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In present paper we reexamine the properties of CABARET numerical scheme formulated for a weakly compressible fluid flow basing the results of free shear layer modeling. Kelvin–Helmholtz instability and successive generation of two-dimensional turbulence provide a wide field for a scheme analysis including temporal evolution of the integral energy and enstrophy curves, the vorticity patterns and energy spectra, as well as the dispersion relation for the instability increment. The most part of calculations is performed for Reynolds number $\text{Re} = 4 \times 10^5$ for square grids sequentially refined in the range of $128^2-2048^2$ nodes. An attention is paid to the problem of underresolved layers generating a spurious vortex during the vorticity layers roll-up. This phenomenon takes place only on a coarse grid with $128^2$ nodes, while the fully regularized evolution pattern of vorticity appears only when approaching $1024^2$-node grid. We also discuss the vorticity resolution properties of grids used with respect to dimensional estimates for the eddies at the borders of the inertial interval, showing that the available range of grids appears to be sufficient for a good resolution of small–scale vorticity patches. Nevertheless, we claim for the convergence achieved for the domains occupied by large-scale structures.

The generated turbulence evolution is consistent with theoretical concepts imposing the emergence of large vortices, which collect all the kinetic energy of motion, and solitary small-scale eddies. The latter resemble the coherent structures surviving in the filamentation process and almost noninteracting with other scales. The dissipative characteristics of numerical method employed are discussed in terms of kinetic energy dissipation rate calculated directly and basing theoretical laws for incompressible (via enstrophy curves) and compressible (with respect to the strain rate tensor and dilatation) fluid models. The asymptotic behavior of the kinetic energy and enstrophy cascades comply with two-dimensional turbulence laws $E(k) \propto k^{−3}, \omega^2(k) \propto k^{−1}$. Considering the instability increment as a function of dimensionless wave number shows a good agreement with other papers, however, commonly used method of instability growth rate calculation is not always accurate, so some modification is proposed. Thus, the implemented CABARET scheme possessing remarkably small numerical dissipation and good vorticity resolution is quite competitive approach compared to other high-order accuracy methods

Based on the modeling method using a mesh system, an algorithm is implemented for solving a unsteady problem with moving bodies The algorithm takes into account the movement and rotation of bodies according to a given law of motion. The algorithm is applied to analysis the flow around an infinite composed of cylinders with an elliptical cross-section, which either move across the flow or rotate with a change in the angle of attack. To simulate the flow of bodies with a sharp edge, characteristic of the profiles of gas turbine machines, an algorithm for constructing a mesh of type C with the inclusion of a certain area behind the profile is implemented. The program for modeling the flow near the profile is implemented within the framework of models of Euler equations, Navier – Stokes equations in the approximation of a thin layer with laminar viscosity and turbulent viscosity in the framework of an algebraic viscosity model. The program has also been adapted to solve the problems of internal gas dynamics of turbomachines. For this purpose, the method of setting the boundary conditions at the entrance and exit from the calculated area from the velocity to the pressure drop, as well as at the lateral boundaries from the free flow to the periodicity, was changed. This made it possible to simulate the flow of gas in the inter-blade channels of compressors and turbines of gas turbine engines. To refine the algorithm, a series of calculations of the aerodynamic parameters of several turbine cascades in various subsonic and supersonic modes and their comparison with the experiment were carried out. Calculations of turbine grating parameters were carried out within the framework of the inviscid and viscous gas model. The calculation and experiment were compared by the distribution of gas parameters near the profile, as well as by the energy losses of the flow in the cascade. Calculations have shown the applicability and correctness of the program to solve this class of problems. To test the program on the problems of external subsonic aerodynamics, calculations of the aerodynamic characteristics of an isolated airfoil in an undisturbed flow were performed. The results obtained allow us to assert the applicability of the hybrid grid method to various classes of problems of applied gas dynamics.

