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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.

By numerical simulation methods the interaction processes of oscillating soliton (breather) with a 180-degree Neel domain wall in the framework of a (2 + 1)-dimensional supersymmetric O(3) nonlinear sigma model is studied. The purpose of this paper is to investigate nonlinear evolution and stability of a system of interacting localized dynamic and topological solutions. To construct the interaction models, were used a stationary breather and domain wall solutions, where obtained in the framework of the two-dimensional sine-Gordon equation by adding specially selected perturbations to the A3-field vector in the isotopic space of the Bloch sphere. In the absence of an external magnetic field, nonlinear sigma models have formal Lorentz invariance, which allows constructing, in particular, moving solutions and analyses the experimental data of the nonlinear dynamics of an interacting solitons system. In this paper, based on the obtained moving localized solutions, models for incident and head-on collisions of breathers with a domain wall are constructed, where, depending on the dynamic parameters of the system, are observed the collisions and reflections of solitons from each other, a long-range interactions and also the decay of an oscillating soliton into linear perturbation waves. In contrast to the breather solution that has the dynamics of the internal degree of freedom, the energy integral of a topologically stable soliton in the all experiments the preserved with high accuracy. For each type of interaction, the range of values of the velocity of the colliding dynamic and topological solitons is determined as a function of the rotation frequency of the A3-field vector in the isotopic space. Numerical models are constructed on the basis of methods of the theory of finite difference schemes, using the properties of stereographic projection, taking into account the group-theoretical features of constructions of the O(N) class of nonlinear sigma models of field theory. On the perimeter of the two-dimensional modeling area, specially developed boundary conditions are established that absorb linear perturbation waves radiated by interacting soliton fields. Thus, the simulation of the interaction processes of localized solutions in an infinite two-dimensional phase space is carried out. A software module has been developed that allows to carry out a complex analysis of the evolution of interacting solutions of nonlinear sigma models of field theory, taking into account it’s group properties in a two-dimensional pseudo-Euclidean space. The analysis of isospin dynamics, as well the energy density and energy integral of a system of interacting dynamic and topological solitons is carried out.

Analysis and practical aspects of implementing developed in the control theory robust control methods in studying economic systems is carried out. The main emphasis is placed on studying results obtained for dynamical systems with structured uncertainty. Practical aspects of implementing such results in control of economic systems on the basis of dynamical models with uncertain parameters and perturbations (stabilization of price on the oil market and inflation in macroeconomic systems) are discussed. With the help of specially constructed aggregate model of oil price dynamics studied the problem of finding control which provides minimal deviation of price from desired levels over middle range period. The second real problem considered in the article consists in determination of stabilizing control providing minimal deviation of inflation from desired levels (on the basis of constructed aggregate macroeconomic model of the USA over middle range period).

Upper levels of parameters uncertainty and control laws guaranteeing stabilizability of the real considered economic systems have been found using the robust method of control with structured uncertainty. At the same time we have come to the conclusion that received estimates of parameters uncertainty upper levels are conservative. Monte-Carlo experiments carried out for the article made it possible to analyze dynamics of oil price and inflation under received limit levels of models parameters uncertainty and under implementing found robust control laws for the worst and the best scenarios. Results of these experiments show that received robust control laws may be successfully used under less stringent uncertainty constraints than it is guaranteed by sufficient conditions of stabilization.

The repressilator 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 our previous paper [Bratsun et al., 2018], we proposed a mathematical model of a delayed repressillator and studied its properties within the framework of a deterministic description. We assume that 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 gene engineering technologies. In this work, we apply the stochastic description of dynamic processes in a delayed repressilator, which is an important addition to deterministic analysis due to the small number of molecules involved in gene regulation. The stochastic study is carried out numerically using the Gillespie algorithm, which is modified for time delay systems. We present the description of the algorithm, its software implementation, and the results of benchmark simulations for a onegene delayed autorepressor. When studying the behavior of a repressilator, we show that a stochastic description in a number of cases gives new information about the behavior of a system, which does not reduce to deterministic dynamics even when averaged over a large number of realizations. We show that in the subcritical range of parameters, where deterministic analysis predicts the absolute stability of the system, quasi-regular oscillations may be excited due to the nonlinear interaction of noise and delay. Earlier, we have discovered within the framework of the deterministic description, that there exists a long-lived transient regime, which is represented in the phase space by a slow manifold. This mode reflects the process of long-term synchronization of protein pulsations in the work of the repressilator genes. In this work, we show that the transition to the cooperative mode of gene operation occurs a two order of magnitude faster, when the effect of the intrinsic noise is taken into account. We have obtained the probability distribution of moment when the phase trajectory leaves the slow manifold and have determined the most probable time for such a transition. The influence of the intrinsic noise of chemical reactions on the dynamic properties of the repressilator is discussed.

