of two coupled populations, identifies zones of monostability and bistability, and gives examples of regular and chaotic attractors. The main focus of the work is in comparing the stability of dynamic regimes against random disturbances in the migration intensity. Noise-induced transitions from a periodic attractor to a chaotic attractor are identified and described using direct numerical simulation methods. The Lyapunov exponents are used to analyze stochastic phenomena. It has been shown that in this model, there is a region of change in the bifurcation parameter in which, even with an increase in the intensity of random perturbations, there is no transition from order to chaos. For the analytical study of noise-induced transitions, the stochastic sensitivity function technique and the confidence domain method are used. The paper demonstrates how this mathematical tool can be employed to predict the critical noise intensity that causes a periodic regime to transform into a chaotic one.



Current issues in computational modeling of thrombosis, fibrinolysis, and thrombolysis
Resumo
Hemostasis system is one of the key body’s defense systems, which is presented in all the liquid tissues and especially important in blood. Hemostatic response is triggered as a result of the vessel injury. The interaction between specialized cells and humoral systems leads to the formation of the initial hemostatic clot, which stops bleeding. After that the slow process of clot dissolution occurs. The formation of hemostatic plug is a unique physiological process, because during several minutes the hemostatic system generates complex structures on a scale ranging from microns for microvessel injury or damaged endothelial cell-cell contacts, to centimeters for damaged systemic arteries. Hemostatic response depends on the numerous coordinated processes, which include platelet adhesion and aggregation, granule secretion, platelet shape change, modification of the chemical composition of the lipid bilayer, clot contraction, and formation of the fibrin mesh due to activation of blood coagulation cascade. Computer modeling is a powerful tool, which is used to study this complex system at different levels of organization. This includes study of intracellular signaling in platelets, modelling humoral systems of blood coagulation and fibrinolysis, and development of the multiscale models of thrombus growth. There are two key issues of the computer modeling in biology: absence of the adequate physico-mathematical description of the existing experimental data due to the complexity of the biological processes, and high computational complexity of the models, which doesn’t allow to use them to test physiologically relevant scenarios. Here we discuss some key unresolved problems in the field, as well as the current progress in experimental research of hemostasis and thrombosis. New findings lead to reevaluation of the existing concepts and development of the novel computer models. We focus on the arterial thrombosis, venous thrombosis, thrombosis in microcirculation and the problems of fibrinolysis and thrombolysis. We also briefly discuss basic types of the existing mathematical models, their computational complexity, and principal issues in simulation of thrombus growth in arteries.



Analysis of the rate of electron transport through photosynthetic cytochrome $b_{6}f$ complex
Resumo
We consider an approach based on linear algebra methods to analyze the rate of electron transport through the cytochrome $b_{6}f$ complex. In the proposed approach, the dependence of the quasi-stationary electron flux through the complex on the degree of reduction of pools of mobile electron carriers is considered a response function characterizing this process. We have developed software in the Python programming language that allows us to construct the master equation for the complex according to the scheme of elementary reactions and calculate quasi-stationary electron transport rates through the complex and the dynamics of their changes during the transition process. The calculations are performed in multithreaded mode, which makes it possible to efficiently use the resources of modern computing systems and to obtain data on the functioning of the complex in a wide range of parameters in a relatively short time. The proposed approach can be easily adapted for the analysis of electron transport in other components of the photosynthetic and respiratory electron-transport chain, as well as other processes in multienzyme complexes containing several reaction centers. Cryo-electron microscopy and redox titration data were used to parameterize the model of cytochrome $b_{6}f$ complex. We obtained dependences of the quasi-stationary rate of plastocyanin reduction and plastoquinone oxidation on the degree of reduction of pools of mobile electron carriers and analyzed the dynamics of rate changes in response to changes in the redox state of the plastoquinone pool. The modeling results are in good agreement with the available experimental data.



MODELS OF ECONOMIC AND SOCIAL SYSTEMS
Assessing the impact of deposit benchmark interest rate on banking loan dynamics
Resumo
Deposit benchmark interest rates are a policy implemented by banking regulators to calculate the interest rates offered to depositors, maintaining equitable and competitive rates within the financial industry. It functions as a benchmark for determining the pricing of different banking products, expenses, and financial choices. The benchmark rate will have a direct impact on the amount of money deposited, which in turn will determine the amount of money available for lending.We are motivated to analyze the influence of deposit benchmark interest rates on the dynamics of banking loans. This study examines the issue using a difference equation of banking loans. In this process, the decision on the loan amount in the next period is influenced by both the present loan volume and the information on its marginal profit. An analysis is made of the loan equilibrium point and its stability. We also analyze the bifurcations that arise in the model. To ensure a stable banking loan, it is necessary to set the benchmark rate higher than the flip value and lower than the transcritical bifurcation values. The confirmation of this result is supported by the bifurcation diagram and its associated Lyapunov exponent. Insufficient deposit benchmark interest rates might lead to chaotic dynamics in banking lending. Additionally, a bifurcation diagram with two parameters is also shown. We do numerical sensitivity analysis by examining contour plots of the stability requirements, which vary with the deposit benchmark interest rate and other parameters. In addition, we examine a nonstandard difference approach for the previous model, assess its stability, and make a comparison with the standard model. The outcome of our study can provide valuable insights to the banking regulator in making informed decisions regarding deposit benchmark interest rates, taking into account several other banking factors.


