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Equations of motion in Newtonian and Hamiltonian forms are used for classical molecular dynamics simulation of particle system time evolution. When Newton equations of motion are used for finding of particle coordinates and velocities in $N$-particle system it takes to solve $3N$ ordinary differential equations of second order at every time step. Traditionally numerical schemes of Verlet method are used for solving Newtonian equations of motion of molecular dynamics. A step of integration is necessary to decrease for Verlet numerical schemes steadiness conservation on sufficiently large time intervals. It leads to a significant increase of the volume of calculations. Numerical schemes of Verlet method with Hamiltonian conservation control (the energy of the system) at every time moment are used in the most software packages of molecular dynamics for numerical integration of equations of motion. It can be used two complement each other approaches to decrease of computational time in molecular dynamics calculations. The first of these approaches is based on enhancement and software optimization of existing software packages of molecular dynamics by using of vectorization, parallelization and special processor construction. The second one is based on the elaboration of efficient methods for numerical integration for equations of motion. A procedure for constructing of explicit, implicit and symmetric symplectic numerical schemes with given approximation accuracy in relation to integration step for solving of molecular dynamic equations of motion in Hamiltonian form is proposed in this work. The approach for construction of proposed in this work procedure is based on the following points: Hamiltonian formulation of equations of motion; usage of Taylor expansion of exact solution; usage of generating functions, for geometrical properties of exact solution conservation, in derivation of numerical schemes. Numerical experiments show that obtained in this work symmetric symplectic third-order accuracy scheme conserves basic properties of the exact solution in the approximate solution. It is more stable for approximation step and conserves Hamiltonian of the system with more accuracy at a large integration interval then second order Verlet numerical schemes.

The paper has methodical character; it is devoted to three classic partial differential equations (Laplace, Diffusion and Wave) solution using simple numerical methods in terms of Cellular Automata. Special attention was payed to the matter conservation law and the offensive effect of excessive hexagonal symmetry.

It has been shown that in contrary to finite-difference approach, in spite of terminological equivalence of CA local transition function to the pattern of computing double layer explicit method, CA approach contains the replacement of matrix technique by iterative ones (for instance, sweep method for three diagonal matrixes). This suggests that discretization of boundary conditions for CA-cells needs more rigid conditions.

The correct local transition function (LTF) of the boundary cells, which is valid at least for the boundaries of the rectangular and circular shapes have been firstly proposed and empirically given for the hexagonal grid and the conservative boundary conditions. The idea of LTF separation into «internal», «boundary» and «postfix» have been proposed. By the example of this problem the value of the Courant-Levy constant was re-evaluated as the CA convergence speed ratio to the solution, which is given at a fixed time, and to the rate of the solution change over time.

This paper is devoted to the application of the method of numerical solution of the Boltzmann equation for the solution of the problem of modeling the behavior of radionuclides in the cavity of the interelectric gap of a multielement electrogenerating channel. The analysis of gas-kinetic processes of thermionic converters is important for proving the design of the power-generating channel. The paper reviews two constructive schemes of the channel: with one- and two-way withdrawal of gaseous fission products into a vacuum-cesium system. The analysis uses a two-dimensional transport equation of the second-order accuracy for the solution of the left-hand side and the projection method for solving the right-hand side — the collision integral. In the course of the work, a software package was implemented that makes it possible to calculate on the cluster architecture by using the algorithm of parallelizing the left-hand side of the equation; the paper contains the results of the analysis of the dependence of the calculation efficiency on the number of parallel nodes. The paper contains calculations of data on the distribution of pressures of gaseous fission products in the gap cavity, calculations use various sets of initial pressures and flows; the dependency of the radionuclide pressure in the collector region was determined as a function of cesium pressures at the ends of the gap. The tests in the loop channel of a nuclear reactor confirm the obtained results.

Verification of the physical-statistical approach within reliability theory for the simplest cases was carried out, which showed its validity. An analytical solution of the one-dimensional basic equation of the physicalstatistical approach is presented under the assumption of a stationary degradation rate. From a mathematical point of view this equation is the well-known continuity equation, where the role of density is played by the density distribution function of goods in its characteristics phase space, and the role of fluid velocity is played by intensity (rate) degradation processes. The latter connects the general formalism with the specifics of degradation mechanisms. The cases of coordinate constant, linear and quadratic degradation rates are analyzed using the characteristics method. In the first two cases, the results correspond to physical intuition. At a constant rate of degradation, the shape of the initial distribution is preserved, and the distribution itself moves equably from the zero. At a linear rate of degradation, the distribution either narrows down to a narrow peak (in the singular limit), or expands, with the maximum shifting to the periphery at an exponentially increasing rate. The distribution form is also saved up to the parameters. For the initial normal distribution, the coordinates of the largest value of the distribution maximum for its return motion are obtained analytically.