In molecular systems with hydrogen bonds the mechanism of proton relaxation can take place. It is caused by redistribution of protons between two steady positions in double walls potential along the line of the hydrogen bond. This redistribution occurs at change of parameters of the double walls potential of the hydrogen bond which is caused by change of an electronic state of molecular system. The relaxation process is carried out due to a tunnel transfer of protons along the line of bonds. It is shown, that relaxation process can define temperature dependence of power parameters (either of the free energy differences ΔG or of the reorganization energy λ) of charge recombination P⁺Q^-_A from RC of Rhodobacter sphaeroides.

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.

The paper is devoted to the study of wave and relaxation effects during the pulsed outflow of a gas mixture with a high content of solid particles from a cylindrical channel during its initial partial filling. The problem is formulated in a two-speed two-temperature formulation and was solved numerically by the hybrid large-particle method of the second order of approximation. The numerical algorithm is implemented in the form of parallel computing using basic Free Pascal language tools. The applicability and accuracy of the method for wave flows of concentrated gas-particles mixtures is confirmed by comparison with test asymptotically accurate solutions. The calculation error on a grid of low detail in the characteristic flow zones of a two-phase medium was 10^-6 . . . 10^-5.

Based on the wave diagram, the analysis of the physical pattern of the outflow of a gas suspension partially filling a cylindrical channel is performed. It is established that, depending on the degree of initial filling of the channel, various outflow modes are formed. The first mode is implemented with a small degree of loading of the high-pressure chamber, at which the left boundary of the gas-particles mixture crosses the outlet section before the arrival of the rarefaction wave reflected from the bottom of the channel. At the same time, the maximum value of the mass flow rate of the mixture is achieved. Other modes are formed in cases of a larger initial filling of the channel, when the rarefaction waves reflected from the bottom of the channel interact with the gas suspension layer and reduce the intensity of its outflow.

The influence of relaxation properties with changing particle size on the dynamics of a limited layer of a gas-dispersed medium is studied. Comparison of the outflow of a limited gas suspension layer with different particle sizes shows that for small particles (the Stokes number is less than 0.001), an anomalous phenomenon of the simultaneous existence of shock wave structures in the supersonic and subsonic flow of gas and suspension is observed. With an increase in the size of dispersed inclusions, the compaction jumps in the region of the two-phase mixture are smoothed out, and for particles (the Stokes number is greater than 0.1), they practically disappear. At the same time, the shock-wave configuration of the supersonic gas flow at the outlet of the channel is preserved, and the positions and boundaries of the energy-carrying volumes of the gas suspension are close when the particle sizes change.

The development of structured molecular systems based on a nucleic acid framework takes into account the ability of single-stranded DNA to form a stable double-stranded structure due to stacking interactions and hydrogen bonds of complementary pairs of nucleotides. To increase the stability of the DNA double helix and to expand the temperature range in the hybridization protocols, it was proposed to use more stable metal-mediated complexes of nucleotide pairs as an alternative to Watson-Crick hydrogen bonds. One of the most frequently considered options is the use of silver ions to stabilize a pair of cytosines from opposite DNA strands. Silver ions specifically bind to N3 cytosines along the helix axis to form, as is believed, a strong N3–Ag⁺–N3 bond, relative to which, two rotational isomers, the cis- and trans-configurations of C–Ag⁺–C can be formed. In present work, a theoretical study and a comparative analysis of the free energy profile of the dissociation of two С–Ag⁺–C isomers were carried out using the combined method of molecular mechanics and quantum chemistry (QM/MM). As a result, it was shown that the cis-configuration is more favorable in energy than the trans- for a single pair of cytosines, and the geometry of the global minimum at free energy profile for both isomers differs from the equilibrium geometries obtained previously by quantum chemistry methods. Apparently, the silver ion stabilization model of the DNA duplex should take into account not only the direct binding of silver ions to cytosines, but also the presence of related factors, such as stacking interaction in extended DNA, interplanar hydrogen bonds, and metallophilic interaction of neighboring silver ions.

