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Muscle contraction is controlled by Ca2+ ions via regulatory proteins, troponin and tropomyosin, associated with thin actin filaments in sarcomeres. Depending on the Ca2+ concentration, the thin filament rearranges so that tropomyosin moves along its surface, opening or closing access to actin for the motor domains of myosin molecules, and causing contraction or relaxation, respectively. Numerous point amino acid substitutions in tropomyosin are known, leading to genetic pathologies — myo- and cardiomyopathies caused by changes in the structural and functional properties of the thin filament. The results of molecular dynamics modeling of a fragment of a thin filament of cardiac muscle sarcomeres formed by fibrillar actin and wildtype tropomyosin or with amino acid substitutions: the double stabilizing substitution D137L/G126R and the cardiomyopathic substitution S215L are presented. For numerical calculations, we used a new model of a thin filament fragment containing 26 actin monomers and 4 tropomyosin dimers, with a refined structure of the region of overlap of neighboring tropomyosin molecules in each of the two tropomyosin strands. The simulation results showed that tropomyosin significantly increases the bending stiffness of the thin filament, as previously found experimentally. The double stabilizing replacement D137L/G126R leads to a further increase in this rigidity, and the replacement S215L, on the contrary, leads to its decrease, which also corresponds to experimental data. At the same time, these substitutions have different effects on the angular mobility of the actin helix and only slightly modulate the angular mobility of tropomyosin cables relative to the actin helix and the population of hydrogen bonds between negatively charged tropomyosin residues and positively charged actin residues. The results of the verification of the new model demonstrate that its quality is sufficient for the numerical study of the effect of single amino acid substitutions on the structure and dynamics of thin filaments and study the effects leading to dysregulation of muscle contraction. This model can be used as a useful tool for elucidating the molecular mechanisms of some genetic diseases and assessing the pathogenicity of newly discovered genetic variants.

In the first part of the paper we present convergence analysis of AGMsDR method on a new class of functions — in general non-convex with $M$-Lipschitz-continuous gradients that satisfy Polyak – Lojasiewicz condition. Method does not need the value of $\mu^{PL}>0$ in the condition and converges linearly with a scale factor $\left(1 - \frac{\mu^{PL}}{M}\right)$. It was previously proved that method converges as $O\left(\frac1{k^2}\right)$ if a function is convex and has $M$-Lipschitz-continuous gradient and converges linearly with a~scale factor $\left(1 - \sqrt{\frac{\mu^{SC}}{M}}\right)$ if the value of strong convexity parameter $\mu^{SC}>0$ is known. The novelty is that one can save linear convergence if $\frac{\mu^{PL}}{\mu^{SC}}$ is not known, but without square root in the scale factor.

The second part presents modification of AGMsDR method for solving problems that allow alternating minimization (Alternating AGMsDR). The similar results are proved.

As the result, we present adaptive accelerated methods that converge as $O\left(\min\left\lbrace\frac{M}{k^2},\,\left(1-{\frac{\mu^{PL}}{M}}\right)^{(k-1)}\right\rbrace\right)$ on a class of convex functions with $M$-Lipschitz-continuous gradient that satisfy Polyak – Lojasiewicz condition. Algorithms do not need values of $M$ and $\mu^{PL}$. If Polyak – Lojasiewicz condition does not hold, the convergence is $O\left(\frac1{k^2}\right)$, but no tuning needed.

We also consider the adaptive catalyst envelope of non-accelerated gradient methods. The envelope allows acceleration up to $O\left(\frac1{k^2}\right)$. We present numerical comparison of non-accelerated adaptive gradient descent which is accelerated using adaptive catalyst envelope with AGMsDR, Alternating AGMsDR, APDAGD (Adaptive Primal-Dual Accelerated Gradient Descent) and Sinkhorn's algorithm on the problem dual to the optimal transport problem.

