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The repressor is the first genetic regulatory network in synthetic biology, which was artificially constructed in 2000. It is a closed network of three genetic elements — $lacI$, $\lambda cI$ and $tetR$, — which have a natural origin, but are not found in nature in such a combination. The promoter of each of the three genes controls the next cistron via the negative feedback, suppressing the expression of the neighboring gene. In this paper, the nonlinear dynamics of a modified repressilator, which has time delays in all parts of the regulatory network, has been studied for the first time. Delay can be both natural, i.e. arises during the transcription/translation of genes due to the multistage nature of these processes, and artificial, i.e. specially to be introduced into the work of the regulatory network using synthetic biology technologies. It is assumed that the regulation is carried out by proteins being in a dimeric form. The considered repressilator has two more important modifications: the location on the same plasmid of the gene $gfp$, which codes for the fluorescent protein, and also the presence in the system of a DNA sponge. In the paper, the nonlinear dynamics has been considered within the framework of the deterministic description. By applying the method of decomposition into fast and slow motions, the set of nonlinear differential equations with delay on a slow manifold has been obtained. It is shown that there exists a single equilibrium state which loses its stability in an oscillatory manner at certain values of the control parameters. For a symmetric repressilator, in which all three genes are identical, an analytical solution for the neutral Andronov–Hopf bifurcation curve has been obtained. For the general case of an asymmetric repressilator, neutral curves are found numerically. It is shown that the asymmetric repressor generally is more stable, since the system is oriented to the behavior of the most stable element in the network. Nonlinear dynamic regimes arising in a repressilator with increase of the parameters are studied in detail. It was found that there exists a limit cycle corresponding to relaxation oscillations of protein concentrations. In addition to the limit cycle, we found the slow manifold not associated with above cycle. This is the long-lived transitional regime, which reflects the process of long-term synchronization of pulsations in the work of individual genes. The obtained results are compared with the experimental data known from the literature. The place of the model proposed in the present work among other theoretical models of the repressilator is discussed.

The paper presents a physico-mathematical model of the perturbed region formed in the lower D-layer of the ionosphere under the action of directed radio emission flux from a terrestrial stand of the megahertz frequency range, obtained as a result of comprehensive theoretical studies. The model is based on the consideration of a wide range of kinetic processes taking into account their nonequilibrium and in the two-temperature approximation for describing the transformation of the radio beam energy absorbed by electrons. The initial data on radio emission achieved by the most powerful radio-heating stands are taken in the paper. Their basic characteristics and principles of functioning, and features of the altitude distribution of the absorbed electromagnetic energy of the radio beam are briefly described. The paper presents the decisive role of the D-layer of the ionosphere in the absorption of the energy of the radio beam. On the basis of theoretical analysis, analytical expressions are obtained for the contribution of various inelastic processes to the distribution of the absorbed energy, which makes it possible to correctly describe the contribution of each of the processes considered. The work considers more than 60 components. The change of the component concentration describe about 160 reactions. All the reactions are divided into five groups according to their physical content: ionization-chemical block, excitation block of metastable electronic states, cluster block, excitation block of vibrational states and block of impurities. Blocks are interrelated and can be calculated both jointly and separately. The paper presents the behavior of the parameters of the perturbed region in daytime and nighttime conditions is significantly different at the same radio flux density: under day conditions, the maximum electron concentration and temperature are at an altitude of ~45–55 km; in night ~80 km, with the temperature of heavy particles rapidly increasing, which leads to the occurrence of a gas-dynamic flow. Therefore, a special numerical algorithm are developed to solve two basic problems: kinetic and gas dynamic. Based on the altitude and temporal behavior of concentrations and temperatures, the algorithm makes it possible to determine the ionization and emission of the ionosphere in the visible and infrared spectral range, which makes it possible to evaluate the influence of the perturbed region on radio engineering and optoelectronic devices used in space technology.

The paper investigates the features of group dynamics of individuals-agents in the computer model of the animal population interacting with each other and with a renewable resource. This type of dynamics was previously found in [Belotelov, Konovalenko, 2016]. The model population consists of a set of individuals. Each individual is characterized by its mass, which is identified with energy. It describes in detail the dynamics of the energy balance of the individual. The habitat of the simulated population is a rectangular area where the resource grows evenly (grass).

Various computer experiments carried out with the model under different parameter values and initial conditions are described. The main purpose of these computational experiments was to study the group (herd) dynamics of individuals. It was found that in a fairly wide range of parameter values and with the introduction of spatial inhomogeneities of the area, the group type of behavior is preserved. The values of the model population parameters under which the regime of spatial oscillations of the population occurs were found numerically. Namely, in the model population periodically group (herd) behavior of animals is replaced by a uniform distribution over space, which after a certain number of bars again becomes a group. Numerical experiments on the preliminary analysis of the factors influencing the period of these solutions are carried out. It turned out that the leading parameters affecting the frequency and amplitude, as well as the number of groups are the mobility of individuals and the rate of recovery of the resource. Numerical experiments are carried out to study the influence of parameters determining the nonlocal interaction between individuals of the population on the group behavior. It was found that the modes of group behavior persist for a long time with the exclusion of fertility factors of individuals. It is confirmed that the nonlocality of interaction between individuals is leading in the formation of group behavior.