A molecular model of phicobilisome complex with a quenching protein OCP which regulates the energy transfer from phicobilisome to photosystem in photosynthetic apparatus of cyanobacteria has been developed. In the model obtained a well known spatial structure of interacting proteins remains intact and also the energy transfer from phycobilisome to OCP with reasonable rates is possible. Free energy of complex formation was calculated using MM–PBSA approach. By the order of magnitude this energy is about tens of kJ/mole. This value correlates well with experimental observed low stability of this complex. The specific surface energy of interaction between hydrophylic phicobilisome and OCP is twice larger than specific surface energy of their interaction with water. This reflects a high molecular complementary of interacting protein surfaces and is a strong pro argument for proposed model.

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.

Metal hydrides are an interesting class of chemical compounds that can reversibly bind a large amount of hydrogen and are, therefore, of interest for energy applications. Understanding the factors affecting the kinetics of hydride formation and decomposition is especially important. Features of the material, experimental setup and conditions affect the mathematical description of the processes, which can undergo significant changes during the processing of experimental data. The article proposes a general approach to numerical modeling of the formation and decomposition of metal hydrides and solving inverse problems of estimating material parameters from measurement data. The models are divided into two classes: diffusive ones, that take into account the gradient of hydrogen concentration in the metal lattice, and models with fast diffusion. The former are more complex and take the form of non-classical boundary value problems of parabolic type. A rather general approach to the grid solution of such problems is described. The second ones are solved relatively simply, but can change greatly when model assumptions change. Our experience in processing experimental data shows that a flexible software tool is needed; a tool that allows, on the one hand, building models from standard blocks, freely changing them if necessary, and, on the other hand, avoiding the implementation of routine algorithms. It also should be adapted for high-performance systems of different paradigms. These conditions are satisfied by the HIMICOS library presented in the paper, which has been tested on a large number of experimental data. It allows simulating the kinetics of formation and decomposition of metal hydrides, as well as related tasks, at three levels of abstraction. At the low level, the user defines the interface procedures, such as calculating the time layer based on the previous layer or the entire history, calculating the observed value and the independent variable from the task variables, comparing the curve with the reference. Special algorithms can be used for solving quite general parabolic-type boundary value problems with free boundaries and with various quasilinear (i.e., linear with respect to the derivative only) boundary conditions, as well as calculating the distance between the curves in different metric spaces and with different normalization. This is the middle level of abstraction. At the high level, it is enough to choose a ready tested model for a particular material and modify it in relation to the experimental conditions.

Mechanical properties of eukaryotic cells play an important role in life cycle conditions and in the development of pathological processes. In this paper we discuss the problem of parameters identification and verification of viscoelastic constitutive models based on force spectroscopy data of living cells. It is proposed to use one-dimensional continuous wavelet transform to calculate the relaxation function. Analytical calculations and the results of numerical simulation are given, which allow to obtain relaxation functions similar to each other on the basis of experimentally determined force curves and theoretical stress-strain relationships using wavelet differentiation algorithms. Test examples demonstrating correctness of software implementation of the proposed algorithms are analyzed. The cell models are considered, on the example of which the application of the proposed procedure of identification and verification of their parameters is demonstrated. Among them are a structural-mechanical model with parallel connected fractional elements, which is currently the most adequate in terms of compliance with atomic force microscopy data of a wide class of cells, and a new statistical-thermodynamic model, which is not inferior in descriptive capabilities to models with fractional derivatives, but has a clearer physical meaning. For the statistical-thermodynamic model, the procedure of its construction is described in detail, which includes the following. Introduction of a structural variable, the order parameter, to describe the orientation properties of the cell cytoskeleton. Setting and solving the statistical problem for the ensemble of actin filaments of a representative cell volume with respect to this variable. Establishment of the type of free energy depending on the order parameter, temperature and external load. It is also proposed to use an oriented-viscous-elastic body as a model of a representative element of the cell. Following the theory of linear thermodynamics, evolutionary equations describing the mechanical behavior of the representative volume of the cell are obtained, which satisfy the basic thermodynamic laws. The problem of optimizing the parameters of the statisticalthermodynamic model of the cell, which can be compared both with experimental data and with the results of simulations based on other mathematical models, is also posed and solved. The viscoelastic characteristics of cells are determined on the basis of comparison with literature data.