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The paper considers the process of flow formation in an outflow of a binary gas mixture through a thin slit into vacuum. An approach to modeling the flows of rarefied gas mixtures in the transient regime is proposed based on the direct solution of the Boltzmann kinetic equation, in which the conservative projection method is used to calculate the collision integrals. Calculation formulas are provided; the calculation procedure is described in detail in relation to the flow of a binary gas mixture. The Lennard–Jones potential is used as an interaction potential of molecules. A software modeling environment has been developed that makes it possible to study the flows of gas mixtures in a transitional regime on systems of cluster architecture. Due to the use of code parallelization technologies, an acceleration of calculations by 50–100 times was obtained. Numerical simulation of a two-dimensional outflow of a binary argon-neon gas mixture from a vessel into vacuum through a thin slit is carried out for various values of the Knudsen number. The graphs of the dependence of gas mixture components output flow on time in the process of establishing the flow are obtained. Non-stationary regions of strong separation of gas mixture components, in which the molecular densities ratio reaches 10 or more, were discovered. The discovered effect can have applications in the problem of gas mixtures separation.

The work is devoted to the study of the influence of nonlinear processes in the boundary layer on the general nature of gas flows in microchannels of technical systems. Such a study is actually concerned with nanotechnology problems. One of the important problems in this area is the analysis of gas flows in microchannels in the case of transient and supersonic flows. The results of this analysis are important for the gas-dynamic spraying techique and for the synthesis of new nanomaterials. Due to the complexity of the implementation of full-scale experiments on micro- and nanoscale, they are most often replaced by computer simulations. The efficiency of computer simulations is achieved by both the use of new multiscale models and the combination of mesh and particle methods. In this work, we use the molecular dynamics method. It is applied to study the establishment of a gas microflow in a metal channel. Nitrogen was chosen as the gaseous medium. The metal walls of the microchannels consisted of nickel atoms. In numerical experiments, the accommodation coefficients were calculated at the boundary between the gas flow and the metal wall. The study of the microsystem in the boundary layer made it possible to form a multicomponent macroscopic model of the boundary conditions. This model was integrated into the macroscopic description of the flow based on a system of quasi-gas-dynamic equations. On the basis of such a transformed gas-dynamic model, calculations of microflow in real microsystem were carried out. The results were compared with the classical calculation of the flow, which does not take into account nonlinear processes in the boundary layer. The comparison showed the need to use the developed model of boundary conditions and its integration with the classical gas-dynamic approach.

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.

Mechanical unfolding of two identical in structure but differ in their amino acid sequences immunoglobulinbinding domains of proteins L and G under the action of external forces have been investigating  using the method of molecular dynamics with explicit model of solvent. Mechanical characteristics of these proteins have been calculated. It has been shown that in the way of the mechanical unfolding of both proteins appear intermediate states. Calculations revealed three significantly different ways of mechanical unfolding of proteins L and G.

In present work we used the methods of molecular dynamics simulations and quantum chemistry to study the concept, according to which aspartic and glutamic residues play a key role in initiation of helix formation in oligopeptides. It has been shown, that the first turn of the alpha-helix can be organized from various amino acid sequences with Asp and Glu residues on the N-terminus. Thermodynamic properties of such a process were analyzed. The obtained results do not interfere with known experimental and statistical data and they substantially elaborate present views on the processes of early peptide folding stages.

Computer simulation of plastic deformation of FCC copper nanocrystal in the process of uniaxial tension in a direction [001] is performed by methods of molecular dynamics and a static relaxation. It is shown that thermoelastic martensite transformation is responsible for plastic deformation, FCC lattice is reconstructed into HCP lattice. Orientation relationship of contacting phases is identified.

By method of molecular dynamics investigated the interaction of nonlinear localized modes with bivacancies Pt crystal Pt₃Al. Identified dependences of the lifetime of the nonlinear localized modes from the initial temperature of the crystal model, the initial atom Al deviation from its equilibrium position, as well as the distance to the introduced bivacancy Pt in (111) plane of the crystal.

Theoretical and experimental investigations of water vapor interaction with porous materials are carried out both at the macro level and at the micro level. At the macro level, the influence of the arrangement structure of individual pores on the processes of water vapor interaction with porous material as a continuous medium is studied. At the micro level, it is very interesting to investigate the dependence of the characteristics of the water vapor interaction with porous media on the geometry and dimensions of the individual pore.