Conducted experiments show faster convergence of alternating AGMsDR in comparison with described catalyst approach and AGMsDR, despite the same asymptotic rate $O\left(\frac1{k^2}\right)$. Such behavior can be explained by linear convergence of AGMsDR method and was tested on quadratic functions. Alternating AGMsDR demonstrated better performance in comparison with AGMsDR.

The data of episodic field measurements of carbon dioxide balance components (soil respiration — R_soil, ecosystem respiration — R_eco, net ecosystem exchange — NEE) of hayfields under use and abandoned one are interpreted by modelling. The field measurements were carried within five field campaigns in 2018 and 2019 on the drained part of the Dubna Peatland in Taldom District, Moscow Oblast, Russia. The territory is within humid continental climate zone. Peatland drainage was done out for milled peat extraction. After extraction was stopped, the residual peat deposit (1–1.5 m) was ploughed and grassed (Poa pratensis L.) for hay production. The current ground water level (GWL) varies from 0.3–0.5 m below the surface during wet and up to 1.0 m during dry periods. Daily dynamics of CO2 fluxes was measured using dynamic chamber method in 2018 (August) and 2019 (May, June, August) for abandoned ditch spacing only with sanitary mowing once in 5 years and the ditch spacing with annual mowing. NEE and Reco were measured on the sites with original vegetation, and Rsoil — after vegetation removal. To model a seasonal dynamics of NEE, the dependence of its components (Reco, Rsoil, and Gross ecosystematmosphere exchange of carbon dioxide — GEE) from soil and air temperature, GWL, photosynthetically active radiation, underground and aboveground plant biomass were used. The parametrization of the models has been carried out considering the stability of coefficients estimated by the bootstrap method. R2 (α = 0.05) between simulated and measured Reco was 0.44 (p < 0.0003) on abandoned and 0.59 (p < 0.04) on under use hayfield, and GEE was 0.57 (p < 0.0002) and 0.77 (p < 0.00001), respectively. Numerical experiments were carried out to assess the influence of different haymaking regime on NEE. It was found that NEE for the season (May 15 – September 30) did not differ much between the hayfield without mowing (4.5±1.0 tC·ha–1·season–1) and the abandoned one (6.2±1.4). Single mowing during the season leads to increase of NEE up to 6.5±0.9, and double mowing — up to 7.5±1.4 tC·ha–1·season–1. This means increase of carbon losses and CO2 emission into the atmosphere. Carbon loss on hayfield for both single and double mowing scenario was comparable with abandoned hayfield. The value of removed phytomass for single and double mowing was 0.8±0.1 tC·ha^–1·season^–1 and 1.4±0.1 (45% carbon content in dry phytomass) or 3.0 and 4.4 t·ha^–1·season^–1 of hay (17% moisture content). In comparison with the fallow, the removal of biomass of 0.8±0.1 at single and 1.4±0.1 tC·ha^–1·season^–1 double mowing is accompanied by an increase in carbon loss due to CO2 emissions, i.e., the growth of NEE by 0.3±0.1 and 1.3±0.6 tC·ha–1·season–1, respectively. This corresponds to the growth of NEE for each ton of withdrawn phytomass per hectare of 0.4±0.2 tС·ha–1·season–1 at single mowing, and 0.9±0.7 tС·ha^–1·season^–1 at double mowing. Therefore, single mowing is more justified in terms of carbon loss than double mowing. Extensive mowing does not increase CO2 emissions into the atmosphere and allows, in addition, to “replace” part of the carbon loss by agricultural production.

