All issues

Microarray datasets are highly dimensional, with a small number of collected samples in comparison to thousands of features. This poses a significant challenge that affects the interpretation, applicability and validation of the analytical results. Matrix factorizations have proven to be a useful method for describing data in terms of a small number of meta-features, which reduces noise, while still capturing the essential features of the data. Three novel and mutually relevant methods are presented in this paper: 1) gradient-based matrix factorization with two adaptive learning rates (in accordance with the number of factor matrices) and their automatic updates; 2) nonparametric criterion for the selection of the number of factors; and 3) nonnegative version of the gradient-based matrix factorization which doesn't require any extra computational costs in difference to the existing methods. We demonstrate effectiveness of the proposed methods to the supervised classification of gene expression data.

In various applications arise problems modeled by nonlinear partial differential equations on graphs (networks, trees). In order to study such problems and various extreme situations arose in the problems of designing and optimizing networks developed the computational model based on solving the corresponding boundary problems for partial differential equations of hyperbolic type on graphs (networks, trees). As applications, three different problems were chosen solved in the framework of the general approach of network computational models. The first was modeling of traffic flow. In solving this problem, a macroscopic approach was used in which the transport flow is described by a nonlinear system of second-order hyperbolic equations. The results of numerical simulations showed that the model developed as part of the proposed approach well reproduces the real situation various sections of the Moscow transport network on significant time intervals and can also be used to select the most optimal traffic management strategy in the city. The second was modeling of data flows in computer networks. In this problem data flows of various connections in packet data network were simulated as some continuous medium flows. Conceptual and mathematical network models are proposed. The numerical simulation was carried out in comparison with the NS-2 network simulation system. The results showed that in comparison with the NS-2 packet model the developed streaming model demonstrates significant savings in computing resources while ensuring a good level of similarity and allows us to simulate the behavior of complex globally distributed IP networks. The third was simulation of the distribution of gas impurities in ventilation networks. It was developed the computational mathematical model for the propagation of finely dispersed or gas impurities in ventilation networks using the gas dynamics equations by numerical linking of regions of different sizes. The calculations shown that the model with good accuracy allows to determine the distribution of gas-dynamic parameters in the pipeline network and solve the problems of dynamic ventilation management.

Verification results of supersonic turbulent jets computational characteristics are presented. Numerical simulation of axisymmetric nozzle operating is realized using FlowVision CFD. Open test cases for CFD are used. The test cases include Seiner tests with exit Mach number of 2.0 both fully-expanded and under-expanded $(P/P_0 = 1.47)$. Fully-expanded nozzle investigated with wide range of flow temperature (300…3000 K). The considered studies include simulation downstream from the nozzle exit diameter. Next numerical investigation is presented at an exit Mach number of 2.02 and a free-stream Mach number of 2.2. Geometric model of convergent- divergent nozzle rebuilt from original Putnam experiment. This study is set with nozzle pressure ratio of 8.12 and total temperature of 317 K.

The paper provides a comparison of obtained FlowVision results with experimental data and another current CFD studies. A comparison of the calculated characteristics and experimental data indicates a good agreement. The best coincidence with Seiner's experimental velocity distribution (about 7 % at far field for the first case) obtained using two-equation $k–\varepsilon$ standard turbulence model with Wilcox compressibility correction. Predicted Mach number distribution at $Y/D = 1$ for Putnam nozzle presents accuracy of 3 %.

General guidelines for simulation of supersonic turbulent jets in the FlowVision software are formulated in the given paper. Grid convergence determined the optimal cell rate. In order to calculate the design regime, it is recommended to build a grid, containing not less than 40 cells from the axis of symmetry to the nozzle wall. In order to calculate an off-design regime, it is necessary to resolve the shock waves. For this purpose, not less than 80 cells is required in the radial direction. Investigation of the influence of turbulence model on the flow characteristics has shown that the version of the SST $k–\omega$ turbulence model implemented in the FlowVision software essentially underpredicts the axial velocity. The standard $k–\varepsilon$ model without compressibility correction also underpredicts the axial velocity. These calculations agree well with calculations in other CFD codes using the standard $k–\varepsilon$ model. The in-home $k–\varepsilon$ turbulence model KEFV with compressibility correction a little bit overpredicts the axial velocity. Since, the best results are obtained using the standard $k–\varepsilon$ model combined with the Wilcox compressibility correction, this model is recommended for the problems discussed.

The developed methodology can be regarded as a basis for numerical investigations of more complex nozzle flows.

The well-known evolutionary equation of mathematical physics, which in modern mathematical literature is called the Kuramoto – Sivashinsky equation, is considered. In this paper, this equation is studied in the original edition of the authors, where it was proposed, together with the homogeneous Neumann boundary conditions.

