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Seismic wave fields in spherically symmetric Earth with high details. Analytical solution
Computer Research and Modeling, 2025, v. 17, no. 5, pp. 903-922An analytical solution is obtained for seismic wave fields in a spherically symmetric Earth. In the case of an arbitrary layered medium, the solution, which includes Bessel functions, is constructed by means of a differential sweep method. Asymptotic of Bessel functions is used for stable calculation of wave fields. It is shown that the classical asymptotic in the case of a sphere of large (in wavelengths) dimensions gives an error in the solution. The new asymptotic is used for efficient calculation of a solution without errors with high detail. A program has been created that makes it possible to carry out calculations for high-frequency (1 hertz and higher) teleseismic wave fields in a discrete (layered) sphere of planetary dimensions. Calculations can be carried even out on personal computers with OpenMP parallelization.
In the works of Burmin (2019) proposed a spherically symmetric model of the Earth. It is characterized by the fact that in it the outer core has a viscosity and, therefore, an effective shear modulus other than zero. For this model of the Earth, a highly detailed calculation was carried out with a carrier frequency of 1 hertz. As a result of the analytical calculation, it was found that highfrequency oscillations of small amplitude, the so-called “precursors”, appear ahead of the PKP waves. An analytical calculation showed that the theoretical seismograms for this model of the Earth are in many respects similar to the experimental data. This confirms the correctness of the ideas underlying its construction.
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Using Docker service containers to build browser-based clinical decision support systems (CDSS)
Computer Research and Modeling, 2026, v. 18, no. 1, pp. 133-147The article presents a technology for building clinical decision support systems (CDSS) based on service containers using Docker and a web interface that runs directly in the browser without installing specialized software on workstation of a clinician. A modular architecture is proposed in which each application module is packaged as an independent service container combining a lightweight web server, a user interface, and computational components for medical image processing. Communication between the browser and the server side is implemented via a persistent bidirectional WebSocket connection with binary message serialization (MessagePack), which provides low latency and efficient transfer of large data. For local storage of images and analysis of results, browser facilities (IndexedDB with the Dexie.js wrapper) are used to speed up repeated data access. Three-dimensional visualization and basic operations with DICOM data are implemented with Three.js and AMI.js: this toolchain supports the integration of interactive elements arising from the task context (annotations, landmarks, markers, 3D models) into volumetric medical images.
Server components and functional modules are assembled as a set of interacting containers managed by Docker. The paper discusses the choice of base images, approaches to minimizing containers down to runtime-only executables without external utilities, and the organization of multi-stage builds with a dedicated build container. It describes a hub service that launches application containers on user request, performs request proxying, manages sessions, and switches a container from shared to exclusive mode at the start of computations. Examples of application modules are provided (fractional flow reserve estimation, quantitative flow ratio computation, aortic valve closure modeling), along with the integration of a React-based interface with a three-dimensional scene, a versioning policy, automated reproducibility checks, and the deployment procedure on the target platform.
It is demonstrated that containerization ensures portability and reproducibility of the software environment, dependency isolation and scalability, while the browser-based interface provides accessibility, reduced infrastructure requirements, and interactive real-time visualization of medical data. Technical limitations are noted (dependence on versions of visualization libraries and data formats) together with practical mitigation measures.
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Application of beta regression to the CD44 alternative splicing problem
Computer Research and Modeling, 2026, v. 18, no. 3, pp. 697-714Aberrant alternative splicing of the CD44 gene drives colorectal cancer progression and facilitates the emergence of cancer stem cells. Although biomedical research recognizes this transmembrane glycoprotein as a major catalyst of malignancy, deciphering its multi-isoform regulatory networks remains a complex analytical challenge. To address this knowledge gap, this study presents a machine learning framework designed to decode these biological mechanisms. The author constructed a neural network regressor based on beta regression to model bounded isoform proportions. This computational architecture jointly estimates both the mean and the precision parameters of the underlying probability distribution. Furthermore, the system employs elastic net regularization to perform quantitative feature selection from highdimensional molecular expression data.
The investigation evaluates the proposed framework using gene expression profiles from colorectal cancer patients. The primary objective involves identifying specific ribonucleic acid-binding proteins acting as regulatory splicing factors. The experimental design contrasts two distinct mathematical modeling strategies. The first configuration incorporates an independent ”one-vs-all” approach that treats each transcript variant as an isolated regression target. The second formulation utilizes a structured ”isoform tree” method that directly mirrors hierarchical exon inclusion relationships. Validation experiments on synthetically generated datasets confirmed the mathematical integrity of the network. The model recovered true distribution parameters with precision and exhibited no systematic bias. Comprehensive empirical comparisons subsequently demonstrated that the independent ”one-vs-all” layout consistently outperforms the hierarchical tree configuration in predictive stability and accuracy.
The computational analysis maps the regulatory landscape of the CD44 gene. The framework validates several established splicing factors while uncovering new candidate proteins, including ACO1, NUDT21, and AGO2. Based on these statistical associations, the paper introduces a biological hypothesis. This concept functionally connects intracellular iron metabolism via the ACO1 protein with the shifting balance of CD44 variants. These discoveries provide deeper insights into oncogenic splicing regulation. Ultimately, they highlight molecular targets for future therapeutic interventions aimed at suppressing the cancer stem cell phenotype.