Studies of the crisis socio-demographic situation in the Russian Far East require not only the use of traditional statistical methods, but also a conceptual analysis of possible development scenarios based on the synergy principles. The article is devoted to the analysis and modeling of the number of employed, unemployed and economically inactive population using nonlinear autonomous differential equations. We studied a basic mathematical model that takes into account the principle of pair interactions, which is a special case of the model for the struggle between conditional information of D. S. Chernavsky. The point estimates for the parameters are found using least squares method adapted for this model. The average approximation error was no more than 5.17%. The calculated parameter values correspond to the unstable focus and the oscillations with increasing amplitude of population number in the asymptotic case, which indicates a gradual increase in disparities between the employed, unemployed and economically inactive population and a collapse of their dynamics. We found that in the parametric space, not far from the inertial scenario, there are domains of blow-up and chaotic regimes complicating the ability to effectively manage. The numerical study showed that a change in only one model parameter (e.g. migration) without complex structural socio-economic changes can only delay the collapse of the dynamics in the long term or leads to the emergence of unpredictable chaotic regimes. We found an additional set of the model parameters corresponding to sustainable dynamics (stable focus) which approximates well the time series of the considered population groups. In the mathematical model, the bifurcation parameters are the outflow rate of the able-bodied population, the fertility (“rejuvenation of the population”), as well as the migration inflow rate of the unemployed. We found that the transition to stable regimes is possible with the simultaneous impact on several parameters which requires a comprehensive set of measures to consolidate the population in the Russian Far East and increase the level of income in terms of compensation for infrastructure sparseness. Further economic and sociological research is required to develop specific state policy measures.

Many properties of ordinary differential equations systems solutions are determined by the properties of the equations in variations. An ODE system, which includes both the original nonlinear system and the equations in variations, will be called an extended system further. When studying the properties of the Cauchy problem for the systems of ordinary differential equations, the transition to extended systems allows one to study many subtle properties of solutions. For example, the transition to the extended system allows one to increase the order of approximation for numerical methods, gives the approaches to constructing a sensitivity function without using numerical differentiation procedures, allows to use methods of increased convergence order for the inverse problem solution. Authors used the Broyden method belonging to the class of quasi-Newtonian methods. The Rosenbroke method with complex coefficients was used to solve the stiff systems of the ordinary differential equations. In our case, it is equivalent to the second order approximation method for the extended system.

As an example of the proposed approach, several related mathematical models of the blood coagulation process were considered. Based on the analysis of the numerical calculations results, the conclusion was drawn that it is necessary to include a description of the factor XI positive feedback loop in the model equations system. Estimates of some reaction constants based on the numerical inverse problem solution were given.

Effect of factor V release on platelet activation was considered. The modification of the mathematical model allowed to achieve quantitative correspondence in the dynamics of the thrombin production with experimental data for an artificial system. Based on the sensitivity analysis, the hypothesis tested that there is no influence of the lipid membrane composition (the number of sites for various factors of the clotting system, except for thrombin sites) on the dynamics of the process.

The paper is devoted to the study of relationships between discrete and continuous models financial processes and their probabilistic characteristics. First, a connection is established between the price processes of stocks, hedging portfolio and options in the models conditioned by binomial perturbations and their limit perturbations of the Brownian motion type. Secondly, analogues in the coefficients of stochastic equations with various random processes, continuous and jumpwise, and in the coefficients corresponding deterministic equations for their probabilistic characteristics. Statement of the results on the connections and finding analogies, obtained in this paper, led to the need for an adequate presentation of preliminary information and results from financial mathematics, as well as descriptions of related objects of stochastic analysis. In this paper, partially new and known results are presented in an accessible form for those who are not specialists in financial mathematics and stochastic analysis, and for whom these results are important from the point of view of applications. Specifically, the following sections are presented.

• In one- and n-period binomial models, it is proposed a unified approach to determining on the probability space a risk-neutral measure with which the discounted option price becomes a martingale. The resulting martingale formula for the option price is suitable for numerical simulation. In the following sections, the risk-neutral measures approach is applied to study financial processes in continuous-time models.

• In continuous time, models of the price of shares, hedging portfolios and options are considered in the form of stochastic equations with the Ito integral over Brownian motion and over a compensated Poisson process. The study of the properties of these processes in this section is based on one of the central objects of stochastic analysis — the Ito formula. Special attention is given to the methods of its application.

• The famous Black – Scholes formula is presented, which gives a solution to the partial differential equation for the function $v(t, x)$, which, when $x = S (t)$ is substituted, where $S(t)$ is the stock price at the moment time $t$, gives the price of the option in the model with continuous perturbation by Brownian motion.

