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Single-point mutations in the transmembrane (TM) region of receptor tyrosine kinases (RTKs) can lead to abnormal ligand-independent activation. We use a combination of computational modeling, NMR spectroscopy and cell experiments to analyze in detail the mechanism of how TM domains contribute to the activation of wild-type (WT) PDGFRA and its oncogenic V536E mutant. Using a computational framework, we scan all positions in PDGFRA TM helix for identification of potential functional mutations for the WT and the mutant and reveal the relationship between the receptor activity and TM dimerization via different interfaces. This strategy also allows us design a novel activating mutation in the WT (I537D) and a compensatory mutation in the V536E background eliminating its constitutive activity (S541G). We show both computationally and experimentally that single-point mutations in the TM region reshape the TM dimer ensemble and delineate the structural and dynamic determinants of spontaneous activation of PDGFRA via its TM domain. Our atomistic picture of the coupling between TM dimerization and PDGFRA activation corroborates the data obtained for other RTKs and provides a foundation for developing novel modulators of the pathological activity of PDGFRA.
A novel method of finding and classifying irreducible invariant surfaces of non-autonomous polynomial dynamical systems in the plane is presented. The general structure of irreducible invariant surfaces and their cofactors is found. The complete set of irreducible invariant surfaces for the classical forced Duffing-van der Pol oscillator is obtained. It is proved that the forced Duffing-van der Pol oscillator possesses only one independent generalized Darboux first integral provided that a constraint on the parameters is valid. In other cases generalized Darboux first integrals do not exist. Consequently, the forced Duffing-van der Pol oscillator is not integrable with two independent generalized Darboux first integrals.
We study the stability conditions of the multiserver queueing system in which each customer requires a random number of servers simultaneously. The input flow is supposed to be a regenerative one and service times of a given customer are independent at the occupied servers. The service time has an exponential, phase-type or hyper-exponential distribution. We define an auxiliary service process that is the number of completed services by all m servers under the assumption that there are always customers in the system. Then we construct the sequence of common regeneration points for the regenerative input flow and the auxiliary service process. It allows us to deduce the stability criterion of the model under consideration. It turns out that the stability condition does not depend on the structure of the input flow, only the rate of this process plays a role. Nevertheless the distribution of the service time is a very important factor. We give examples which show that the stability condition can not be expressed in terms of the mean of the service time.
Plasmon spectroscopy methods are highly sensitive to the small volumes of material due to subwavelength localization of light increasing light-matter interaction. Recent research has shown a high potential of plasmon quantum generator (spaser) or amplifier (sped) for sensing in the infrared optical region. Trinitrotoluene (TNT) molecules fingerprints are considered as an example. Basing on Lindblad equations, we implement full quantum mechanical theory of graphene plasmon generator to investigate how a small amount of absorbing atoms influences the spectrum of a graphene spaser. We analyze the optimal type of an active medium, the number of active molecules, and the pump level to achieve the highest sensitivity and show that optimized structure is sensitive to dozens of atoms. Our research is useful for the development of near- and mid-IR spectroscopy based on plasmon quantum amplifier.
We point out that superconducting quantum computers are prospective for the simulation of the dynamics of spin models far from equilibrium, including nonadiabatic phenomena and quenches. The important advantage of these machines is that they are programmable, so that different spin models can be simulated in the same chip, as well as various initial states can be encoded into it in a controllable way. This opens an opportunity to use superconducting quantum computers in studies of fundamental problems of statistical physics such as the absence or presence of thermalization in the free evolution of a closed quantum system depending on the choice of the initial state as well as on the integrability of the model. In the present paper, we performed proof-of-principle digital simulations of two spin models, which are the central spin model and the transverse-field Ising model, using 5- and 16-qubit superconducting quantum computers of the IBM Quantum Experience. We found that these devices are able to reproduce some important consequences of the symmetry of the initial state for the system’s subsequent dynamics, such as the excitation blockade. However, lengths of algorithms are currently limited due to quantum gate errors. We also discuss some heuristic methods which can be used to extract valuable information from the imperfect experimental data.
model for deep bed filtration of a monodisperse suspension in a porous medium with multiple geometric
particle capture mechanisms is considered. It is assumed that identical suspended particles can block pores of
different sizes. The pores smaller than the particle size are clogged by single particles; if the pore size exceeds
the diameter of the particles, it can be blocked by bridging— several particles forming various stable structures.