The paper presents an analysis of the nonlinear equation of spin wave transport by the method of characteristics. The conclusion of a new mathematical model of spin wave propagation is presented for the solution of which the characteristic is applied. The behavior analysis of the behavior of the real and imaginary parts of the wave and its amplitude is performed. The phase portraits demonstrate the dependence of the desired function on the nonlinearity coefficient. It is established that the real and imaginary parts of the wave oscillate by studying the nature of the evolution of the initial wave profile by the phase plane method. The transition of trajectories from an unstable focus to a limiting cycle, which corresponds to the oscillation of the real and imaginary parts, is shown. For the amplitude of the wave, such a transition is characterized by its amplification or attenuation (depending on the nonlinearity coefficient and the chosen initial conditions) up to a certain threshold value. It is shown that the time of the transition process from amplification (attenuation) to stabilization of the amplitude also depends on the nonlinearity parameter. It was found out that at the interval of amplification of the amplitude of the spin wave, the time of the transition process decreases, and lower amplitude values correspond to higher parameters of nonlinearity.

In the last few years, significant progress has been observed in the field of rotating detonation engines for aircrafts. Scientific laboratories around the world conduct both fundamental researches related, for example, to the issues of effective mixing of fuel and oxidizer with the separate supply, and applied development of existing prototypes. The paper provides a brief overview of the main results of the most significant recent computational work on the study of propagation of a onedimensional pulsating gaseous detonation wave in a non-uniform medium. The general trends observed by the authors of these works are noted. In these works, it is shown that the presence of parameter perturbations in front of the wave front can lead to regularization and to resonant amplification of pulsations behind the detonation wave front. Thus, there is an appealing opportunity from a practical point of view to influence the stability of the detonation wave and control it. The aim of the present work is to create an instrument to study the gas-dynamic mechanisms of these effects.

The mathematical model is based on one-dimensional Euler equations supplemented by a one-stage model of the kinetics of chemical reactions. The defining system of equations is written in the shock-attached frame that leads to the need to add a shock-change equations. A method for integrating this equation is proposed, taking into account the change in the density of the medium in front of the wave front. So, the numerical algorithm for the simulation of detonation wave propagation in a non-uniform medium is proposed.

Using the developed algorithm, a numerical study of the propagation of stable detonation in a medium with variable density as carried out. A mode with a relatively small oscillation amplitude is investigated, in which the fluctuations of the parameters behind the detonation wave front occur with the frequency of fluctuations in the density of the medium. It is shown the relationship of the oscillation period with the passage time of the characteristics C₊ and C₀ over the region, which can be conditionally considered an induction zone. The phase shift between the oscillations of the velocity of the detonation wave and the density of the gas before the wave is estimated as the maximum time of passage of the characteristic C₊ through the induction zone.

The coconut tree is often mentioned as the “tree of life” due to its immense benefits to the human community ranging from edible products to building materials. Rugose spiraling whitefly (RSW), a natural enemy seems to be a major threat to farmers in bringing up these coconut trees. A mathematical model to study the dynamics of pest population in the presence of predator and parasite is developed. The biologically feasible equilibrium points are derived. Local asymptotic stability as well as global asymptotic stability is analyzed at the points. Furthermore, in order to educate farmers on pest control, we have added the impact of awareness programs in the model. The conditions of existence and stability properties of all feasible steady states of this model are analyzed. The result reveals that predator and parasite play a major role in reducing the immature pest. It also shows that pest control activities through awareness programs further reduce the mature pest population which decreases the egg laying rate which in turn reduces the immature population.

