All issues

A vector-matrix approach to the theoretical design of metabolic pathways converting chemical compounds, viz., preset substrates, into desirable products is described. It is a mathematical basis for computer–aided generation of alternative biochemical reaction sets executing the given substrate–product conversion. The pathways are retrieved from the used database of biochemical reactions and utilize the reaction stoichiometry and restrictions based on the irreversibility of a part of them. Particular attention is paid to the analysis of restriction interrelations. It is shown that the number of restrictions can be notably reduced due to the existence of families of parallel restricting planes in the space of reaction flows. Coinciding planes of contradirectional restrictions result in the existence of fixed reaction flow values. The problem of exclusion of so called futile cycles is also considered. Utilization of these factors allows essential lowering of the problem complexity and necessary computational resources. An example of alternative biochemical pathway computation for conversion of glucose and glycerol into succinic acid is given. It is found that for a preset “substrate–product” pair many pathways have the same high-energy bond balance.

The paper considers mathematical modeling of layered Benard–Marangoni convection of a viscous incompressible fluid. The fluid moves in an infinitely extended layer. The Oberbeck–Boussinesq system describing layered Benard–Marangoni convection is overdetermined, since the vertical velocity is zero identically. We have a system of five equations to calculate two components of the velocity vector, temperature and pressure (three equations of impulse conservation, the incompressibility equation and the heat equation). A class of exact solutions is proposed for the solvability of the Oberbeck–Boussinesq system. The structure of the proposed solution is such that the incompressibility equation is satisfied identically. Thus, it is possible to eliminate the «extra» equation. The emphasis is on the study of heat exchange on the free layer boundary, which is considered rigid. In the description of thermocapillary convective motion, heat exchange is set according to the Newton’s law of cooling. The application of this heat distribution law leads to the third-kind initial-boundary value problem. It is shown that within the presented class of exact solutions to the Oberbeck–Boussinesq equations the overdetermined initial-boundary value problem is reduced to the Sturm–Liouville problem. Consequently, the hydrodynamic fields are expressed using trigonometric functions (the Fourier basis). A transcendental equation is obtained to determine the eigenvalues of the problem. This equation is solved numerically. The numerical analysis of the solutions of the system of evolutionary and gradient equations describing fluid flow is executed. Hydrodynamic fields are analyzed by a computational experiment. The existence of counterflows in the fluid layer is shown in the study of the boundary value problem. The existence of counterflows is equivalent to the presence of stagnation points in the fluid, and this testifies to the existence of a local extremum of the kinetic energy of the fluid. It has been established that each velocity component cannot have more than one zero value. Thus, the fluid flow is separated into two zones. The tangential stresses have different signs in these zones. Moreover, there is a fluid layer thickness at which the tangential stresses at the liquid layer equal to zero on the lower boundary. This physical effect is possible only for Newtonian fluids. The temperature and pressure fields have the same properties as velocities. All the nonstationary solutions approach the steady state in this case.

In this paper we consider the controlled motion of a helical body with three blades in an ideal fluid, which is executed by rotating three internal rotors. We set the problem of selecting control actions, which ensure the motion of the body near the predetermined trajectory. To determine controls that guarantee motion near the given curve, we propose methods based on the application of hybrid genetic algorithms (genetic algorithms with real encoding and with additional learning of the leader of the population by a gradient method) and artificial neural networks. The correctness of the operation of the proposed numerical methods is estimated using previously obtained differential equations, which define the law of changing the control actions for the predetermined trajectory.

In the approach based on hybrid genetic algorithms, the initial problem of minimizing the integral functional reduces to minimizing the function of many variables. The given time interval is broken up into small elements, on each of which the control actions are approximated by Lagrangian polynomials of order 2 and 3. When appropriately adjusted, the hybrid genetic algorithms reproduce a solution close to exact. However, the cost of calculation of 1 second of the physical process is about 300 seconds of processor time.

To increase the speed of calculation of control actions, we propose an algorithm based on artificial neural networks. As the input signal the neural network takes the components of the required displacement vector. The node values of the Lagrangian polynomials which approximately describe the control actions return as output signals . The neural network is taught by the well-known back-propagation method. The learning sample is generated using the approach based on hybrid genetic algorithms. The calculation of 1 second of the physical process by means of the neural network requires about 0.004 seconds of processor time, that is, 6 orders faster than the hybrid genetic algorithm. The control calculated by means of the artificial neural network differs from exact control. However, in spite of this difference, it ensures that the predetermined trajectory is followed exactly.

A mathematical model describing the irreversible processes of polarization and deformation of polycrystalline ferroelectrics in external electric and mechanical fields of high intensity is presented, as a result of which the internal structure changes and the properties of the material change. Irreversible phenomena are modeled in a three-dimensional setting for the case of simultaneous action of an electric field and mechanical stresses. The object of the research is a representative volume in which the residual phenomena in the form of the induced and irreversible parts of the polarization vector and the strain tensor are investigated. The main task of modeling is to construct constitutive relations connecting the polarization vector and strain tensor, on the one hand, and the electric field vector and mechanical stress tensor, on the other hand. A general case is considered when the direction of the electric field may not coincide with any of the main directions of the tensor of mechanical stresses. For reversible components, the constitutive relations are constructed in the form of linear tensor equations, in which the modules of elasticity and dielectric permeability depend on the residual strain, and the piezoelectric modules depend on the residual polarization. The constitutive relations for irreversible parts are constructed in several stages. First, an auxiliary model was constructed for the ideal or unhysteretic case, when all vectors of spontaneous polarization can rotate in the fields of external forces without mutual influence on each other. A numerical method is proposed for calculating the resulting values of the maximum possible polarization and deformation values of an ideal case in the form of surface integrals over the unit sphere with the distribution density obtained from the statistical Boltzmann law. After that the estimates of the energy costs required for breaking down the mechanisms holding the domain walls are made, and the work of external fields in real and ideal cases is calculated. On the basis of this, the energy balance was derived and the constitutive relations for irreversible components in the form of equations in differentials were obtained. A scheme for the numerical solution of these equations has been developed to determine the current values of the irreversible required characteristics in the given electrical and mechanical fields. For cyclic loads, dielectric, deformation and piezoelectric hysteresis curves are plotted.

