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Determination of post-reconstruction correction factors for quantitative assessment of pathological bone lesions using gamma emission tomography
Computer Research and Modeling, 2025, v. 17, no. 4, pp. 677-696In single-photon emission computed tomography (SPECT), patients with bone disorders receive a radiopharmaceutical (RP) that accumulates selectively in pathological lesions. Accurate quantification of RP uptake plays a critical role in disease staging, prognosis, and the development of personalized treatment strategies. Traditionally, the accuracy of quantitative assessment is evaluated through in vitro clinical trials using the standardized physical NEMA IEC phantom, which contains six spheres simulating lesions of various sizes. However, such experiments are limited by high costs and radiation exposure to researchers. This study proposes an alternative in silico approach based on numerical simulation using a digital twin of the NEMA IEC phantom. The computational framework allows for extensive testing under varying conditions without physical constraints. Analogous to clinical protocols, we calculated the recovery coefficient (RCmax), defined as the ratio of the maximum activity in a lesion to its known true value. The simulation settings were tailored to clinical SPECT/CT protocols involving 99mTc for patients with bone-related diseases. For the first time, we systematically analyzed the impact of lesion-to-background ratios and post-reconstruction filtering on RCmax values. Numerical experiments revealed the presence of edge artifacts in reconstructed lesion images, consistent with those observed in both real NEMA IEC phantom studies and patient scans. These artifacts introduce instability into the iterative reconstruction process and lead to errors in activity quantification. Our results demonstrate that post-filtering helps suppress edge artifacts and stabilizes the solution. However, it also significantly underestimates activity in small lesions. To address this issue, we introduce post-reconstruction correction factors derived from our simulations to improve the accuracy of quantification in lesions smaller than 20 mm in diameter.
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The use of cluster analysis methods for the study of a set of feasible solutions of the phase problem in biological crystallography
Computer Research and Modeling, 2010, v. 2, no. 1, pp. 91-101Views (last year): 2.X-ray diffraction experiment allows determining of magnitudes of complex coefficients in the decomposition of the studied electron density distribution into Fourier series. The determination of the lost in the experiment phase values poses the central problem of the method, namely the phase problem. Some methods for solving of the phase problem result in a set of feasible solutions. Cluster analysis method may be used to investigate the composition of this set and to extract one or several typical solutions. An essential feature of the approach is the estimation of the closeness of two solutions by the map correlation between two aligned Fourier syntheses calculated with the use of phase sets under comparison. An interactive computer program ClanGR was designed to perform this analysis.
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Views (last year): 3.
The BES-III experiment at the IHEP CAS, Beijing, is running at the high-luminosity e+e- collider BEPC-II to study physics of charm quarks and tau leptons. The world largest samples of J/psi and psi' events are already collected, a number of unique data samples in the energy range 2.5–4.6 GeV have been taken. The data volume is expected to increase by an order of magnitude in the coming years. This requires to move from a centralized computing system to a distributed computing environment, thus allowing the use of computing resources from remote sites — members of the BES-III Collaboration. In this report the general information, latest results and development plans of the BES-III distributed computing system are presented.
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Substantiation of optimum planting schemes for forest plantations: a computer experiment
Computer Research and Modeling, 2016, v. 8, no. 2, pp. 333-343Views (last year): 2. Citations: 2 (RSCI).The article presents the results of computer simulations aimed to assess the influence of tree spatial locations (planting schemes) on the productivity and the dynamics of soil fertility in forest plantations. The growth of aspen (Populus tremula L.) in plantations with short rotation (30 years) was simulated in the EFIMOD system of models with the soil and climatic data matching forested lands in the Mari El Republic. The outcome reveals that higher biomass rates, increase in soil organic matter stocks, and the minimal loss of soil nitrogen can be obtained when the distance between trees in the row equals 1–4 m and 4–6 м in aisles.
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Detection of influence of upper working roll’s vibrayion on thickness of sheet at cold rolling with the help of DEFORM-3D software
Computer Research and Modeling, 2017, v. 9, no. 1, pp. 111-116Views (last year): 12. Citations: 1 (RSCI).Technical diagnosis’ current trends are connected to application of FEM computer simulation, which allows, to some extent, replace real experiments, reduce costs for investigation and minimize risks. Computer simulation, just at the stage of research and development, allows carrying out of diagnostics of equipment to detect permissible fluctuations of parameters of equipment’s work. Peculiarity of diagnosis of rolling equipment is that functioning of rolling equipment is directly tied with manufacturing of product with required quality, including accuracy. At that design of techniques of technical diagnosis and diagnostical modelling is very important. Computer simulation of cold rolling of strip was carried out. At that upper working roll was doing vibrations in horizontal direction according with published data of experiments on continuous 1700 rolling mill. Vibration of working roll in a stand appeared due to gap between roll’s craft and guide in a stand and led to periodical fluctuations of strip’s thickness. After computer simulation with the help of DEFORM software strip with longitudinal and transversal thickness variation was gotten. Visualization of strip’s geometrical parameters, according with simulation data, corresponded to type of inhomogeneity of surface of strip rolled in real. Further analysis of thickness variation was done in order to identify, on the basis of simulation, sources of periodical components of strip’s thickness, whose reasons are malfunctions of equipment. Advantage of computer simulation while searching the sources of forming of thickness variation is that different hypothesis concerning thickness formations may be tested without conducting real experiments and costs of different types may be reduced. Moreover, while simulation, initial strip’s thickness will not have fluctuations as opposed to industrial or laboratorial experiments. On the basis of spectral analysis of random process, it was established that frequency of changing of strip’s thickness after rolling in one stand coincides with frequency of working roll’s vibration. Results of computer simulation correlate with results of the researches for 1700 mill. Therefore, opportunity to apply computer simulation to find reasons of formation of thickness variation of strip on the industrial rolling mill is shown.
