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The study tested correctness of three interatomic potentials available in the scientific literature in reproducing a vacancy diffusion in concentrated Fe–Cr alloys by molecular dynamic simulations. It was necessary for further detailed study of vacancy diffusion mechanism in these alloys with Cr content 5–25 at.% at temperatures in the range of 600–1000 K. The analysis of the potentials was performed on alloys models with Cr content 10, 20, 50 at.%. The consideration of the model with chromium content 50 at.% was necessary for further study of diffusion processes in chromium-rich precipitates in these alloys. The formation energies and the atomic mobilities of iron and chromium atoms were calculated and analyzed in the alloys via an artificially created vacancy for all used potentials. A time dependence of mean squared displacement of atoms was chosen as а main characteristic for the analysis of atomic mobilities. The simulation of vacancy formation energies didn’t show qualitative differences between the investigated potentials. The study of atomic mobilities showed a poor reproduction of vacancy diffusion in the simulated alloys by the concentration-dependent model (CDM), which strongly underestimated the mobility of chromium atoms via vacancy in the investigated range of temperature and chromium content. Also it was established, that the two-band model (2BM) of potentials in its original and modified version doesn’t have such drawbacks. This allows one to use these potentials in simulations of vacancy diffusion mechanism in Fe–Cr alloys. Both potentials show a significant dependence of the ratio of chromium and iron atomic mobilities on temperature and Cr content in simulated alloys. The quantitative data of the diffusion coefficients of atoms obtained by these potentials also differ significantly.

The effect of the nonlinear supratransmission in crystal of A₃B stoichiometry is studied by molecular dynamics on the example of Pt₃Al alloy. This effect is the transfer of energy at frequencies outside the phonon spectrum of the crystal. Research of the mechanisms of energy transport from the material surface to the interior is the important task, both from the theoretical point of view and from the prospects for practical application in the modification of near-surface layers by treatment with intense external influence of various types. The model was a three-dimensional face-centered cubic crystal whose atoms interact by means of the multiparticle potential obtained by the embedded atom method, which provides greater realism of the model in comparison with the use of pair potentials. Various forms of oscillation of the external influence region are considered. The possibility of energy transport from the crystal surface to the interior is shown by excitation of quasi-breathers near the region of influence and their subsequent destruction in the crystal and scattering of the energy stored on them. The quasibreathers are high-amplitude nonlinear atoms' oscillations of the alloy lightweight component at frequencies outside the phonon spectrum of the crystal. This effect was observed not with every oscillation's form of the region of influence. Quasi-breathers appeared most intensely near the region of influence with sinusoidal form oscillations. The results obtained indicate that the contribution of quasi-breathers to the energy transfer through the crystal increases with increasing amplitude of the influence. The range of amplitudes from 0.05 to 0.5 Å is considered. The frequency of the influence varied from 0.2 to 15 THz, which ensured the coverage of the entire spectrum of lowamplitude oscillations for this crystal's model. The minimum magnitude of the external effect amplitude at which this effect was observed was found to be 0.15 Å. At amplitudes greater than 0.5 Å, the cell rapidly decays for frequencies close to the optical branch of the phonon spectrum. The results of the study can be useful for laser processing of materials, surface treatment by low-energy plasma, and also in radiation materials science.

The equilibrium configurations of charged electrons, confined in the hard disk potential, are analysed by means of the hybrid numerical algorithm. The algorithm is based on the interpolation formulas, that are obtained from the analysis of the equilibrium configurations, provided by the variational principle developed in the circular model. The solution of the nonlinear equations of the circular model yields the formation of the shell structure which is composed of the series of rings. Each ring contains a certain number of particles, which decreases as one moves from the boundary ring to the central one. The number of rings depends on the total number of electrons. The interpolation formulas provide the initial configurations for the molecular dynamics calculations. This approach makes it possible to significantly increase the speed at which an equilibrium configuration is reached for an arbitrarily chosen number of particles compared to the Metropolis annealing simulation algorithm and other algorithms based on global optimization methods.

