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In this paper, a comparative analysis of the characteristics, advantages and disadvantages of five different types of magnetoresistive random access memories has been carried out. An optimal mathematical model for investigation of composition and structure of materials for spintronics devices is selected. A review of the combined mathematical model consisting of the molecular dynamics method and the model of spin dynamics of particles with interatomic interaction potential based on a modified embedded atom method is presented. An analysis is performed of modeling of magnetic properties of cobalt and iron bilayer film under conditions of the uniform external magnetic field. The iron layer was characterized by the formation of skirmions, while regions with different magnetic domains were found in the cobalt nanofilms. The overall magnetization of the Co-Fe system was found to be low due to the lack of the priority direction of the magnetic moment. The magnetization rates of cobalt, iron of different thicknesses and the Co-Fe system as a whole were compared separately.

Employing results of our molecular dynamics experiments performed by using the LAMMPS program and embedded atom method, phase diagrams for binary Ag-Cu and Cu-Ni nanoalloys (binary nanoparticles containing 2000 and 5000 atoms) were constructed and analyzed. The concentration dependence of the melting temperature of nanoparticles was interpreted as the liquidus line. It was found that for the Ag-Cu nanoalloy, the phase diagram corresponds to the simple eutectic, and for the Cu-Ni nanoalloy, it corresponds to the phase diagram of an alloy with unlimited mutual solubility of components. The above results agree with the phase diagrams for the corresponding bulk alloys. It was found that the eutectic temperature decreases with decreasing nanoparticle size; and the value of the mole fraction corresponding to the eutectic point and equal to 0,4 coincides with the value corresponding to the bulk alloy. A hypothesis is put forward about the relationship between the surface segregation of one of the components of the binary alloy/nanoalloy and the eutectic type of the phase diagram. It is concluded that the surface segregation effect is a necessary condition for the eutectic behavior, but is not the sufficient condition.

Melting of cuboctahedral nanoclusters of fcc metals (Ag, Au, Cu, Ni, Pd и Pt) containing 561 atoms and a transition to icosahedral isomers preceding their melting were simulated using the isothermal molecular dynamics. The heating process was simulated in the NVT ensemble using the well-known open LAMMPS program, the Verlet velocity algorithm and the Nosé-Hoover thermostat. The interatomic interactions in metal nanoparticles were reproduced by employing the embedded atom method. At a relatively low for MD experiments heating rate of 0,15 K/ps, the cuboctahedron → icosahedron transition was observed in the face-centered cubic nanoparticles of all the above metals, except for Ag nanoparticles. However, an increase in the heating rate to 1,5 K/ps led to the fact that the cuboctahedron → icosahedron transition began to be observed in Ag nanoclusters as well. Unlike nanoparticles of other metals, the cuboctahedron → icosahedron transition in Pt nanoclusters occurs at a very low temperature, close to the initial temperature preceding the heating of the particles and equal to 10 K. In contrast, in Ni particles the cuboctahedron → icosahedron transition was observed at a temperature close to the melting point.

The present study employs molecular dynamics simulations to investigate the interactions between quercetin, amyloid fibrils, and POPC lipid bilayers. The results demonstrate that quercetin does not significantly affect the molecular organization of the bilayer, while IAPP fibrils induce substantial structural changes, particularly in the outer monolayer. Quercetin mitigates these effects by reducing the impact on headgroup and glycerol regions and causing a more superficial positioning of IAPP. Additionally, quercetin slightly decreases the order of sn-2 acyl chains, indicating a disordering effect. In a ternary system with POPC, quercetin, and IAPP, the reduction in the deuterium order parameter of sn-2 acyl chains is less pronounced, underscoring quercetin's protective role. Unlike IAPP, ApoAI and insulin fibrils undergo significant structural reorganization in the membrane-bound state. Quercetin attenuative effects are observed only with ApoAI, highlighting its potential as a protective agent against amyloid-induced membrane disruption. These findings provide valuable insights into the interactions between polyphenols, amyloid fibrils, and lipid membranes, contributing to the understanding of membrane-associated amyloid pathologies.

