Most viewed papers

561. Ilyin O.V.
     The modeling of nonlinear pulse waves in elastic vessels using the Lattice Boltzmann method
     Computer Research and Modeling, 2019, v. 11, no. 4, pp. 707-722

     In the present paper the application of the kinetic methods to the blood flow problems in elastic vessels is studied. The Lattice Boltzmann (LB) kinetic equation is applied. This model describes the discretized in space and time dynamics of particles traveling in a one-dimensional Cartesian lattice. At the limit of the small times between collisions LB models describe hydrodynamic equations which are equivalent to the Navier – Stokes for compressible if the considered flow is slow (small Mach number). If one formally changes in the resulting hydrodynamic equations the variables corresponding to density and sound wave velocity by luminal area and pulse wave velocity then a well-known 1D equations for the blood flow motion in elastic vessels are obtained for a particular case of constant pulse wave speed.

     In reality the pulse wave velocity is a function of luminal area. Here an interesting analogy is observed: the equation of state (which defines sound wave velocity) becomes pressure-area relation. Thus, a generalization of the equation of state is needed. This procedure popular in the modeling of non-ideal gas and is performed using an introduction of a virtual force. This allows to model arbitrary pressure-area dependence in the resulting hemodynamic equations.

     Two test case problems are considered. In the first problem a propagation of a sole nonlinear pulse wave is studied in the case of the Laplace pressure-area response. In the second problem the pulse wave dynamics is considered for a vessel bifurcation. The results show good precision in comparison with the data from literature.

     Keywords: hemodynamics, lattice Boltzmann method, elastic vessels.
     Views (last year): 2.
562. Minkevich I.G.
     Estimation of maximal values of biomass growth yield based on the mass-energy balance of cell metabolism
     Computer Research and Modeling, 2019, v. 11, no. 4, pp. 723-750

     The biomass growth yield is the ratio of the newly synthesized substance of growing cells to the amount of the consumed substrate, the source of matter and energy for cell growth. The yield is a characteristic of the efficiency of substrate conversion to cell biomass. The conversion is carried out by the cell metabolism, which is a complete aggregate of biochemical reactions occurring in the cells.

     This work newly considers the problem of maximal cell growth yield prediction basing on balances of the whole living cell metabolism and its fragments called as partial metabolisms (PM). The following PM’s are used for the present consideration. During growth on any substrate we consider i) the standard constructive metabolism (SCM) which consists of identical pathways during growth of various organisms on any substrate. SCM starts from several standard compounds (nodal metabolites): glucose, acetyl-CoA 2-oxoglutarate, erythrose-4-phosphate, oxaloacetate, ribose-5- phosphate, 3-phosphoglycerate, phosphoenolpyruvate, and pyruvate, and ii) the full forward metabolism (FM) — the remaining part of the whole metabolism. The first one consumes high-energy bonds (HEB) formed by the second one. In this work we examine a generalized variant of the FM, when the possible presence of extracellular products, as well as the possibilities of both aerobic and anaerobic growth are taken into account. Instead of separate balances of each nodal metabolite formation as it was made in our previous work, this work deals at once with the whole aggregate of these metabolites. This makes the problem solution more compact and requiring a smaller number of biochemical quantities and substantially less computational time. An equation expressing the maximal biomass yield via specific amounts of HEB formed and consumed by the partial metabolisms has been derived. It includes the specific HEB consumption by SCM which is a universal biochemical parameter applicable to the wide range of organisms and growth substrates. To correctly determine this parameter, the full constructive metabolism and its forward part are considered for the growth of cells on glucose as the mostly studied substrate. We used here the found earlier properties of the elemental composition of lipid and lipid-free fractions of cell biomass. Numerical study of the effect of various interrelations between flows via different nodal metabolites has been made. It showed that the requirements of the SCM in high-energy bonds and NAD(P)H are practically constants. The found HEB-to-formed-biomass coefficient is an efficient tool for finding estimates of maximal biomass yield from substrates for which the primary metabolism is known. Calculation of ATP-to-substrate ratio necessary for the yield estimation has been made using the special computer program package, GenMetPath.

     Keywords: biomass growth yield, cell metabolism, constructive metabolism, nodal metabolites, high-energy bonds, reductivity carriers, mass-energy balance.
     Views (last year): 2.
563. Zaburdaeva E.A.
     Calibration of diversity indexes and search for ecologically tolerable levels of abiotic factors (case study: water objects of the Don river)
     Computer Research and Modeling, 2009, v. 1, no. 2, pp. 199-207

     With the data obtained by hydrobiological monitoring of water objects of Don river for many years (1978-1988) calculation of rank distribution parameters and indexes of dominance for phytoplankton species abundance was conducted. The borders of investigated characteristics are calculated. They correspond to borders of ecological well-being - trouble conditions of phytoplankton communities. Ecologically tolerable levels for the core abiotic factors are found. Contribution of each of analyzed factors to a degree of ecological trouble is established.

     Keywords: phytoplankton, ecological monitoring, ETL.
     Views (last year): 1.
564. Elizarova T.G., Zherikov A.V., Kalachinskaya I.S.
     Numerical solution of quasi-hydrodynamic equations on non-structured triangle mesh
     Computer Research and Modeling, 2009, v. 1, no. 2, pp. 181-188

     A new flow modeling method on unstructured grid was proposed. As a basis system this method used quasi-hydro-dynamic equations. The finite volume method vas used for solving these equations. The Delaunay triangulation was used for constructing mesh. This proposed method was tested in modeling of incompressible flow through a channel with complex profile. The acquired results showed that the proposed method could be used in flow modeling in unstructured grid.