A method is proposed for analyzing the tremor of the earth’s surface, measured by means of space geodesy, in order to highlight the prognostic effects of seismicity activation. The method is illustrated by the example of a joint analysis of a set of synchronous time series of daily vertical displacements of the earth’s surface on the Japanese Islands for the time interval 2009–2023. The analysis is based on dividing the source data (1047 time series) into blocks (clusters of stations) and sequentially applying the principal component method. The station network is divided into clusters using the K-means method from the maximum pseudo-F-statistics criterion, and for Japan the optimal number of clusters was chosen to be 15. The Huang decomposition method into a sequence of independent empirical oscillation modes (EMD — Empirical Mode Decomposition) is applied to the time series of principal components from station blocks. To provide the stability of estimates of the waveforms of the EMD decomposition, averaging of 1000 independent additive realizations of white noise of limited amplitude was performed. Using the Cholesky decomposition of the covariance matrix of the waveforms of the first three EMD components in a sliding time window, indicators of abnormal tremor behavior were determined. By calculating the correlation function between the average indicators of anomalous behavior and the released seismic energy in the vicinity of the Japanese Islands, it was established that bursts in the measure of anomalous tremor behavior precede emissions of seismic energy. The purpose of the article is to clarify common hypotheses that movements of the earth’s crust recorded by space geodesy may contain predictive information. That displacements recorded by geodetic methods respond to the effects of earthquakes is widely known and has been demonstrated many times. But isolating geodetic effects that predict seismic events is much more challenging. In our paper, we propose one method for detecting predictive effects in space geodesy data.

A vertically distributed three-component model of marine ecosystem is considered. State of the plankton community with nutrients is analyzed under the active movement of zooplankton in a vertical column of water. The necessary conditions of the Turing instability in the vicinity of the spatially homogeneous equilibrium are obtained. Stability of the spatially homogeneous equilibrium, the Turing instability and the oscillatory instability are examined depending on the biological characteristics of zooplankton and spatial movement of plankton. It is shown that at low values of zooplankton grazing rate and intratrophic interaction rate the system is Turing instable when the taxis rate is low. Stabilization occurs either through increased decline of zooplankton either by increasing the phytoplankton diffusion. With the increasing rate of consumption of phytoplankton range of parameters that determine the stability is reduced. A type of instability depends on the phytoplankton diffusion. For large values of diffusion oscillatory instability is observed, with a decrease in the phytoplankton diffusion zone of Turing instability is increases. In general, if zooplankton grazing rate is faster than phytoplankton growth rate the spatially homogeneous equilibrium is Turing instable or oscillatory instable. Stability is observed only at high speeds of zooplankton departure or its active movements. With the increase in zooplankton search activity spatial distribution of populations becomes more uniform, increasing the rate of diffusion leads to non-uniform spatial distribution. However, under diffusion the total number of the population is stabilized when the zooplankton grazing rate above the rate of phytoplankton growth. In general, at low rate of phytoplankton consumption the spatial structures formation is possible at low rates of zooplankton decline and diffusion of all the plankton community. With the increase in phytoplankton predation rate the phytoplankton diffusion and zooplankton spatial movement has essential effect on the spatial instability.

Base long-term modern scenarios of hydrochemical and temperature regimes of the Sea of Azov were considered. New schemes of modeling mechanisms of algal adaptation to changes in the hydrochemical regime and temperature were proposed. In comparison to the traditional ecological-evolutionary schemes, these models have a relatively small dimension, high speed and allow carrying out various calculations on long-term perspective (evolutionally significant times). Based on the ecology-evolutionary model of the lower trophic levels the impact of these environmental factors on the dynamics and microevolution of algae in the Sea of Azov was estimated. In each scenario, the calculations were made for 100 years, with the final values of the variables and parameters not depending on the choice of the initial values. In the process of such asymptotic computer analysis, it was found that as a result of climate warming and temperature adaptation of organisms, the average annual biomass of thermophilic algae (Pyrrophyta and Cyanophyta) naturally increases. However, for a number of diatom algae (Bacillariophyta), even with their temperature adaptation, the average annual biomass may unexpectedly decrease. Probably, this phenomenon is associated with a toughening of competition between species with close temperature parameters of existence. The influence of the variation in the chemical composition of the Don River’s flow on the dynamics of nutrients and algae of the Sea of Azov was also investigated. It turned out that the ratio of organic forms of nitrogen and phosphorus in sea waters varies little. This stabilization phenomenon will take place for all high-productive reservoirs with low flow, due to autochthonous origin of larger part of organic matter in water bodies of this type.