• The analogue of the Black – Scholes formula for the case of the model with a jump-like perturbation by the Poisson process is suggested. The derivation of this formula is based on the technique of risk-neutral measures and the independence lemma.

Dynamic scenarios leading to multistability in the form of continuous families of stable solutions are studied for a system of autonomous differential equations. The approach is based on determining the cosymmetries of the problem, calculating stationary solutions, and numerically-analytically studying their stability. The analysis is carried out for equations of the Lotka –Volterra type, describing the interaction of two predators feeding on two related prey species. For a system of ordinary differential equations of the 4th order with 11 real parameters, a numerical-analytical study of possible interaction scenarios was carried out. Relationships are found analytically between the control parameters under which the cosymmetry linear in the variables of the problem is realized and families of stationary solutions (equilibria) arise. The case of multicosymmetry is established and explicit formulas for a two-parameter family of equilibria are presented. The analysis of the stability of these solutions made it possible to reveal the division of the family into regions of stable and unstable equilibria. In a computational experiment, the limit cycles branching off from unstable stationary solutions are determined and their multipliers corresponding to multistability are calculated. Examples of the coexistence of families of stable stationary and non-stationary solutions are presented. The analysis is carried out for the growth functions of logistic and “hyperbolic” types. Depending on the parameters, scenarios can be obtained when only stationary solutions (coexistence of prey without predators and mixed combinations), as well as families of limit cycles, are realized in the phase space. The multistability scenarios considered in the work allow one to analyze the situations that arise in the presence of several related species in the range. These results are the basis for subsequent analysis when the parameters deviate from cosymmetric relationships.

The paper presents the results of applying a scheme of very high accuracy and resolution to obtain numerical solutions of the Navier – Stokes equations of a compressible gas describing the occurrence and development of instability of a two-dimensional laminar boundary layer on a flat plate. The peculiarity of the conducted studies is the absence of commonly used artificial exciters of instability in the implementation of direct numerical modeling. The multioperator scheme used made it possible to observe the subtle effects of the birth of unstable modes and the complex nature of their development caused presumably by its small approximation errors. A brief description of the scheme design and its main properties is given. The formulation of the problem and the method of obtaining initial data are described, which makes it possible to observe the established non-stationary regime fairly quickly. A technique is given that allows detecting flow fluctuations with amplitudes many orders of magnitude smaller than its average values. A time-dependent picture of the appearance of packets of Tollmien – Schlichting waves with varying intensity in the vicinity of the leading edge of the plate and their downstream propagation is presented. The presented amplitude spectra with expanding peak values in the downstream regions indicate the excitation of new unstable modes other than those occurring in the vicinity of the leading edge. The analysis of the evolution of instability waves in time and space showed agreement with the main conclusions of the linear theory. The numerical solutions obtained seem to describe for the first time the complete scenario of the possible development of Tollmien – Schlichting instability, which often plays an essential role at the initial stage of the laminar-turbulent transition. They open up the possibilities of full-scale numerical modeling of this process, which is extremely important for practice, with a similar study of the spatial boundary layer.

This work is devoted to molecular dynamic modeling of the thermal impact processes on the metal sample consisting of nickel atoms. For the solution of this problem, a continuous mathematical model on the basis of the classical Newton mechanics equations has been used; a numerical method based on the Verlet scheme has been chosen; a parallel algorithm has been offered, and its realization within the MPI and OpenMP technologies has been executed. By means of the developed parallel program, the investigation of thermodynamic equilibrium of nickel atoms’ system under the conditions of heating a sample to desired temperature has been executed. In numerical experiments both optimum parameters of calculation procedure and physical parameters of analyzed process have been defined. The obtained numerical results are well corresponding to known theoretical and experimental data.

The paper presents a software system aimed at finding best (in some sense) parameters of an algorithm. The system handles both discrete and continuous parameters and employs massive parallelism offered by public clouds. The paper presents an overview of the system, a method to measure algorithm's performance in the cloud and numerical results of system's use on several problem sets.