In this paper, a study was carried out by means of mathematical modelling of the processes of water vapor interaction with suffering pore of the cylindrical type. The calculations were performed using a model of a hybrid type combining a molecular-dynamic and a macro-diffusion approach for describing water vapor interaction with an individual pore. The processes of evolution to the state of thermodynamic equilibrium of macroscopic characteristics of the system such as temperature, density, and pressure, depending on external conditions with respect to pore, were explored. The dependence of the evolution parameters on the distribution of the diffusion coefficient in the pore, obtained as a result of molecular dynamics modelling, is examined. The relevance of these studies is due to the fact that all methods and programs used for the modelling of the moisture and heat conductivity are based on the use of transport equations in a porous material as a continuous medium with known values of the transport coefficients, which are usually obtained experimentally.

Now days the main research activity in the field of nanotechnology is aimed at the creation, study and application of new materials and new structures. Recently, much attention has been attracted by the possibility of controlling magnetic properties using a superconducting current, as well as the influence of magnetic dynamics on the current–voltage characteristics of hybrid superconductor/ferromagnet (S/F) nanostructures. In particular, such structures include the S/F/S Josephson junction or molecular nanomagnets coupled to the Josephson junctions. Theoretical studies of the dynamics of such structures need processes of a large number of coupled nonlinear equations. Numerical modeling of hybrid superconductor/magnet nanostructures implies the calculation of both magnetic dynamics and the dynamics of the superconducting phase, which strongly increases their complexity and scale, so it is advisable to use heterogeneous computing systems.

In the course of studying the physical properties of these objects, it becomes necessary to numerically solve complex systems of nonlinear differential equations, which requires significant time and computational resources.

The currently existing micromagnetic algorithms and frameworks are based on the finite difference or finite element method and are extremely useful for modeling the dynamics of magnetization on a wide time scale. However, the functionality of existing packages does not allow to fully implement the desired computation scheme.

The aim of the research is to develop a unified environment for modeling hybrid superconductor/magnet nanostructures, providing access to solvers and developed algorithms, and based on a heterogeneous computing paradigm that allows research of superconducting elements in nanoscale structures with magnets and hybrid quantum materials. In this paper, we investigate resonant phenomena in the nanomagnet system associated with the Josephson junction. Such a system has rich resonant physics. To study the possibility of magnetic reversal depending on the model parameters, it is necessary to solve numerically the Cauchy problem for a system of nonlinear equations. For numerical simulation of hybrid superconductor/magnet nanostructures, a computing environment based on the heterogeneous HybriLIT computing platform is implemented. During the calculations, all the calculation times obtained were averaged over three launches. The results obtained here are of great practical importance and provide the necessary information for evaluating the physical parameters in superconductor/magnet hybrid nanostructures.

Based on the Holstein Hamiltonian, the dynamics of the charge introduced into the molecular chain of sites was modeled at different temperatures. In the calculation, the temperature of the chain is set by the initial data ¡ª random Gaussian distributions of velocities and site displacements. Various options for the initial charge density distribution are considered. Long-term calculations show that the system moves to fluctuations near a new equilibrium state. For the same initial velocities and displacements, the average kinetic energy, and, accordingly, the temperature of the T chain, varies depending on the initial distribution of the charge density: it decreases when a polaron is introduced into the chain, or increases if at the initial moment the electronic part of the energy is maximum. A comparison is made with the results obtained previously in the model with a Langevin thermostat. In both cases, the existence of a polaron is determined by the thermal energy of the entire chain.

According to the simulation results, the transition from the polaron mode to the delocalized state occurs in the same range of thermal energy values of a chain of $N$ sites ~ $NT$ for both thermostat options, with an additional adjustment: for the Hamiltonian system the temperature does not correspond to the initially set one, but is determined after long-term calculations from the average kinetic energy of the chain.

In the polaron region, the use of different methods for simulating temperature leads to a number of significant differences in the dynamics of the system. In the region of the delocalized state of charge, for high temperatures, the results averaged over a set of trajectories in a system with a random force and the results averaged over time for a Hamiltonian system are close, which does not contradict the ergodic hypothesis. From a practical point of view, for large temperatures T ≈ 300 K, when simulating charge transfer in homogeneous chains, any of these options for setting the thermostat can be used.