An exact solution is obtained for constant filtration coefficients. Exact solutions for non-constant filtration
functions are obtained on the concentrations front of the suspended and retained particles and at the porous
medium inlet. Asymptotic solutions are constructed near these lines. For small and close to constant filtration
functions, global asymptotic solutions are obtained.
A basic model with two mechanisms of particle capture is studied in detail. Asymptotic solutions are compared
to the results of numerical simulation. The applicability of various types of asymptotics is analyzed.
In the article, it is considered a modification of an integral model of an unsteady turbulent jet with a pressure force. Stationary solutions of the presented model are compared with well-known analytical results of classical models. It is shown that the inclusion of the pressure forces changes the dynamic parameters of a jet by about 12%. Analytical solutions of a steady forced buoyant jet of the atmospheric convective boundary layer and a spontaneous jet of a surface layer are presented. The simplest model of an ensemble of spontaneous jets of convective surface layer is constructed. It is shown that an ensemble of spontaneous jets forms a dependence of the turbulent moments and heat eddy diffusivity on the altitude within the convective boundary layer.
The effect of an interplay between electrostatic and excluded volume interactions on the conformational behavior of a dipolar chain has been studied theoretically and by means of molecular dynamics simulations. Every monomer unit of the dipolar chain comprises a dipole formed by a charged group of the chain and an oppositely charged counterion.
The counterion is assumed to freelymove around the chain but keeping the distance between oppositely charged ions (the dipole length) fixed. The novelty of the developed mean-field theory is that variations of the dipole parameters (the dipole length and the counterion size) have been accounted for in both electrostatic and excluded volume
contributions to the total free energy of the dipolar chain. It has been shown that conformational transitions between swollen and collapsed states of the chain can be induced by fine-tuning the balance between electrostatic and excluded volume interactions. In particular, in lowpolar media not only globule but also extended coil conformations can be realized even under strong electrostatic attraction. The results ofMD simulations of a dipolar chain with variable dipolar length support theoretical conclusions.
The anomalous magnetic moment (AMM) for excited states of an electron in a constant magnetic field has been calculated within the framework of two-dimensional electrodynamics. The analytical results for the interaction energy of the anomalous magnetic moment with the external magnetic field are obtained in two limiting cases of nonrelativistic and relativistic energy values in a comparatively weak magnetic field. It is shown that the interaction energy of the spin with the external field does not contain infrared divergence and tends to zero as magnetic field decreases, while the electron’s AMM increases logarithmically.
In this paper we propose a method for solving systems of nonlinear inequalities with predefined accuracy based on nonuniform covering concept formerly adopted for global optimization. The method generates inner and outer approximations of the solution set. We describe the general concept and three ways of numerical implementation of the method. The first one is applicable only in a few cases when a minimum and a maximum of the constraints convolution function can be found analytically. The second implementation uses a global optimization method to find extrema of the constraints convolution function numerically. The third one is based on extrema approximation with Lipschitz under- and overestimations. We obtain theoretical bounds on the complexity and the accuracy of the generated approximations as well as compare proposed approaches theoretically and experimentally.
We study properties of generalized $K$-functionals and generalized moduli of smoothness in $L_p(\R)$ spaces with $1 \le p \le +\infty$. We obtain the direct Jackson type estimate and the inverse Bernstein type estimate for them. We state equivalence between approximation error of convolution integrals generated by an arbitrary generator with compact support generalized $K$-functionals generated by homogeneous function and generalized moduli of smoothness generated by $2\pi$-periodic generator subject to equivalence of their generators. We show that generalized $K$-functionals and generalized moduli of smoothness contain, as their special cases many well-known constructions of $K$-functionals and moduli of smoothness with an appropriate choice of the generators.
The stochastic ensemble of convective thermals (vortices), forming the fine structure of a turbulent
convective atmospheric layer, is considered. The proposed ensemble model assumes all thermals in
the mixed-layer to have the same determinate buoyancies and considers them as solid spheres of
variable volumes. The values of radii and vertical velocities of the thermals are assumed random. The
motion of the stochastic system of convective vortices is described by the nonlinear Langevin equation
with a linear drift coefficient and a random force, whose structure is known for a system of Brownian
particles. The probability density of the thermal ensemble in velocity phase space is shown to satisfy
an associated K-form of the Fokker-Planck equation with variable coefficients. Maxwell velocity
distribution of convective thermals is constructed as a steady-state solution of a simplified Fokker-
Planck equation. The obtained Maxwell velocity distribution is shown to give a good approximation
of experimental distributions in a turbulent convective mixed-layer.