In the quadratic case, the formal solution demonstrates counterintuitive behavior. It consists in the fact that the solution is uniquely defined only on a part of an infinite half-plane, vanishes along with all derivatives on the boundary, and is ambiguous when crossing the boundary. If you continue it to another area in accordance with the analytical solution, it has a two-humped appearance, retains the amount of substance and, which is devoid of physical meaning, periodically over time. If you continue it with zero, then the conservativeness property is violated. The anomaly of the quadratic case is explained, though not strictly, by the analogy of the motion of a material point with an acceleration proportional to the square of velocity. Here we are dealing with a mathematical curiosity. Numerical calculations are given for all cases. Additionally, the entropy of the probability distribution and the reliability function are calculated, and their correlation is traced.

An essential class of problems describes physical processes occurring in non-convex domains containing a corner greater than 180 degrees on the boundary. The solution in a neighborhood of a corner is singular and its finding using classical approaches entails a loss of accuracy. In the paper, we consider stationary, linearized by Picard’s iterations, Navier – Stokes equations governing the flow of a incompressible viscous fluid in the convection form in $L$-shaped domain. An $R_\nu$-generalized solution of the problem in special sets of weighted spaces is defined. A special finite element method to find an approximate $R_\nu$-generalized solution is constructed. Firstly, functions of the finite element spaces satisfy the law of conservation of mass in the strong sense, i.e. at the grid nodes. For this purpose, Scott – Vogelius element pair is used. The fulfillment of the condition of mass conservation leads to the finding more accurate, from a physical point of view, solution. Secondly, basis functions of the finite element spaces are supplemented by weight functions. The degree of the weight function, as well as the parameter $\nu$ in the definition of an $R_\nu$-generalized solution, and a radius of a neighborhood of the singularity point are free parameters of the method. A specially selected combination of them leads to an increase almost twice in the order of convergence rate of an approximate solution to the exact one in relation to the classical approaches. The convergence rate reaches the first order by the grid step in the norms of Sobolev weight spaces. Thus, numerically shown that the convergence rate does not depend on the corner value.

The purpose of this work is to develop a universal computer program (solver) which solves kinetic Boltzmann equation for simulations of rarefied gas flows in complexly shaped devices. The structure of the solver is described in details. Its efficiency is demonstrated on an example of calculations of a modern many tubes Knudsen pump. The kinetic Boltzmann equation is solved by finite-difference method on discrete grid in spatial and velocity spaces. The differential advection operator is approximated by finite difference method. The calculation of the collision integral is based on the conservative projection method.

In the developed computational program the unstructured spatial mesh is generated using GMSH and may include prisms, tetrahedrons, hexahedrons and pyramids. The mesh is denser in areas of flow with large gradients of gas parameters. A three-dimensional velocity grid consists of cubic cells of equal volume.

A huge amount of calculations requires effective parallelization of the algorithm which is implemented in the program with the use of Message Passing Interface (MPI) technology. An information transfer from one node to another is implemented as a kind of boundary condition. As a result, every MPI node contains the information about only its part of the grid.

The main result of the work is presented in the graph of pressure difference in 2 reservoirs connected by a multitube Knudsen pump from Knudsen number. This characteristic of the Knudsen pump obtained by numerical methods shows the quality of the pump. Distributions of pressure, temperature and gas concentration in a steady state inside the pump and the reservoirs are presented as well.

The correctness of the solver is checked using two special test solutions of more simple boundary problems — test with temperature distribution between 2 planes with different temperatures and test with conservation of total gas mass.

The correctness of the obtained data for multitube Knudsen pump is checked using denser spatial and velocity grids, using more collisions in collision integral per time step.

The paper considers mathematical modeling of layered Benard–Marangoni convection of a viscous incompressible fluid. The fluid moves in an infinitely extended layer. The Oberbeck–Boussinesq system describing layered Benard–Marangoni convection is overdetermined, since the vertical velocity is zero identically. We have a system of five equations to calculate two components of the velocity vector, temperature and pressure (three equations of impulse conservation, the incompressibility equation and the heat equation). A class of exact solutions is proposed for the solvability of the Oberbeck–Boussinesq system. The structure of the proposed solution is such that the incompressibility equation is satisfied identically. Thus, it is possible to eliminate the «extra» equation. The emphasis is on the study of heat exchange on the free layer boundary, which is considered rigid. In the description of thermocapillary convective motion, heat exchange is set according to the Newton’s law of cooling. The application of this heat distribution law leads to the third-kind initial-boundary value problem. It is shown that within the presented class of exact solutions to the Oberbeck–Boussinesq equations the overdetermined initial-boundary value problem is reduced to the Sturm–Liouville problem. Consequently, the hydrodynamic fields are expressed using trigonometric functions (the Fourier basis). A transcendental equation is obtained to determine the eigenvalues of the problem. This equation is solved numerically. The numerical analysis of the solutions of the system of evolutionary and gradient equations describing fluid flow is executed. Hydrodynamic fields are analyzed by a computational experiment. The existence of counterflows in the fluid layer is shown in the study of the boundary value problem. The existence of counterflows is equivalent to the presence of stagnation points in the fluid, and this testifies to the existence of a local extremum of the kinetic energy of the fluid. It has been established that each velocity component cannot have more than one zero value. Thus, the fluid flow is separated into two zones. The tangential stresses have different signs in these zones. Moreover, there is a fluid layer thickness at which the tangential stresses at the liquid layer equal to zero on the lower boundary. This physical effect is possible only for Newtonian fluids. The temperature and pressure fields have the same properties as velocities. All the nonstationary solutions approach the steady state in this case.