β-Lactoglobulin (β-lg), the predominant whey protein, is renowned for its nutritional and functional attributes, including its ability to bind hydrophobic and charged molecules. These properties make β-lg a promising candidate for applications such as drug delivery systems, nutraceutical carriers, and nanocomposites for environmental remediation, particularly in detecting and removing heavy metals. Despite its potential, the impact of heavy metal binding on β-lg's structure and stability remains insufficiently explored, posing challenges for its advanced applications. In this study, molecular dynamics (MD) simulations were employed to investigate the structural and dynamic responses of β-lg to the binding of heavy metal ions—Cd²⁺, Ni²⁺, Co³⁺, Pb²⁺, and Pt²⁺. A series of 200-ns MD simulations for the metal-protein complexes was conducted at 300 K using GROMACS software and the CHARMM General Force Field. Key structural parameters analyzed included backbone root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and root-mean-square fluctuations (RMSF). The results demonstrated that binding of Cd²⁺, Ni²⁺, Co³⁺, Pb²⁺, and Pt²⁺ destabilized the protein's structure, with notable effects observed in critical regions such as the EF loop, H-strand, and AB loop. The extent of destabilization varied depending on the specific heavy metal ion. These findings emphasize the need for detailed residue-level analyses to fully elucidate the structural changes induced by metal binding and their implications for β-lg's functional properties. This work provides valuable insights into the behavior of β-lg under heavy metal binding and lays the groundwork for developing β-lg-based nanosystems for environmental and biomedical applications.

Protein-based drug nanocarriers are increasingly recognized as promising candidates for effective drug delivery, owing to a multitude of beneficial advantages over synthetic materials including low cytotoxicity, biocompatibility, biodegradability, abundance, renewability, and high drug loading capacity mediated by diverse functional groups and interactions. In the present study the molecular dynamics simulation was employed to explore the stability of lysozyme-based drug delivery nanosystems functionalized by the antiviral drugs (favipiravir, molnupiravir, nirmatrelvir and ritonavir) and cyanine dyes (AK7-5, AK5-6, AK3-11). A series of 5 ns or 100 ns MD simulations for the top-scored docked drug-dye-protein complexes, obtained using the PatchDock server was performed at 310 K with GROMACS software using the CHARMM General Force Field. The MD results have been analyzed in terms of the parameters, such as the backbone root mean-square deviation, gyration radius, solvent accessible surface area, the root means square fluctuations. The analysis of calculated parameters for the studied systems enabled us to improve the previously acquired molecular docking data. Taken together, the results obtained indicate that Lz-F-AK3-11, Lz-R-AK75, Lz-R-AK56, Lz-N-AK75, Lz-N-AK3-11, and Lz-M-AK75 systems exhibit the highest stability among the examined dye-drug-protein systems and represent potential candidates for the targeted delivery of the explored antiviral agents.

Being the first part of a two-part series, published in this issue of the journal, this paper combines a brief overview of theoretical and experimental studies, as well as the results of atomistic simulations of surface melting in bulk bodies and nanoparticles with presentation of our own molecular dynamics results. We have studied the patterns and mechanisms of surface melting in metal nanoparticles (gold, silver, copper, lead and nickel). The patterns and mechanisms of this phenomenon were studied in most detail on gold and silver nanoparticles. It has been established that the effect of surface premelting is characteristic for nanoparticles of all the above metals, although with decreasing particle size this effect manifests itself to a lesser extent. In addition, our molecular dynamics results do not confirm theoretical predictions of some authors about the existence of a quite definite characteristic (critical) radius of nanoparticles, below which the effect of surface melting is completely absent.

Taking into account results of our molecular dynamics experiments, we have concluded that of the three commonly considered alternative models of nanoparticle melting (homogeneous melting, liquid shell, nucleation of liquid and growth), the latter is the most adequate. At the same time, a more adequate model corresponds to a combination of continuous melting at the initial stage of the process with its subsequent abrupt completion. In other words, nucleation and growth of a liquid-like surface layer occur until a certain critical radius of the crystalline core of the particle is reached, and then melting is completed very quickly, almost abruptly (in fractions of a nanosecond) at a temperature interpreted as the nanoparticle melting temperature Tm. Then, the role of surface melting in nanoparticle sintering is discussed. According to our results, the sintering of metal nanoparticles at high temperatures cannot be reduced to a single mechanism: a certain role play surface melting, surface and bulk diffusion, deformation in the contact zone, and collective effects associated with the displacements of groups (clusters) of atoms rather than of individual atoms. We also have put forward and substantiated the hypothesis that the previously introduced redetermined Tamman temperature TT=0,5Tm corresponds to the switching of the scenario of sintering of metal nanoparticles from formation of a dumbbell-shaped nanocrystal at low temperatures to the scenario corresponding to coalescence of solid nanoparticles resulting in the formation of a defective nanocrystal of a shape close to spherical.