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Regarding the dynamics of cosymmetric predator – prey systems
Computer Research and Modeling, 2017, v. 9, no. 5, pp. 799-813Views (last year): 12. Citations: 3 (RSCI).To study nonlinear effects of biological species interactions numerical-analytical approach is being developed. The approach is based on the cosymmetry theory accounting for the phenomenon of the emergence of a continuous family of solutions to differential equations where each solution can be obtained from the appropriate initial state. In problems of mathematical ecology the onset of cosymmetry is usually connected with a number of relationships between the parameters of the system. When the relationships collapse families vanish, we get a finite number of isolated solutions instead of a continuum of solutions and transient process can be long-term, dynamics taking place in a neighborhood of a family that has vanished due to cosymmetry collapse.
We consider a model for spatiotemporal competition of predators or prey with an account for directed migration, Holling type II functional response and nonlinear prey growth function permitting Alley effect. We found out the conditions on system parameters under which there is linear with respect to population densities cosymmetry. It is demonstated that cosymmetry exists for any resource function in case of heterogeneous habitat. Numerical experiment in MATLAB is applied to compute steady states and oscillatory regimes in case of spatial heterogeneity.
The dynamics of three population interactions (two predators and a prey, two prey and a predator) are considered. The onset of families of stationary distributions and limit cycle branching out of equlibria of a family that lose stability are investigated in case of homogeneous habitat. The study of the system for two prey and a predator gave a wonderful result of species coexistence. We have found out parameter regions where three families of stable solutions can be realized: coexistence of two prey in absence of a predator, stationary and oscillatory distributions of three coexisting species. Cosymmetry collapse is analyzed and long-term transient dynamics leading to solutions with the exclusion of one of prey or extinction of a predator is established in the numerical experiment.
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On the computer experiments of Kasman
Computer Research and Modeling, 2019, v. 11, no. 3, pp. 503-513Views (last year): 23.In 2007 Kasman conducted a series of original computer experiments with sine-Gordon kinks moving along artificial DNA sequences. Two sequences were considered. Each consisted of two parts separated by a boundary. The left part of the first sequence contained repeating TTA triplets that encode leucines, and the right part contained repeating CGC triplets that encode arginines. In the second sequence, the left part contained repeating CTG triplets encoding leucines, and the right part contained repeating AGA triplets encoding arginines. When modeling the kink movement, an interesting effect was discovered. It turned out that the kink, moving in one of the sequences, stopped without reaching the end of the sequence, and then “bounced off” as if he had hit a wall. At the same time, the kink movement in the other sequence did not stop during the entire time of the experiment. In these computer experiments, however, a simple DNA model proposed by Salerno was used. It takes into account differences in the interactions of complementary bases within pairs, but does not take into account differences in the moments of inertia of nitrogenous bases and in the distances between the centers of mass of the bases and the sugar-phosphate chain. The question of whether the Kasman effect will continue with the use of more accurate DNA models is still open. In this paper, we investigate the Kasman effect on the basis of a more accurate DNA model that takes both of these differences into account. We obtained the energy profiles of Kasman's sequences and constructed the trajectories of the motion of kinks launched in these sequences with different initial values of the energy. The results of our investigations confirmed the existence of the Kasman effect, but only in a limited interval of initial values of the kink energy and with a certain direction of the kinks movement. In other cases, this effect did not observe. We discussed which of the studied sequences were energetically preferable for the excitation and propagation of kinks.
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Linear and nonlinear optimization models of multiple covering of a bounded plane domain with circles
Computer Research and Modeling, 2019, v. 11, no. 6, pp. 1101-1110Problems of multiple covering ($k$-covering) of a bounded set $G$ with equal circles of a given radius are well known. They are thoroughly studied under the assumption that $G$ is a finite set. There are several papers concerned with studying this problem in the case where $G$ is a connected set. In this paper, we study the problem of minimizing the number of circles that form a $k$-covering, $k \geqslant 1$, provided that $G$ is a bounded convex plane domain.