Experimental, theoretical and numerical investigations of equatorial spread F, equatorial plasma bubbles (EPBs), plasma depletion shells, and plasma clouds are continued at new variety articles. Nonlinear growth, bifurcation, pinching, atomic and molecular ion dynamics are considered at there articles. But the authors of this article believe that not all parameters of EPB development are correct. For example, EPB bifurcation is highly questionable.

A maximum speed inside EPBs and a development time of EPB are defined and studied. EPBs starting from one, two or three zones of the increased density (initial plasma clouds). The development mechanism of EPB is the Rayleigh-Taylor instability (RTI). Time of the initial stage of EPB development went into EPB favorable time interval (in this case the increase linear increment is more than zero) and is 3000–7000 c for the Earth equatorial ionosphere.

Numerous computing experiments were conducted with use of the original two-dimensional mathematical and numerical model MI2, similar USA standard model SAMI2. This model MI2 is described in detail. The received results can be used both in other theoretical works and for planning and carrying out natural experiments for generation of F-spread in Earth ionosphere.

Numerical simulating was carried out for the geophysical conditions favorable for EPBs development. Numerical researches confirmed that development time of EPBs from initial irregularities with the increased density is significantly more than development time from zones of the lowered density. It is shown that developed irregularities interact among themselves strongly and not linearly even then when initial plasma clouds are strongly removed from each other. In addition, this interaction is stronger than interaction of EPBs starting from initial irregularities with the decreased density. The numerical experiments results showed the good consent of developed EPB parameters with experimental data and with theoretical researches of other authors.

Seasonal migrations and herd instinct are traditionally recognized as wild reindeer (Rangifer tarandus L.) species-specific behavioral signs. These animals are forced to overcome water obstacles during the migrations. Behaviour peculiarities are considered as the result of the selection process, which has chosen among the sets of strategies, as the only evolutionarily stable one, determining the reproduction and biological survival of wild reindeer as a species. Natural processes in the Taimyr population wild reindeer are currently occurring against the background of an increase in the influence of negative factors due to the escalation of the industrial development of the Arctic. That is why the need to identify the ethological features of these animals completely arose. This paper presents the results of applying the classical methods of the theory of optimal control and differential games to the wild reindeer study of the migration patterns in overcoming water barriers, including major rivers. Based on these animals’ ethological features and behavior forms, the herd is presented as a controlled dynamic system, which presents also two classes of individuals: the leader and the rest of the herd, for which their models, describing the trajectories of their movement, are constructed. The models are based on hypotheses, which are the mathematical formalization of some animal behavior patterns. This approach made it possible to find the trajectory of the important one using the methods of the optimal control theory, and in constructing the trajectories of other individuals, apply the principle of control with a guide. Approbation of the obtained results, which can be used in the formation of a common “platform” for the adaptive behavior models systematic construction and as a reserve for the cognitive evolution models fundamental development, is numerically carried out using a model example with observational data on the Werchnyaya Taimyra River.

In real problems of exploration seismology we deal with a heterogeneity of the nature of elastic waves interaction with the surface of a fracture by the propagation through it. The fracture is a complex heterogeneous structure. In some locations the surfaces of fractures are placed some distance apart and are separated by filling fluid or emptiness, in some places we can observe the gluing of surfaces, when under the action of pressure forces the fracture surfaces are closely adjoined to each other. In addition, fractures can be classified by the nature of saturation: fluid or gas. Obviously, for such a large variety in the structure of fractures, one cannot use only one model that satisfies all cases.

This article is concerned with description of developed mathematical fracture models which can be used for numerical solution of exploration seismology problems using the grid-characteristic method on unstructured triangular (in 2D-case) and tetrahedral (in 3D-case) meshes. The basis of the developed models is the concept of an infinitely thin fracture, whose aperture does not influence the wave processes in the fracture area. These fractures are represented by bound areas and contact boundaries with different conditions on contact and boundary surfaces. Such an approach significantly reduces the consumption of computer resources since there is no need to define the mesh inside the fracture. On the other side, it allows the fractures to be given discretely in the integration domain, therefore, one can observe qualitatively new effects, such as formation of diffractive waves and multiphase wave front due to multiple reflections between the surfaces of neighbor fractures, which cannot be observed by using effective fracture models actively used in computational seismology.

The computational modeling of seismic waves propagation through layers of mesofractures was produced using developed fracture models. The results were compared with the results of physical modeling in problems in the same statements.

The paper presents a mathematical model that describes the process of obtaining biogas from livestock waste. This model describes the processes occurring in a biogas plant for mesophilic and thermophilic media, as well as for continuous and periodic modes of substrate inflow. The values of the coefficients of this model found earlier for the periodic mode, obtained by solving the problem of model identification from experimental data using a genetic algorithm, are given.