A procedure has been proposed for calculating limited orbits around the L2 libration points of the Sun–Earth system. The motion of a spacecraft in the vicinity of the libration point has been considered a superposition of three components, i.e., decreasing (stable), increasing (unstable), and limited. The proposed procedure makes it possible to correct the state vector of the spacecraft so as to neutralize the unstable component of the motion. Using this procedure, the calculation of orbits around various types of libration points has been carried out and the dependence on the orbit type on the initial conditions has been studied.
The filtration problem in a porous medium is an important part of underground hydromechanics. Filtration of suspensions and colloids determines the processes of strengthening the soil and creating waterproof walls in the ground while building the foundations of buildings and underground structures. It is assumed that the formation of a deposit is dominated by the size-exclusion mechanism of pore blocking: solid particles pass freely through large pores and get stuck at the inlet of pores smaller than the diameter of the particles. A one-dimensional mathematical model for the filtration of a monodisperse suspension includes the equation for the mass balance of suspended and retained particles and the kinetic equation for the growth of the deposit. For the blocking filtration coefficient with a double root, the exact solution is given implicitly. The asymptotics of the filtration problem is constructed for large time. The numerical calculation of the problem is carried out by the finite differences method. It is shown that asymptotic approximations rapidly converge to a solution with the increase of the expansion order.
Molecular dynamics calculations are performed to calculate vapor–liquid equilibrium of methane–n-butane mixture. Three force-field models are tested: the TraPPE-UA united-atom forcefield, LOPLS-AA all-atom forcefield and a fully flexible version of the TraPPEEH all-atom forcefield. All those forcefields reproduce well the composition of liquid phase in the mixture as a function of pressure at the 300 K isotherm, while significant discrepancies from experimental data are observed in the saturated vapor compositions with OPLS-AA and TraPPE-UA forcefields. The best agreement with the experimental phase diagram is found with TraPPE-EH forcefield which accurately reproduces compositions of both liquid and vapor phase. This forcefield can be recommended for simulation of two-phase hydrocarbon systems.
Control of Discrete-Time Descriptor Systems takes an anisotropy-based approach to the explanation of random input disturbance with an information-theoretic representation. It describes the random input signal more precisely, and the anisotropic norm minimization included in the book enables readers to tune their controllers better through the mathematical methods provided. The book contains numerous examples of practical applications of descriptor systems in various fields, from robotics to economics, and presents an information-theoretic approach to the mathematical description of coloured noise. Anisotropy-based analysis and design for descriptor systems is supplied along with proofs of basic statements, which help readers to understand the algorithms proposed, and to undertake their own numerical simulations. This book serves as a source of ideas for academic researchers and postgraduate students working in the control of discrete-time systems. The control design procedures outlined are numerically effective and easily implementable in MATLAB®
A one-dimensional model for the deep bed filtration of a
monodisperse suspension in a porous medium with variable porosity and
permeability and multiple pore-blocking mechanisms is considered. It is
assumed that the small pores are clogged by separate particles; pores of
medium size, exceeding the diameter of the particles, can be blocked by
arched bridges, forming stable structures at the pore throats. These poreblocking
mechanisms - size-exclusion and different types of bridging act
simultaneously. Exact solutions are obtained for constant coefficients, on
the concentrations front and at the porous medium inlet.
It is often suggested that inter-particle distance in stable dusty plasma structures decreases with cooling as a square root of neutral gas temperature. Deviations from this dependence (up to the increase at cryogenic temperatures) found in the experimental results for the pressures range 0.1–8.0 mbar and for the currents range 0.1–1.0 mA are given. Inter-particle distance dependences on the charge of particles, parameter of the trap and the screening length in surrounding plasma are obtained for different conditions from molecular dynamics simulations. They are well approximated by power functions in the mentioned range of parameters. It is found that under certain assumptions thermophoretical force is responsible for inter-particle distance increase at cryogenic temperatures
Modern Elbrus-4S and Elbrus-8S processors show floating point performance comparable to the popular Intel processors in the field of high-performance computing. Tasks oriented to take advantage of the VLIW architecture show even greater efficiency on Elbrus processors. In this paper the efficiency of the most popular materials science codes in the field of classical molecular dynamics and quantum-mechanical calculations is considered. A comparative analysis of the performance of these codes on Elbrus processor and other modern processors is carried out