The question of the existence and stability of local attractors formed by spatially inhomogeneous solutions of the boundary value problem under study has been studied. This issue has become particularly relevant recently in connection with the simulation of the formation of nanostructures on the surface of semiconductors under the influence of an ion flux or laser radiation. The question of the existence and stability of second-order equilibrium states has been studied in two different ways. In the first of these, the Galerkin method was used. The second approach is based on using strictly grounded methods of the theory of dynamic systems with infinite-dimensional phase space: the method of integral manifolds, the theory of normal forms, asymptotic methods.

In the work, in general, the approach from the well-known work of D.Armbruster, D.Guckenheimer, F.Holmes is repeated, where the approach based on the application of the Galerkin method is used. The results of this analysis are substantially supplemented and developed. Using the capabilities of modern computers has helped significantly complement the analysis of this task. In particular, to find all the solutions in the fourand five-term Galerkin approximations, which for the studied boundary-value problem should be interpreted as equilibrium states of the second kind. An analysis of their stability in the sense of A. M. Lyapunov’s definition is also given.

In this paper, we compare the results obtained using the Galerkin method with the results of a bifurcation analysis of a boundary value problem based on the use of qualitative analysis methods for infinite-dimensional dynamic systems. Comparison of two variants of results showed some limited possibilities of using the Galerkin method.

An algorithm for solving the conjugation of aerodynamic and ballistic problems, which is based on the method of modeling with the help of a grid system, has been complemented by a numerical mechanism that allows to take into account the relative movement and rotation of bodies relative to their centers of mass. For a given configuration of the bodies a problem of flow is solved by relaxation method. After that the state of the system is recalculated after a short amount of time. With the use of iteration it is possible to trace the dynamics of the system over a large period of time. The algorithm is implemented for research of flight of systems of bodies taking into account their relative position and rotation. The algorithm was tested on the problem of flow around a body with segmental-conical form. A good correlation of the results with experimental studies was shown. The algorithm is used to calculate the problem of the supersonic fight of a rotating body. For bodies of rectangular shape, imitating elongated fragments of a meteoroid, it is shown that for elongated bodies the aerodynamically more stable position is flight with a larger area across the direction of flight. This de facto leads to flight of bodies with the greatest possible aerodynamic resistance due to the maximum midship area. The algorithm is used to calculate the flight apart of two identical bodies of a rectangular shape, taking into account their rotation. Rotation leads to the fact that the bodies fly apart not only under the action of the pushing aerodynamic force but also the additional lateral force due to the acquisition of the angle of attack. The velocity of flight apart of two fragments with elongated shape of a meteoric body increases to three times with the account of rotation in comparison with the case, when it is assumed that the bodies do not rotate. The study was carried out in order to evaluate the influence of various factors on the velocity of fragmentation of the meteoric body after destruction in order to construct possible trajectories of fallen on earth meteorites. A developed algorithm for solving the conjugation of aerodynamic and ballistic problems, taking into account the relative movement and rotation of the bodies, can be used to solve technical problems, for example, to study the dynamics of separation of aircraft stages.

This work is dedicated to application of bicompact schemes to numerical solution of evolutionary hyperbolic equations. The main advantage of this class of schemes lies in combination of two beneficial properties: the first one is spatial approximation of high even order on a stencil that always occupies only one mesh cell; the second one is spectral resolution which is better in comparison to classic compact finite-difference schemes of the same order of spatial approximation. One feature of bicompact schemes is considered: their spatial approximation is rigidly tied to Cartesian meshes (with parallelepiped-shaped cells in three-dimensional case). This feature makes rather challenging any application of bicompact schemes to problems with complex computational domains as treated in the framework of unstructured meshes. This problem is proposed to be solved using well-known methods for treating complex-shaped boundaries and their corresponding boundary conditions on Cartesian meshes. The generalization of bicompact schemes on problems in geometrically complex domains is made in case of gas dynamics problems and Euler equations. The free boundary method is chosen as a particular tool to introduce the influence of arbitrary-shaped solid boundaries on gas flows on Cartesian meshes. A brief description of this method is given, its governing equations are written down. Bicompact schemes of fourth order of approximation in space with locally one-dimensional splitting are constructed for equations of the free boundary method. Its compensation flux is discretized with second order of accuracy. Time stepping in the obtained schemes is done with the implicit Euler method and the third order accurate $L$-stable stiffly accurate three-stage singly diagonally implicit Runge–Kutta method. The designed bicompact schemes are tested on three two-dimensional problems: stationary supersonic flows with Mach number three past one circular cylinder and past three circular cylinders; the non-stationary interaction of planar shock wave with a circular cylinder in a channel with planar parallel walls. The obtained results are in a good agreement with other works: influence of solid bodies on gas flows is physically correct, pressure in control points on solid surfaces is calculated with the accuracy appropriate to the chosen mesh resolution and level of numerical dissipation.

