All issues

Hemostasis system is one of the key body’s defense systems, which is presented in all the liquid tissues and especially important in blood. Hemostatic response is triggered as a result of the vessel injury. The interaction between specialized cells and humoral systems leads to the formation of the initial hemostatic clot, which stops bleeding. After that the slow process of clot dissolution occurs. The formation of hemostatic plug is a unique physiological process, because during several minutes the hemostatic system generates complex structures on a scale ranging from microns for microvessel injury or damaged endothelial cell-cell contacts, to centimeters for damaged systemic arteries. Hemostatic response depends on the numerous coordinated processes, which include platelet adhesion and aggregation, granule secretion, platelet shape change, modification of the chemical composition of the lipid bilayer, clot contraction, and formation of the fibrin mesh due to activation of blood coagulation cascade. Computer modeling is a powerful tool, which is used to study this complex system at different levels of organization. This includes study of intracellular signaling in platelets, modelling humoral systems of blood coagulation and fibrinolysis, and development of the multiscale models of thrombus growth. There are two key issues of the computer modeling in biology: absence of the adequate physico-mathematical description of the existing experimental data due to the complexity of the biological processes, and high computational complexity of the models, which doesn’t allow to use them to test physiologically relevant scenarios. Here we discuss some key unresolved problems in the field, as well as the current progress in experimental research of hemostasis and thrombosis. New findings lead to reevaluation of the existing concepts and development of the novel computer models. We focus on the arterial thrombosis, venous thrombosis, thrombosis in microcirculation and the problems of fibrinolysis and thrombolysis. We also briefly discuss basic types of the existing mathematical models, their computational complexity, and principal issues in simulation of thrombus growth in arteries.

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.

The problem of active control of the mechanical equilibrium of an inhomogeneously heated fluid in a thermosyphon is studied theoretically and experimentally. The control is performed by using a feedback subsystem which inhibits convection by changing the orientation of thermosyphon in space. It is shown that excess feedback leads to the excitation of oscillations which are related to a delay in the controller work. In the presense of noise, the oscillations arise even when deterministic description predicts stationary behaviour. The experimental data and theory are in good agreement.

It proposes a new alternative approach to explain the flat spectrum of the velocity for stars orbital motion on the periphery of spiral galaxies. In particular, that velocity significant excess of speed calculated according to the virial theorem. The concept is the assumption of the existence for gravitational field of the Central body of the galaxy cylindrical, and not spherical, symmetry. The configuration of this field can be explained by the presence on galaxy axis the cosmic string, the length of which covers the diameter of the disk of the galaxy. This model will be subjected to comparison with the more traditional concept of the availability of the spiral galaxy ball halo of dark matter. For this approach it will also be offered a kinematic model, and the hypothesis about the nature of dark matter. It examines the data of astronomical observations about the presence of cosmic strings in the zones adjacent to galaxies.

This paper is devoted to investigation of the swirl flows. Such flows are widely used in various industrial processes. Swirl flows can be accompanied by time-dependent effects, for example, precession of the vortex core. In turn, the large-scale fluctuations due to the precession of the vortex can cause damage of structures and reduce of equipment reliability. Thus, for engineering calculations approaches that sufficiently well described such flows are required. This paper presents the technique of swirl flows calculation, tested for CFD packages Fluent and SigmaFlow. A numerical simulation of several swirl flow test problems was carried out. Obtained results are compared with each other and with the experimental data.

We consider a new set of tests which assigns to detection of human capability for parallel calculation. The new tests support the homogenous statistical distribution of results in distinction to the tests discussed in our previous works. This feature simplifies the analysis of test results and decreases the estimate of statistical error. The new experimental data is close to results obtained in previous experiments.

Here we demonstrate the results of kinetic modeilng of DNA double-strand breaks induction and repair and phosphorilated histone H2AX ($\gamma$-H2AX) and Rad51 foci formation in primary human fibroblasts exposed to low-LET ionizing radiation (IR). The model describes two major paths of DNA double-strand breaks repair: non-homologous end joining (NHEJ) and homologous recombination (HR) and considers interactions between DNA and several repair proteins (DNA-PKcs, ATM, Ku70/80, XRCC1, XRCC4, Rad51, RPA, etc.) using mass action equations and Michaelis–Menten kinetics. Experimental data on DNA rejoining kinetics and $\gamma$-H2AX and Rad51 foci formation in vicinity of double strand breaks in primary human fibroblasts exposed to low-LET IR with various dose rates and exposure times was utilized for training and statistical validation of the model.

A hybrid cluster implies the use of computational devices with radically different architectures. Usually, these are conventional CPU architecture (e.g. x86_64) and GPU architecture (e. g. NVIDIA CUDA). Creating and exploiting such a cluster requires some experience: in order to harness all computational power of the described system and get substantial speedup for computational tasks many factors should be taken into account. These factors consist of hardware characteristics (e.g. network infrastructure, a type of data storage, GPU architecture) as well as software stack (e.g. MPI implementation, GPGPU libraries). So, in order to run scientific applications GPU capabilities, software features, task size and other factors should be considered.

This report discusses opportunities and problems of hybrid computations. Some statistics from tests programs and applications runs will be demonstrated. The main focus of interest is open source applications (e. g. OpenFOAM) that support GPGPU (with some parts rewritten to use GPGPU directly or by replacing libraries).

There are several approaches to organize heterogeneous computations for different GPU architectures out of which CUDA library and OpenCL framework are compared. CUDA library is becoming quite typical for hybrid systems with NVIDIA cards, but OpenCL offers portability opportunities which can be a determinant factor when choosing framework for development. We also put emphasis on multi-GPU systems that are often used to build hybrid clusters. Calculations were performed on a hybrid cluster of SPbU computing center.

A mathematical model that reflects the main features of the protests is constructed in this paper. An analytical solution was found with assuming that only excited part of the population involved in protests. The numerical value of the model coefficients was estimated from the real data for the cascade of protests that took place in Leipzig in 1989. The changes of the participants number in the protest action with influence the model coefficients was analysed.

The article covered results of three-dimensional modeling of ecologic situation of shallow water on the example of the Azov Sea with using schemes of increased order of accuracy on multiprocessor computer system of Southern Federal University. Discrete analogs of convective and diffusive transfer operators of the fourth order of accuracy in the case of partial occupancy of cells were constructed and studied. The developed scheme of the high (fourth) order of accuracy were used for solving problems of aquatic ecology and modeling spatial distribution of polluting nutrients, which caused growth of phytoplankton, many species of which are toxic and harmful. The use of schemes of the high order of accuracy are improved the quality of input data and decreased the error in solutions of model tasks of aquatic ecology. Numerical experiments were conducted for the problem of transportation of substances on the basis of the schemes of the second and fourth orders of accuracy. They’re showed that the accuracy was increased in 48.7 times for diffusion-convection problem. The mathematical algorithm was proposed and numerically implemented, which designed to restore the bottom topography of shallow water on the basis of hydrographic data (water depth at individual points or contour level). The map of bottom relief of the Azov Sea was generated with using this algorithm. It’s used to build fields of currents calculated on the basis of hydrodynamic model. The fields of water flow currents were used as input data of the aquatic ecology models. The library of double-layered iterative methods was developed for solving of nine-diagonal difference equations. It occurs in discretization of model tasks of challenges of pollutants concentration, plankton and fish on multiprocessor computer system. It improved the precision of the calculated data and gave the possibility to obtain operational forecasts of changes in ecologic situation of shallow water in short time intervals.