This article discusses the mechanical properties of carbon nanotube (CNT)-reinforced platinum under uniaxial tensile loading using the molecular dynamics method. A review of current computational and experimental studies on the use of carbon nanotube-reinforced composites from a structural point of view. However, quantitative and qualitative studies of CNTs to improve the properties of composites are still rare. Composite selection is a promising application for platinum alloys in many cases where they may be subjected to mechanical stress, including in biocompatibility sources. Pt-reinforced with CNTs may have additional possibilities for implantation of the implant and at the same time obtain the required mechanical characteristics.

The structure of the composite is composed of a Pt crystal with a face-centered cubic lattice with a constant of 3.92 Å and a carbon nanotube. The Pt matrix has the shape of a cube with dimensions of $43.1541 Å \times 43.1541 Å \times 43.1541 Å$. The hole size in the average platinum dimension is the radius of the carbon nanotube of the «zigzag» type (8,0), which is 2.6 Å. A carbon nanotube is placed in a hole with a radius of 4.2 Å. At such parameters, the maximum energy level was mutually observed. The model under consideration is contained in 320 atomic bombs and 5181 atomic platinum. The volume fraction of deaths in the Pt-C composite is 5.8%. At the first stage of the study, the strain rate was analyzed for stress-strain and energy change during uniaxial action on the Pt-C composite.

Analysis of the strain rate study showed that the consumption yield strength increases with high strain rate, and the elasticity has increased density with decreasing strain rate. This work also increased by 40% for Pt-C, the elasticity of the composite decreased by 42.3%. In general, fracture processes are considered in detail, including plastic deformation on an atomistic scale.

The study of the structural characteristics of composites and nanostructures is of fundamental importance in materials science. Theoretical and numerical modeling and simulation of the mechanical properties of nanostructures is the main tool that allows for complex studies that are difficult to conduct only experimentally. One example of nanostructures considered in this work are carbon nanotubes (CNTs), which have good thermal and electrical properties, as well as low density and high Young’s modulus, making them the most suitable reinforcement element for composites, for potential applications in aerospace, automotive, metallurgical and biomedical industries. In this review, we reviewed the modeling methods, mechanical properties, and applications of CNT-reinforced metal matrix composites. Some modeling methods applicable in the study of composites with polymer and metal matrices are also considered. Methods such as the gradient descent method, the Monte Carlo method, methods of molecular statics and molecular dynamics are considered. Molecular dynamics simulations have been shown to be excellent for creating various composite material systems and studying the properties of metal matrix composites reinforced with carbon nanomaterials under various conditions. This paper briefly presents the most commonly used potentials that describe the interactions of composite modeling systems. The correct choice of interaction potentials between parts of composites directly affects the description of the phenomenon being studied. The dependence of the mechanical properties of composites on the volume fraction of the diameter, orientation, and number of CNTs is detailed and discussed. It has been shown that the volume fraction of carbon nanotubes has a significant effect on the tensile strength and Young’s modulus. The CNT diameter has a greater impact on the tensile strength than on the elastic modulus. An example of works is also given in which the effect of CNT length on the mechanical properties of composites is studied. In conclusion, we offer perspectives on the direction of development of molecular dynamics modeling in relation to metal matrix composites reinforced with carbon nanomaterials.

A correct model of lipid molecule (distearoylphosphatidylcholine, DSPC) and lipid membrane in water was constructed. Model lipid membrane is stable and has a reliable energy distribution among degrees of freedom. Also after equilibration model system has spatial parameters very similar to those of real DSPC membrane in liquid-crystalline phase. This model was used for studying of lipid membrane permeability to oxygen and water molecules and sodium ion. We obtained the values for transmembrane mobility and diffusion coefficients profiles, which we used for effective permeability coefficients calculation. We found lipid membranes to have significant diffusional resistance to penetration not only by charged particles, such as ions, but also by nonpolar molecules, such as oxygen molecule. We propose theoretical approach for calculation of particle flow across a membrane, as well as methods for estimation of distribution coefficients between bilayer and water phase.

Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent require a reliable source of pseudorandom numbers generated at each step of calculation. We present the two main approaches for implementation of pseudorandom number generators on a GPU. In the first approach, inherent in CPU-based calculations, one PRNG produces a stream of pseudorandom numbers in each thread of execution, whereas the second approach builds on the ability of different threads to communicate, thus, sharing random seeds across the entire device. We exemplify the use of these approaches through the development of Ran2, Hybrid Taus, and Lagged Fibonacci algorithms. As an application-based test of randomness, we carry out LD simulations of N independent harmonic oscillators coupled to a stochastic thermostat. This model allows us to assess statistical quality of pseudorandom numbers. We also profile performance of these generators in terms of the computational time, memory usage, and the speedup factor (CPU/GPU time).

We present a semiphenomenological model of the two molecular motors: kinesin and myosin V, which play a great role in intracellular transport. The temporal dynamics of changes in the characteristic geometric parameters and the elastic stresses generated during the movement of motors is studied. The rates of movement of kinesin and myosin V, and their dependence on the concentration of ATP are discussed.

Experimental, theoretical and numerical investigations of equatorial spread F, equatorial plasma bubbles (EPBs), plasma depletion shells, and plasma clouds are continued at new variety articles. Nonlinear growth, bifurcation, pinching, atomic and molecular ion dynamics are considered at there articles. But the authors of this article believe that not all parameters of EPB development are correct. For example, EPB bifurcation is highly questionable.

A maximum speed inside EPBs and a development time of EPB are defined and studied. EPBs starting from one, two or three zones of the increased density (initial plasma clouds). The development mechanism of EPB is the Rayleigh-Taylor instability (RTI). Time of the initial stage of EPB development went into EPB favorable time interval (in this case the increase linear increment is more than zero) and is 3000–7000 c for the Earth equatorial ionosphere.

Numerous computing experiments were conducted with use of the original two-dimensional mathematical and numerical model MI2, similar USA standard model SAMI2. This model MI2 is described in detail. The received results can be used both in other theoretical works and for planning and carrying out natural experiments for generation of F-spread in Earth ionosphere.

Numerical simulating was carried out for the geophysical conditions favorable for EPBs development. Numerical researches confirmed that development time of EPBs from initial irregularities with the increased density is significantly more than development time from zones of the lowered density. It is shown that developed irregularities interact among themselves strongly and not linearly even then when initial plasma clouds are strongly removed from each other. In addition, this interaction is stronger than interaction of EPBs starting from initial irregularities with the decreased density. The numerical experiments results showed the good consent of developed EPB parameters with experimental data and with theoretical researches of other authors.

The development of structured molecular systems based on a nucleic acid framework takes into account the ability of single-stranded DNA to form a stable double-stranded structure due to stacking interactions and hydrogen bonds of complementary pairs of nucleotides. To increase the stability of the DNA double helix and to expand the temperature range in the hybridization protocols, it was proposed to use more stable metal-mediated complexes of nucleotide pairs as an alternative to Watson-Crick hydrogen bonds. One of the most frequently considered options is the use of silver ions to stabilize a pair of cytosines from opposite DNA strands. Silver ions specifically bind to N3 cytosines along the helix axis to form, as is believed, a strong N3–Ag⁺–N3 bond, relative to which, two rotational isomers, the cis- and trans-configurations of C–Ag⁺–C can be formed. In present work, a theoretical study and a comparative analysis of the free energy profile of the dissociation of two С–Ag⁺–C isomers were carried out using the combined method of molecular mechanics and quantum chemistry (QM/MM). As a result, it was shown that the cis-configuration is more favorable in energy than the trans- for a single pair of cytosines, and the geometry of the global minimum at free energy profile for both isomers differs from the equilibrium geometries obtained previously by quantum chemistry methods. Apparently, the silver ion stabilization model of the DNA duplex should take into account not only the direct binding of silver ions to cytosines, but also the presence of related factors, such as stacking interaction in extended DNA, interplanar hydrogen bonds, and metallophilic interaction of neighboring silver ions.