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The paper proposes a set of fairly simple analysis algorithms that can be used to analyze a wide range of protein-protein interactions. In this work, we jointly use the methods of Brownian and molecular dynamics to describe the process of formation of a complex of plastocyanin and cytochrome f proteins in higher plants. In the diffusion-collision complex, two clusters of structures were revealed, the transition between which is possible with the preservation of the position of the center of mass of the molecules and is accompanied only by a rotation of plastocyanin by 134 degrees. The first and second clusters of structures of collisional complexes differ in that in the first cluster with a positively charged region near the small domain of cytochrome f, only the “lower” plastocyanin region contacts, while in the second cluster, both negatively charged regions. The “upper” negatively charged region of plastocyanin in the first cluster is in contact with the amino acid residue of lysine K122. When the final complex is formed, the plastocyanin molecule rotates by 69 degrees around an axis passing through both areas of electrostatic contact. With this rotation, water is displaced from the regions located near the cofactors of the molecules and formed by hydrophobic amino acid residues. This leads to the appearance of hydrophobic contacts, a decrease in the distance between the cofactors to a distance of less than 1.5 nm, and further stabilization of the complex in a position suitable for electron transfer. Characteristics such as contact matrices, rotation axes during the transition between states, and graphs of changes in the number of contacts during the modeling process make it possible to determine the key amino acid residues involved in the formation of the complex and to reveal the physicochemical mechanisms underlying this process.

A numerical simulation of fluid flow in a blood pump was performed using the FlowVision software package. This test problem, provided by the Center for Devices and Radiological Health of the US. Food and Drug Administration, involved considering fluid flow according to several design modes. At the same time for each case of calculation a certain value of liquid flow rate and rotor speed was set. Necessary data for calculations in the form of exact geometry, flow conditions and fluid characteristics were provided to all research participants, who used different software packages for modeling. Numerical simulations were performed in FlowVision for six calculation modes with the Newtonian fluid and standard $k-\varepsilon$ turbulence model, in addition, the fifth mode with the $k-\omega$ SST turbulence model and with the Caro rheological fluid model were performed. In the first stage of the numerical simulation, the convergence over the mesh was investigated, on the basis of which a final mesh with a number of cells of the order of 6 million was chosen. Due to the large number of cells, in order to accelerate the study, part of the calculations was performed on the Lomonosov-2 cluster. As a result of numerical simulation, we obtained and analyzed values of pressure difference between inlet and outlet of the pump, velocity between rotor blades and in the area of diffuser, and also, we carried out visualization of velocity distribution in certain cross-sections. For all design modes there was compared the pressure difference received numerically with the experimental data, and for the fifth calculation mode there was also compared with the experiment by speed distribution between rotor blades and in the area of diffuser. Data analysis has shown good correlation of calculation results in FlowVision with experimental results and numerical simulation in other software packages. The results obtained in FlowVision for solving the US FDA test suggest that FlowVision software package can be used for solving a wide range of hemodynamic problems.

The results of theoretical researches of molecular probe diffusion as well as its impact to probe fluorescence spectra are represented in this paper. The case with compound introduction to biological liquid as an injection has been considered. Shown, fluorescence spectra shifts of injected probe is a result of diffusion processes in biological liquid as well as its immobilization to contained structures (compound of peptides nature, different cell types and others).

The possibility of numerical 3D simulation of thrombi formation is considered.

The developed up to now detailed mathematical models describing formation of thrombi and clots include a great number of equations. Being implemented in a CFD code, the detailed mathematical models require essential computer resources for simulation of the thrombi growth in a blood flow. A reasonable alternative way is using reduced mathematical models. Two models based on the reduced mathematical model for the thrombin generation are described in the given paper.

The first model describes growth of a thrombus in a great vessel (artery). The artery flows are essentially unsteady. They are characterized by pulse waves. The blood velocity here is high compared to that in the vein tree. The reduced model for the thrombin generation and the thrombus growth in an artery is relatively simple. The processes accompanying the thrombin generation in arteries are well described by the zero-order approximation.

A vein flow is characterized lower velocity value, lower gradients, and lower shear stresses. In order to simulate the thrombin generation in veins, a more complex system of equations has to be solved. The model must allow for all the non-linear terms in the right-hand sides of the equations.

The simulation is carried out in the industrial software FlowVision.

The performed numerical investigations have shown the suitability of the reduced models for simulation of thrombin generation and thrombus growth. The calculations demonstrate formation of the recirculation zone behind a thrombus. The concentration of thrombin and the mass fraction of activated platelets are maximum here. Formation of such a zone causes slow growth of the thrombus downstream. At the upwind part of the thrombus, the concentration of activated platelets is low, and the upstream thrombus growth is negligible.

When the blood flow variation during a hart cycle is taken into account, the thrombus growth proceeds substantially slower compared to the results obtained under the assumption of constant (averaged over a hard cycle) conditions. Thrombin and activated platelets produced during diastole are quickly carried away by the blood flow during systole. Account of non-Newtonian rheology of blood noticeably affects the results.

The article proposes a space-time approach to modeling the diffusion of information and communication technologies based on the Fisher –Kolmogorov– Petrovsky – Piskunov equation, in which the diffusion kinetics is described by the Bass model, which is widely used to model the diffusion of innovations in the market. For this equation, its equilibrium positions are studied, and based on the singular perturbation theory, was obtained an approximate solution in the form of a traveling wave, i. e. a solution that propagates at a constant speed while maintaining its shape in space. The wave speed shows how much the “spatial” characteristic, which determines the given level of technology dissemination, changes in a single time interval. This speed is significantly higher than the speed at which propagation occurs due to diffusion. By constructing such an autowave solution, it becomes possible to estimate the time required for the subject of research to achieve the current indicator of the leader.

The obtained approximate solution was further applied to assess the factors affecting the rate of dissemination of information and communication technologies in the federal districts of the Russian Federation. Various socio-economic indicators were considered as “spatial” variables for the diffusion of mobile communications among the population. Growth poles in which innovation occurs are usually characterized by the highest values of “spatial” variables. For Russia, Moscow is such a growth pole; therefore, indicators of federal districts related to Moscow’s indicators were considered as factor indicators. The best approximation to the initial data was obtained for the ratio of the share of R&D costs in GRP to the indicator of Moscow, average for the period 2000–2009. It was found that for the Ural Federal District at the initial stage of the spread of mobile communications, the lag behind the capital was less than one year, for the Central Federal District, the Northwestern Federal District — 1.4 years, for the Volga Federal District, the Siberian Federal District, the Southern Federal District and the Far Eastern Federal District — less than two years, in the North Caucasian Federal District — a little more 2 years. In addition, estimates of the delay time for the spread of digital technologies (intranet, extranet, etc.) used by organizations of the federal districts of the Russian Federation from Moscow indicators were obtained.