The article describes an improved paired comparison method, which systematizes in tables the rules of logical conclusions and formulas of checking indices for comparison of technical systems. To achieve this goal, the authors formulate rational rules of logical conclusions in making a paired comparison of the systems. In addition, for the purpose of consistency check of the results of the assessment, the authors introduce parameters such as «the number of scores gained by one system» and «systems’ quality index»; moreover, they design corresponding calculation formulas. For the purposes of practical application of this method to design computer programs, the authors propose to use formalized variants of interconnected tables: a table for processing and systematization of expert information, a table of possible logical conclusions based on the results of comparison of a set number of technical systems and a table of check values in the paired comparison method used in quality assessment of a definite number of technical systems. These tables allow one to organize procedures of the information processing in a more rational way and to predominantly exclude the influence of mistakes on the results of quality assessment of technical systems at the stage of data input. The main positive effect from the implementation of the paired comparison method is observed in a considerable reduction of time and resources needed to organize experts work, process expert information, and to prepare and conduct distant interviews with experts (on the Internet or a local computer network of an organization). This effect is achieved by a rational use of input data of the quality of the systems to be assessed. The proposed method is applied to computer programs used in assessing the effectiveness and stability of large technical systems.

The paper presents the results of numerical simulation of different-temperature water flows turbulent mixing in a T-junctions in the FlowVision software package. The article describes in detail an experimental stand specially designed to obtain boundary conditions that are simple for most computational fluid dynamics software systems. Values of timeaveraged temperatures and velocities in the control sensors and planes were obtained according to the test results. The article presents the system of partial differential equations used in the calculation describing the process of heat and mass transfer in a liquid using the Smagorinsky turbulence model. Boundary conditions are specified that allow setting the random velocity pulsations at the entrance to the computational domain. Distributions of time-averaged water velocity and temperature in control sections and sensors are obtained. The simulation is performed on various computational grids, for which the axes of the global coordinate system coincide with the directions of hot and cold water flows. The possibility for FlowVision PC to construct a computational grid in the simulation process based on changes in flow parameters is shown. The influence of such an algorithm for constructing a computational grid on the results of calculations is estimated. The results of calculations on a diagonal grid using a beveled scheme are given (the direction of the coordinate lines does not coincide with the direction of the tee pipes). The high efficiency of the beveled scheme is shown when modeling flows whose general direction does not coincide with the faces of the calculated cells. A comparison of simulation results on various computational grids is carried out. The numerical results obtained in the FlowVision PC are compared with experimental data and calculations performed using other computing programs. The results of modeling turbulent mixing of water flow of different temperatures in the FlowVision PC are closer to experimental data in comparison with calculations in CFX ANSYS. It is shown that the application of the LES turbulence model on relatively small computational grids in the FlowVision PC allows obtaining results with an error within 5%.

Exact solution of the stationary problem of wind-induced flow of two-layered viscous fluid is found for two-dimensional in vertical plane current and for drift current in three-dimensional case. The condition of sliding is set on the bottom of a water body. The condition of nonpassage is set on the lateral surface. Results of some calculations are given in comparison with those obtained using Ekman’s model (which does not take into account horizontal viscosity of the layer).

The technique of simplification of mathematical model of a chemical reaction by reducing the number of steps of the reaction scheme, based on an analysis of sensitivity to changes in the objective function of the model parameters, is proposed. The reduced scheme of model reaction of formaldehyde oxidation is received. Functional characterizes the measure of proximity to the calculated values for the initial kinetic reaction scheme and the scheme resulting disturbance of its parameters. The advantage of this technique is the ability to analyze complex kinetic schemes and reduction of kinetic models to a size suitable for practical use. The results of computational experiments under different reaction conditions can be included in the functional and thus to receive the reduce scheme, which is consistent the detailed scheme for the desired range of conditions. Sensitivity analysis of the functional model allows to identify those parameters, which provide the largest (or smallest) the contribution to the result of the process simulation. The mathematical model can contain parameters, which change of values do not affect the qualitative and quantitative description of the process. The contribution of these parameters in the functional value won’t be of great importance. Thus it can be eliminated from consideration, which do not serve for modeling kinetic curves substances. The kinetic scheme of formaldehyde oxidation, the detailed mechanism which includes 25 stages and 15 substances, were investigated using this method. On the basis of the local and global sensitivity analysis, the most important stage of the process that affect the overall dynamics of the target concentrations of the reaction. The reduced scheme of model reaction of formaldehyde oxidation is received. This scheme also describes the behavior of the main substances, as detailed scheme, but has a much smaller number of reaction stages. The results of the comparative analysis of modeling of formaldehyde oxidation on detailed and reduced schemes are given. Computational aspects of the problems of chemical kinetics by Sobol’ global method an example of this reaction are specified. The comparison results are local, global and total sensitivity indices are given.