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Currently, different nonlinear numerical schemes of the spatial approximation are used in numerical simulation of boundary value problems for hyperbolic systems of partial differential equations (e. g. gas dynamics equations, MHD, deformable rigid body, etc.). This is due to the need to improve the order of accuracy and perform simulation of discontinuous solutions that are often occurring in such systems. The need for non-linear schemes is followed from the barrier theorem of S. K. Godunov that states the impossibility of constructing a linear scheme for monotone approximation of such equations with approximation order two or greater. One of the most accurate non-linear type schemes are ENO (essentially non oscillating) and their modifications, including WENO (weighted, essentially non oscillating) scemes. The last received the most widespread, since the same stencil width has a higher order of approximation than the ENO scheme. The benefit of ENO and WENO schemes is the ability to maintain a high-order approximation to the areas of non-monotonic solutions. The main difficulty of the analysis of such schemes comes from the fact that they themselves are nonlinear and are used to approximate the nonlinear equations. In particular, the linear stability condition was obtained earlier only for WENO5 scheme (fifth-order approximation on smooth solutions) and it is a numerical one. In this paper we consider the problem of construction and stability for WENO5, WENO7, WENO9, WENO11, and WENO13 finite volume schemes for the Hopf equation. In the first part of this article we discuss WENO methods in general, and give the explicit expressions for the coefficients of the polynomial weights and linear combinations required to build these schemes. We prove a series of assertions that can make conclusions about the order of approximation depending on the type of local solutions. Stability analysis is carried out on the basis of the principle of frozen coefficients. The cases of a smooth and discontinuous behavior of solutions in the field of linearization with frozen coefficients on the faces of the final volume and spectra of the schemes are analyzed for these cases. We prove the linear stability conditions for a variety of Runge-Kutta methods applied to WENO schemes. As a result, our research provides guidance on choosing the best possible stability parameter, which has the smallest effect on the nonlinear properties of the schemes. The convergence of the schemes is followed from the analysis.

Optical systems with two-dimensional feedback demonstrate wide possibilities for studying the nucleation and development processes of dissipative structures. Feedback allows to influence the dynamics of the optical system by controlling the transformation of spatial variables performed by prisms, lenses, dynamic holograms and other devices. A nonlinear interferometer with a mirror image of a field in two-dimensional feedback is one of the simplest optical systems in which is realized the nonlocal nature of light fields.

A mathematical model of optical systems with two-dimensional feedback is a nonlinear parabolic equation with rotation transformation of a spatial variable and periodicity conditions on a circle. Such problems are investigated: bifurcation of the traveling wave type stationary structures, how the form of the solution changes as the diffusion coefficient decreases, dynamics of the solution’s stability when the bifurcation parameter leaves the critical value. For the first time as a parameter bifurcation was taken of diffusion coefficient.

The method of central manifolds and the Galerkin’s method are used in this paper. The method of central manifolds and the Galerkin’s method are used in this paper. The method of central manifolds allows to prove a theorem on the existence and form of the traveling wave type solution neighborhood of the bifurcation value. The first traveling wave born as a result of the Andronov –Hopf bifurcation in the transition of the bifurcation parameter through the сritical value. According to the central manifold theorem, the first traveling wave is born orbitally stable.

Since the above theorem gives the opportunity to explore solutions are born only in the vicinity of the critical values of the bifurcation parameter, the decision to study the dynamics of traveling waves of change during the withdrawal of the bifurcation parameter in the supercritical region, the formalism of the Galerkin method was used. In accordance with the method of the central manifold is made Galerkin’s approximation of the problem solution. As the bifurcation parameter decreases and its transition through the critical value, the zero solution of the problem loses stability in an oscillatory manner. As a result, a periodic solution of the traveling wave type branches off from the zero solution. This wave is born orbitally stable. With further reduction of the parameter and its passage through the next critical value from the zero solution, the second solution of the traveling wave type is produced as a result of the Andronov –Hopf bifurcation. This wave is born unstable with an instability index of two.

Numerical calculations have shown that the application of the Galerkin’s method leads to correct results. The results obtained are in good agreement with the results obtained by other authors and can be used to establish experiments on the study of phenomena in optical systems with feedback.

WENO schemes (weighted, essentially non oscillating) are currently having a wide range of applications as approximate high order schemes for discontinuous solutions of partial differential equations. These schemes are used for direct numerical simulation (DNS) and large eddy simmulation in the gas dynamic problems, problems for DNS in MHD and even neutron kinetics. This work is dedicated to clarify some characteristics of WENO schemes and numerical simulation of specific tasks. Results of the simulations can be used to clarify the field of application of these schemes. The first part of the work contained proofs of the approximation properties, stability and convergence of WENO5, WENO7, WENO9, WENO11 and WENO13 schemes. In the second part of the work the modified wave number analysis is conducted that allows to conclude the dispersion and dissipative properties of schemes. Further, a numerical simulation of a number of specific problems for hyperbolic equations is conducted, namely for advection equations (one-dimensional and two-dimensional), Hopf equation, Burgers equation (with low dissipation) and equations of non viscous gas dynamics (onedimensional and two-dimensional). For each problem that is implying a smooth solution, the practical calculation of the order of approximation via Runge method is performed. The influence of a time step on nonlinear properties of the schemes is analyzed experimentally in all problems and cross checked with the first part of the paper. In particular, the advection equations of a discontinuous function and Hopf equations show that the failure of the recommendations from the first part of the paper leads first to an increase in total variation of the solution and then the approximation is decreased by the non-linear dissipative mechanics of the schemes. Dissipation of randomly distributed initial conditions in a periodic domain for one-dimensional Burgers equation is conducted and a comparison with the spectral method is performed. It is concluded that the WENO7–WENO13 schemes are suitable for direct numerical simulation of turbulence. At the end we demonstrate the possibility of the schemes to be used in solution of initial-boundary value problems for equations of non viscous gas dynamics: Rayleigh–Taylor instability and the reflection of the shock wave from a wedge with the formation a complex configuration of shock waves and discontinuities.

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.