The developed model can be implanted into a finite element complex for calculating inhomogeneous residual polarization and deformation fields with subsequent determination of the physical modules of inhomogeneously polarized ceramics as a locally anisotropic body.

This paper investigates the effectiveness of Retrieval-Augmented Generation (RAG) combined with various Large Language Models (LLMs) for document retrieval and information access in corporate information systems. We survey typical use-cases of LLMs in enterprise environments, outline the RAG architecture, and discuss the major challenges that arise when integrating LLMs into a RAG pipeline. A system architecture is proposed that couples a text-vector encoder with an LLM. The encoder builds a vector database that indexes a library of corporate documents. For every user query, relevant contextual fragments are retrieved from this library via the FAISS engine and appended to the prompt given to the LLM. The LLM then generates an answer grounded in the supplied context. The overall structure and workflow of the proposed RAG solution are described in detail. To justify the choice of the generative component, we benchmark a set of widely used LLMs — ChatGPT, GigaChat, YandexGPT, Llama, Mistral, Qwen, and others — when employed as the answer-generation module. Using an expert-annotated test set of queries, we evaluate the accuracy, completeness, linguistic quality, and conciseness of the responses. Model-specific characteristics and average response latencies are analysed; the study highlights the significant influence of available GPU memory on the throughput of local LLM deployments. An overall ranking of the models is derived from an aggregated quality metric. The results confirm that the proposed RAG architecture provides efficient document retrieval and information delivery in corporate environments. Future research directions include richer context augmentation techniques and a transition toward agent-based LLM architectures. The paper concludes with practical recommendations on selecting an optimal RAG–LLM configuration to ensure fast and precise access to enterprise knowledge assets.

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.

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 short-term prediction of road traffic condition is one of the main tasks of transportation modelling. The main purpose of which are traffic control, reporting of accidents, avoiding traffic jams due to knowledge of traffic flow and subsequent transportation planning. A number of solutions exist — both model-driven and data driven had proven to be successful in capturing the dynamics of traffic flow. Nevertheless, most space-time models suffer from high mathematical complexity and low efficiency. Artificial Neural Networks, one of the prominent datadriven approaches, show promising performance in modelling the complexity of traffic flow. We present a neural network architecture for traffic flow prediction on a real-world road network graph. The model is based on the combination of a recurrent neural network and graph convolutional neural network. Where a recurrent neural network is used to model temporal dependencies, and a convolutional neural network is responsible for extracting spatial features from traffic. To make multiple few steps ahead predictions, the encoder-decoder architecture is used, which allows to reduce noise propagation due to inexact predictions. To model the complexity of traffic flow, we employ multilayered architecture. Deeper neural networks are more difficult to train. To speed up the training process, we use skip-connections between each layer, so that each layer teaches only the residual function with respect to the previous layer outputs. The resulting neural network was trained on raw data from traffic flow detectors from the US highway system with a resolution of 5 minutes. 3 metrics: mean absolute error, mean relative error, mean-square error were used to estimate the quality of the prediction. It was found that for all metrics the proposed model achieved lower prediction error than previously published models, such as Vector Auto Regression, LSTM and Graph Convolution GRU.

Inhibitors of histone deacetylases (HDACi) have considered as a promising class of drugs for the treatment of cancers because of their effects on cell growth, differentiation, and apoptosis. Angiogenesis play an important role in the growth of most solid tumors and the progression of metastasis. The vascular endothelial growth factor (VEGF) is a key angiogenic agent, which is secreted by malignant tumors, which induces the proliferation and the migration of vascular endothelial cells. Currently, the most promising strategy in the fight against cancer is the creation of hybrid drugs that simultaneously act on several physiological targets. In this work, a series of hybrids bearing N-phenylquinazolin-4-amine and hydroxamic acid moieties were studied as dual VEGFR-2/HDAC inhibitors using simplex representation of the molecular structure and Support Vector Machine (SVM). The total sample of 42 compounds was divided into training and test sets. Five-fold cross-validation (5-fold) was used for internal validation. Satisfactory quantitative structure—activity relationship (QSAR) models were constructed (R²_test = 0.64–0.87) for inhibitors of HDAC, VEGFR-2 and human breast cancer cell line MCF-7. The interpretation of the obtained QSAR models was carried out. The coordinated effect of different molecular fragments on the increase of antitumor activity of the studied compounds was estimated. Among the substituents of the N-phenyl fragment, the positive contribution of para bromine for all three types of activity can be distinguished. The results of the interpretation were used for molecular design of potential dual VEGFR-2/HDAC inhibitors. For comparative QSAR research we used physicochemical descriptors calculated by the program HYBOT, the method of Random Forest (RF), and on-line version of the expert system OCHEM (https://ochem.eu). In the modeling of OCHEM PyDescriptor descriptors and extreme gradient boosting was chosen. In addition, the models obtained with the help of the expert system OCHEM were used for virtual screening of 300 compounds to select promising VEGFR-2/HDAC inhibitors for further synthesis and testing.

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.