For the model of methanogenesis, an optimal control problem is formulated in the form of a Lagrange problem, whose criterial functionality is the output of biogas over a certain period of time. The controlling parameter of the task is the rate of substrate entry into the biogas plant. An algorithm for solving this problem is proposed, based on the numerical implementation of the Pontryagin maximum principle. In this case, a hybrid genetic algorithm with an additional search in the vicinity of the best solution using the method of conjugate gradients was used as an optimization method. This numerical method for solving an optimal control problem is universal and applicable to a wide class of mathematical models.

In the course of the study, various modes of submission of the substrate to the digesters, temperature environments and types of raw materials were analyzed. It is shown that the rate of biogas production in the continuous feed mode is 1.4–1.9 times higher in the mesophilic medium (1.9–3.2 in the thermophilic medium) than in the periodic mode over the period of complete fermentation, which is associated with a higher feed rate of the substrate and a greater concentration of nutrients in the substrate. However, the yield of biogas during the period of complete fermentation with a periodic mode is twice as high as the output over the period of a complete change of the substrate in the methane tank at a continuous mode, which means incomplete processing of the substrate in the second case. The rate of biogas formation for a thermophilic medium in continuous mode and the optimal rate of supply of raw materials is three times higher than for a mesophilic medium. Comparison of biogas output for various types of raw materials shows that the highest biogas output is observed for waste poultry farms, the least — for cattle farms waste, which is associated with the nutrient content in a unit of substrate of each type.

Theory of anomalous diffusion, which describe a vast number of transport processes with power law mean squared displacement, is actively advancing in recent years. Diffusion of liquids in porous media, carrier transport in amorphous semiconductors and molecular transport in viscous environments are widely known examples of anomalous deceleration of transport processes compared to the standard model.

Direct Monte Carlo simulation is a convenient tool for studying such processes. An efficient stochastic simulation algorithm is developed in the present paper. It is based on simple renewal process with interarrival times that have power law asymptotics. Analytical derivations show a deep connection between this class of random process and equations with fractional derivatives. The algorithm is further generalized by coupling it with chemical reaction simulation. It makes stochastic approach especially useful, because the exact form of integrodifferential evolution equations for reaction — subdiffusion systems is still a matter of debates.

Proposed algorithm relies on non-markovian random processes, hence one should carefully account for qualitatively new effects. The main question is how molecules leave the system during chemical reactions. An exact scheme which tracks all possible molecule combinations for every reaction channel is computationally infeasible because of the huge number of such combinations. It necessitates application of some simple heuristic procedures. Choosing one of these heuristics greatly affects obtained results, as illustrated by a series of numerical experiments.

The paper considers the process of flow formation in an outflow of a binary gas mixture through a thin slit into vacuum. An approach to modeling the flows of rarefied gas mixtures in the transient regime is proposed based on the direct solution of the Boltzmann kinetic equation, in which the conservative projection method is used to calculate the collision integrals. Calculation formulas are provided; the calculation procedure is described in detail in relation to the flow of a binary gas mixture. The Lennard–Jones potential is used as an interaction potential of molecules. A software modeling environment has been developed that makes it possible to study the flows of gas mixtures in a transitional regime on systems of cluster architecture. Due to the use of code parallelization technologies, an acceleration of calculations by 50–100 times was obtained. Numerical simulation of a two-dimensional outflow of a binary argon-neon gas mixture from a vessel into vacuum through a thin slit is carried out for various values of the Knudsen number. The graphs of the dependence of gas mixture components output flow on time in the process of establishing the flow are obtained. Non-stationary regions of strong separation of gas mixture components, in which the molecular densities ratio reaches 10 or more, were discovered. The discovered effect can have applications in the problem of gas mixtures separation.

In this work, we develop a model of the immune response to respiratory viral infections taking into account some particular properties of the SARS-CoV-2 infection. The model represents a system of ordinary differential equations for the concentrations of epithelial cells, immune cells, virus and inflammatory cytokines. Conventional analysis of the existence and stability of stationary points is completed by numerical simulations in order to study dynamics of solutions. Behavior of solutions is characterized by large peaks of virus concentration specific for acute respiratory viral infections.

At the first stage, we study the innate immune response based on the protective properties of interferon secreted by virus-infected cells. On the other hand, viral infection down-regulates interferon production. Their competition can lead to the bistability of the system with different regimes of infection progression with high or low intensity. In the case of infection outbreak, the incubation period and the maximal viral load depend on the initial viral load and the parameters of the immune response. In particular, increase of the initial viral load leads to shorter incubation period and higher maximal viral load.

In order to study the emergence and dynamics of cytokine storm, we consider proinflammatory cytokines produced by cells of the innate immune response. Depending on parameters of the model, the system can remain in the normal inflammatory state specific for viral infections or, due to positive feedback between inflammation and immune cells, pass to cytokine storm characterized by excessive production of proinflammatory cytokines. Furthermore, inflammatory cell death can stimulate transition to cytokine storm. However, it cannot sustain it by itself without the innate immune response. Assumptions of the model and obtained results are in qualitative agreement with the experimental and clinical data.