     Keywords: quasi-hydrodynamic equations, Delaunay triangulation, finite volume method.
     Views (last year): 1.
565. Korchak A.B., Evdokimov A.V.
     Tool for integration of heterogeneous models and its application to loosely coupled sets of differential equations
     Computer Research and Modeling, 2009, v. 1, no. 2, pp. 127-136

     We develop the software tool for integration of dynamics models, which are inhomogeneous over mathematical properties and/or over requirements to the time step. The family of algorithms for the parallel computation of heterogeneous models with different time steps is offered. Analytical estimates and direct measurements of the error of these algorithms are made with reference to weakly coupled ODE sets. The advantage of the algorithms in the time cost as compared to accurate methods is shown.

     Keywords: heterogeneous models, differential equations solving, parallel computation.
     Views (last year): 1.
566. Brazhe A.R., Brazhe N.A., Sosnovtseva O.V., Pavlov A.N., Mosekilde E., Maksimov G.V.
     Wavelet-based analysis of cell dynamics measured by interference microscopy
     Computer Research and Modeling, 2009, v. 1, no. 1, pp. 77-83

     Laser interference microscopy was used to study morphology and intracellular dynamics of erythrocytes, neurons and mast cells. We have found that changes of the local refractive index (RI) of cells have regular components that relate to the cooperative processes in the cellular submembrane and centre regions. We have shown that characteristic frequencies of RI dynamics differ for various cell types and can be used as markers of specific cellular processes.

     Keywords: laser interference microscopy, wavelet-based analysis.
     Views (last year): 1. Citations: 5 (RSCI).
567. Koganov A.V.
     Representation of groups by automorphisms of normal topological spaces
     Computer Research and Modeling, 2009, v. 1, no. 3, pp. 243-249

     The famous fact [3, 5] of existence of an exact representation for any finite group in the form of the full automorphism group of a finite graph was generalize in [4]. For an arbitrary group exact representation exists in the form of the full automorphism group of Kolmogorov topological space (weak type of separability T₀). For a finite group a finite space may be chosen, thus allowing to restore a finite graph with the same number of vertices and having the same automorphism group. Such topological spaces and graphs are called topological imprints and graph imprints of a group (T-imprints and G-imprints, respectively). The question of maximum type of separability of a topological space for which T-imprint can be obtained for any group is open. The author proves that the problem can be solved for the class of normal topology (maximal type of separability T₄+T₀). Special finite T-imprint for a symmetric group may be obtained as a discrete topology; for any other group minimal cardinality of normal T-imprint is countable. There is a generic procedure to construct a T-imprint for any group. For a finite group this procedure allows finite space partitioning into subspaces having G-imprint of the original group as their connectivity graphs.

     Keywords: group theory, automorphisms, topological spaces.
     Views (last year): 1.
568. Kargovsky A.V.
     Anharmonic vibrational resonances in small water clusters
     Computer Research and Modeling, 2009, v. 1, no. 3, pp. 321-336

     Numerical calculations of structures and vibrational spectra of small water clusters are performed by solution of the molecular Schrodinger equation in the density functional theory framework using B3LYP and X3LYP hybrid functionals. Spectral features and evolution of hydrogen bond properties in clusters with their size increasing are discussed. The vibrotational Hamiltonian parameters and Fermi and Darling-Dennison anharmonic resonances in small water oligomers are determined. Obtained results may be used in quantum mechanics/molecular dynamics simulations of water and processes in active site of enzyme.

     Keywords: vibrational spectra, hydrogen bonds, water clusters.
     Views (last year): 1. Citations: 4 (RSCI).
569. Koganov A.V.
     Occurence of contradictions in Zermelo–Fraenkel theory under extension of base language by recursion functions
     Computer Research and Modeling, 2009, v. 1, no. 4, pp. 367-380

     It is shown that the extension of base language in Zermelo–Fraenkel theory, which allows a relations on recursion function of natural argument, may lead in Set Theory to contradictive constructions on arithmetic level.

     Keywords: Zermelo–Fraenkel theory, recursion functions, set theory.
     Views (last year): 1. Citations: 2 (RSCI).
570. Khoraskina Y.S., Komarov A.S., Bezrukova M.G., Zhiyanski M.K.
     Modeling of calcium dynamics in soil organic layers
     Computer Research and Modeling, 2010, v. 2, no. 1, pp. 103-110

     Calcium is a major nutrient regulating metabolism in a plant. Deficiency of calcium results in a growth decline of plant tissues. Ca may be lost from forest soils due to acidic atmospheric deposition and tree harvesting. Plant-available calcium compounds are in the soil cation exchange complex and soil waters. Model of soil calcium dynamics linking it with the model of soil organic matter dynamics ROMUL in forest ecosystems is developed. ROMUL describes the mineralization and humification of the fraction of fresh litter which is further transformed into complex of partially humified substance (CHS) and then to stable humus (H) in dependence on temperature, soil moisture and chemical composition of the fraction (nitrogen, lignin and ash contents, pH). Rates of decomposition and humification being coefficients in the system of ordinary differential equations are evaluated using laboratory experiments and verified on a set of field experiments. Model of soil calcium dynamics describes calcium flows between pools of soil organic matter. Outputs are plant nutrition, leaching, synthesis of secondary minerals. The model describes transformation and mineralization of forest floor in detail. Experimental data for calibration model was used from spruсe forest of Bulgaria.

     Keywords: calcium turnover, mathematical modeling of ecosystems, secondary minerals.
     Views (last year): 1.

• About Journal
• Open Access Policy
• Publishing Ethics
• Editorial board
• Author index
• For authors
• For Reviewers
• Contacts
• Most viewed papers
• Most cited papers
• Submit publication ONLINE