The two significant geometric parameters are proposed that affect the physical quantities interpolation in the smoothed particle hydrodynamics method (SPH). They are: the smoothing coefficient which the particle size and the smoothing radius are connecting and the volume coefficient which determine correctly the particle mass for a given particles distribution in the medium.

In paper proposes a technique for these parameters influence assessing on the SPH method interpolations accuracy when the hydrostatic problem solving. The analytical functions of the relative error for the density and pressure gradient in the medium are introduced for the accuracy estimate. The relative error functions are dependent on the smoothing factor and the volume factor. Designating a specific interpolation form in SPH method allows the differential form of the relative error functions to the algebraic polynomial form converting. The root of this polynomial gives the smoothing coefficient values that provide the minimum interpolation error for an assigned volume coefficient.

In this work, the derivation and analysis of density and pressure gradient relative errors functions on a sample of popular nuclei with different smoothing radius was carried out. There is no common the smoothing coefficient value for all the considered kernels that provides the minimum error for both SPH interpolations. The nuclei representatives with different smoothing radius are identified which make it possible the smallest errors of SPH interpolations to provide when the hydrostatic problem solving. As well, certain kernels with different smoothing radius was determined which correct interpolation do not allow provide when the hydrostatic problem solving by the SPH method.

Actin is a conserved structural protein that is expressed in all eukaryotic cells. When polymerized, it forms long filaments of fibrillar actin, or F-actin, which are involved in the formation of the cytoskeleton, in muscle contraction and its regulation, and in many other processes. The dynamic and mechanical properties of actin are important for interaction with other proteins and the realization of its numerous functions in the cell. We performed 204.8 ns long molecular dynamics (MD) simulations of an actin filament segment consisting of 24 monomers in the absence and the presence of MgADP at 300 K in the presence of a solvent and at physiological ionic strength using the AMBER99SBILDN and CHARMM36 force fields in the GROMACS software environment, using modern structural models as the initial structure obtained by high-resolution cryoelectron microscopy. MD calculations have shown that the stationary regime of fluctuations in the structure of the F-actin long segment is developed 80–100 ns after the start of the MD trajectory. Based on the results of MD calculations, the main parameters of the actin helix and its bending, longitudinal, and torsional stiffness were estimated using a section of the calculation model that is far enough away from its ends. The estimated subunit axial (2.72–2.75 nm) and angular (165–168^◦) translation of the F-actin helix, its bending (2.8–4.7 · 10⁻²⁶ N·m²), longitudinal (36–47·10⁻⁹ N), and torsional (2.6–3.1·10⁻²⁶ N·m²) stiffness are in good agreement with the results of the most reliable experiments. The results of MD calculations have shown that modern structural models of F-actin make it possible to accurately describe its dynamics and mechanical properties, provided that computational models contain a sufficiently large number of monomers, modern force fields, and relatively long MD trajectories are used. The inclusion of actin partner proteins, in particular, tropomyosin and troponin, in the MD model can help to understand the molecular mechanisms of such important processes as the regulation of muscle contraction.

Investigation of logical deterministic cellular automata models of population dynamics allows to reveal detailed individual-based mechanisms. The search for such mechanisms is important in connection with ecological problems caused by overexploitation of natural resources, environmental pollution and climate change. Classical models of population dynamics have the phenomenological nature, as they are “black boxes”. Phenomenological models fundamentally complicate research of detailed mechanisms of ecosystem functioning. We have investigated the role of fecundity and duration of resources regeneration in mechanisms of population growth using four models of ecosystem with one species. These models are logical deterministic cellular automata and are based on physical axiomatics of excitable medium with regeneration. We have modeled catastrophic death of population arising from increasing of resources regeneration duration. It has been shown that greater fecundity accelerates population extinction. The investigated mechanisms are important for understanding mechanisms of sustainability of ecosystems and biodiversity conservation. Prospects of the presented modeling approach as a method of transparent multilevel modeling of complex systems are discussed.