For the above-mentioned problem, we state a 0-1 linear model, a general integer linear model, and a nonlinear model, imposing a constraint on the minimum distance between the centers of covering circles. The latter constraint is due to the fact that in practice one can place at most one device at each point. We establish necessary and sufficient solvability conditions for the linear models and describe one (easily realizable) variant of these conditions in the case where the covered set $G$ is a rectangle.
We propose some methods for finding an approximate number of circles of a given radius that provide the desired $k$-covering of the set $G$, both with and without constraints on distances between the circles’ centers. We treat the calculated values as approximate upper bounds for the number of circles. We also propose a technique that allows one to get approximate lower bounds for the number of circles that is necessary for providing a $k$-covering of the set $G$. In the general linear model, as distinct from the 0-1 linear model, we require no additional constraint. The difference between the upper and lower bounds for the number of circles characterizes the quality (acceptability) of the constructed $k$-covering.
We state a nonlinear mathematical model for the $k$-covering problem with the above-mentioned constraints imposed on distances between the centers of covering circles. For this model, we propose an algorithm which (in certain cases) allows one to find more exact solutions to covering problems than those calculated from linear models.
For implementing the proposed approach, we have developed computer programs and performed numerical experiments. Results of numerical experiments demonstrate the effectiveness of the method.
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The applicability of the approximation of single scattering in pulsed sensing of an inhomogeneous medium
Computer Research and Modeling, 2020, v. 12, no. 5, pp. 1063-1079The mathematical model based on the linear integro-differential Boltzmann equation is considered in this article. The model describes the radiation transfer in the scattering medium irradiated by a point source. The inverse problem for the transfer equation is defined. This problem consists of determining the scattering coefficient from the time-angular distribution of the radiation flux density at a given point in space. The Neumann series representation for solving the radiation transfer equation is analyzed in the study of the inverse problem. The zero member of the series describes the unscattered radiation, the first member of the series describes a single-scattered field, the remaining members of the series describe a multiple-scattered field. When calculating the approximate solution of the radiation transfer equation, the single scattering approximation is widespread to calculated an approximate solution of the equation for regions with a small optical thickness and a low level of scattering. An analytical formula is obtained for finding the scattering coefficient by using this approximation for problem with additional restrictions on the initial data. To verify the adequacy of the obtained formula the Monte Carlo weighted method for solving the transfer equation is constructed and software implemented taking into account multiple scattering in the medium and the space-time singularity of the radiation source. As applied to the problems of high-frequency acoustic sensing in the ocean, computational experiments were carried out. The application of the single scattering approximation is justified, at least, at a sensing range of about one hundred meters and the double and triple scattered fields make the main impact on the formula error. For larger regions, the single scattering approximation gives at the best only a qualitative evaluation of the medium structure, sometimes it even does not allow to determine the order of the parameters quantitative characteristics of the interaction of radiation with matter.
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Investigation of the averaged model of coked catalyst oxidative regeneration
Computer Research and Modeling, 2021, v. 13, no. 1, pp. 149-161The article is devoted to the construction and investigation of an averaged mathematical model of an aluminum-cobalt-molybdenum hydrocracking catalyst oxidative regeneration. The oxidative regeneration is an effective means of restoring the activity of the catalyst when its granules are coating with coke scurf.
The mathematical model of this process is a nonlinear system of ordinary differential equations, which includes kinetic equations for reagents’ concentrations and equations for changes in the temperature of the catalyst granule and the reaction mixture as a result of isothermal reactions and heat transfer between the gas and the catalyst layer. Due to the heterogeneity of the oxidative regeneration process, some of the equations differ from the standard kinetic ones and are based on empirical data. The article discusses the scheme of chemical interaction in the regeneration process, which the material balance equations are compiled on the basis of. It reflects the direct interaction of coke and oxygen, taking into account the degree of coverage of the coke granule with carbon-hydrogen and carbon-oxygen complexes, the release of carbon monoxide and carbon dioxide during combustion, as well as the release of oxygen and hydrogen inside the catalyst granule. The change of the radius and, consequently, the surface area of coke pellets is taken into account. The adequacy of the developed averaged model is confirmed by an analysis of the dynamics of the concentrations of substances and temperature.
The article presents a numerical experiment for a mathematical model of oxidative regeneration of an aluminum-cobalt-molybdenum hydrocracking catalyst. The experiment was carried out using the Kutta–Merson method. This method belongs to the methods of the Runge–Kutta family, but is designed to solve stiff systems of ordinary differential equations. The results of a computational experiment are visualized.
The paper presents the dynamics of the concentrations of substances involved in the oxidative regeneration process. A conclusion on the adequacy of the constructed mathematical model is drawn on the basis of the correspondence of the obtained results to physicochemical laws. The heating of the catalyst granule and the release of carbon monoxide with a change in the radius of the granule for various degrees of initial coking are analyzed. There are a description of the results.
In conclusion, the main results and examples of problems which can be solved using the developed mathematical model are noted.
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