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Modeling of helix formation in peptides containing aspartic and glutamic residues
Computer Research and Modeling, 2010, v. 2, no. 1, pp. 83-90Views (last year): 2. Citations: 4 (RSCI).In present work we used the methods of molecular dynamics simulations and quantum chemistry to study the concept, according to which aspartic and glutamic residues play a key role in initiation of helix formation in oligopeptides. It has been shown, that the first turn of the alpha-helix can be organized from various amino acid sequences with Asp and Glu residues on the N-terminus. Thermodynamic properties of such a process were analyzed. The obtained results do not interfere with known experimental and statistical data and they substantially elaborate present views on the processes of early peptide folding stages.
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DNA conformational dynamics: approach to the physical mapping of genome
Computer Research and Modeling, 2010, v. 2, no. 4, pp. 419-428Views (last year): 2. Citations: 2 (RSCI).Recently we have developed a new method for studying DNA based on ultrasound - induced cleavage of DNA sugar-phosphate backbone. Relative cleavage rates of the phosphodiester bonds in all 16 dinucleotides have been determined. The increased amount of data sampling (of more than 20 000 nucleotides) made it also possible to obtain cleavage rates in all 256 possible tetranucleotides. These values quantitatively characterize sequence effects on conformational dynamics of DNA sugar phosphate backbone. Same type of DNA heterogeneity have been discovered and studied using its chemical cleavage induced by various chemical agents and DNAse I. The presence of essential heterogeneity in structural properties of DNA might be a key for physical mapping of the genomes, i.e. determining the structural profiles being responsible for DNA recognition by gene expression regulation machinery.
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Mathematical model of hydride phase change in a symmetrical powder particle
Computer Research and Modeling, 2012, v. 4, no. 3, pp. 569-584Views (last year): 2. Citations: 2 (RSCI).In the paper we construct the model of phase change. Process of hydriding / dehydriding is taken as an example. A single powder particle is considered under the assumption about its symmetry. A ball, a cylinder, and a flat plate are examples of such symmetrical shapes. The model desribes both the "shrinking core"(when the skin of the new phase appears on the surface of the particle) and the "nucleation and growth"(when the skin does not appear till complete vanishing of the old phase) scenarios. The model is the non-classical boundary-value problem with the free boundary and nonlinear Neumann boundary condition. The symmetry assumptions allow to reduce the problem to the single spatial variable. The model was tested on the series of experimental data. We show that the particle shape’s influence on the kinetics is insignificant. We also show that a set of particles of different shapes with size distribution can be approxomated by the single particle of the "average" size and of a simple shape; this justifies using single particle approximation and simple shapes in mathematical models.
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On the investigation of plasma turbulence by the analysis of the spectra
Computer Research and Modeling, 2012, v. 4, no. 4, pp. 793-802Views (last year): 2. Citations: 4 (RSCI).The article describes the examples of the analysis of the experimental data spectra for identifying typical structures of processes forming plasma turbulence. The method is based on the original algorithm which is close to the one-sample bootstrap. The base model for description of the fine structure of stochastic processes is finite local-scale normal mixtures. For finding the statistical estimates (maximum likelihood estimates) well known EM algorithm is used. The efficiency of the proposed research technique is demonstrated for a number of spectra’s set obtained in different modes of low-frequency plasma turbulence.
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Searching for connections between biological and physico-chemical characteristics of Rybinsk reservoir ecosystem. Part 3. Calculation of the boundaries of water quality classes
Computer Research and Modeling, 2013, v. 5, no. 3, pp. 451-471Views (last year): 4. Citations: 4 (RSCI).Approbation of calculation of borders of water quality classes for the purpose of ecological diagnosis and standardization by data of the Rybinsk reservoir is carried out. For bioindication indicators of phytoplankton fluorescence and the contents of pigments of phytoplankton are used. Chesnokov's importance coefficient proved to be the most preferred measure of connection for analyzing the effects of environmental factors on indicators. The factors important for environmental condition are identified. Comparison of borders between quality classes “valid” and “invalid” of factors values and boundaries of the classifications of water quality.
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Deformation model of polymer nanocomposites based on cellular automata
Computer Research and Modeling, 2014, v. 6, no. 1, pp. 131-136Views (last year): 3. Citations: 2 (RSCI).This paper discusses the modeling of the deformation of polymer nanocomposites containing "hard" and "soft" inclusions, using cellular automata and parallel computing. The paper describes an algorithm based on the model, a comparison with experimental data is shown, software for the numerical experiment is described.
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Empirical testing of institutional matrices theory by data mining
Computer Research and Modeling, 2015, v. 7, no. 4, pp. 923-939The paper has a goal to identify a set of parameters of the environment and infrastructure with the most significant impact on institutional-matrices that dominate in different countries. Parameters of environmental conditions includes raw statistical indices, which were directly derived from the databases of open access, as well as complex integral indicators that were by method of principal components. Efficiency of discussed parameters in task of dominant institutional matrices type recognition (X or Y type) was evaluated by a number of methods based on machine learning. It was revealed that greatest informational content is associated with parameters characterizing risk of natural disasters, level of urbanization and the development of transport infrastructure, the monthly averages and seasonal variations of temperature and precipitation.
Keywords: institutional matrices theory, machine learning.Views (last year): 7. Citations: 13 (RSCI).
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