To date, many derivatives and analogs of nucleic acids (NAs) have been developed. Some of them have found uses in scientific research and biomedical applications. Their effective use is based on the data about their properties. Some of the most important physicochemical properties of oligonucleotides are thermodynamic parameters of the formation of their duplexes with DNA and RNA. These parameters can be calculated only for a few NA derivatives: locked NAs, bridged oligonucleotides, and peptide NAs. Existing predictive approaches are based on an analysis of experimental data and the consequent construction of predictive models. The ongoing pilot studies aimed at devising methods for predicting the properties of NAs by computational modeling techniques are based only on knowledge about the structure of oligonucleotides. In this work, we studied the applicability of the weighted histogram analysis method (WHAM) in combination with umbrella sampling to the calculation of thermodynamic parameters of DNA duplex formation (changes in enthalpy ∆H°, entropy ∆S°, and Gibbs free energy ∆G37° ). A procedure was designed involving WHAM for calculating the hybridization properties of oligodeoxyribonucleotides. Optimal parameters for modeling and calculation of thermodynamic parameters were determined. The feasibility of calculation of ∆H°, ∆S°, and ∆G37° was demonstrated using a representative sample of 21 oligonucleotides 4–16 nucleotides long with a GC content of 14–100 %. Error of the calculation of the thermodynamic parameters was 11.4, 12.9, and 11.8 % for ∆H°, ∆S°, and ∆G37° , respectively, and the melting temperature was predicted with an average error of 5.5 °C. Such high accuracy of computations is comparable with the accuracy of the experimental approach and of other methods for calculating the energy of NA duplex formation. In this paper, the use of WHAM for computation of the energy of DNA duplex formation was systematically investigated for the first time. Our results show that a reliable calculation of the hybridization parameters of new NA derivatives is possible, including derivatives not yet synthesized. This work opens up new horizons for a rational design of constructs based on NAs for solving problems in biomedicine and biotechnology.

A comparative molecular dynamics simulation of the gas-phase synthesis of Ag nanoparticles is carried out employing two different types of many-particle potentials of the interatomic interaction: a potential corresponding to the embedded atom method and the tight-binding potential. The initial temperature was varied from 1000 to 3000 K, and then it gradually decreased to 77 K, which corresponded to the temperature of liquid nitrogen. The results obtained using alternative force fields are consistent with each other, but, at the same time, they significantly differ both in the dynamics of evolution of the system and in the obtained final configurations of nanoparticles. Increasing the cutoff radius of the tight binding potential significantly changes the rate of the nanoparticle formation. However, an increase in the cutoff radius when using the embedded atom method does not affect the evolution of the system. The configurations obtained as a result of simulation using the embedded atom method are characterized by a smaller size and a shape close to spherical, while when using the tight binding potential, larger nanocrystals with an elongated shape are formed.

The paper is devoted to the substantiation and further development of the approach to the analysis of the mesoscopic and integral structure of binary metal nanoparticles from the radial distributions of the local density of the components. As an example, the local density distributions of Ni and Al obtained using the results of molecular dynamics modeling of binary Ni-Al nanoparticles with an initial uniform distribution of components and Ni@Al core-shell icosahedral nanostructures are considered. Both patterns demonstrate the surface segregation of Al atoms during relaxation and subsequent quenching of the initial configurations containing 5000 atoms in 1:1 ratio (nanoparticle radius 3 nm). During cooling, the temperature of the nanoparticles decreased from 1000 K to 0,01 K with a low for atomistic simulation cooling rate. Experimentally binary Ni-Al nanoparticles with a radius of about 100 nm (76Ni:24Al at.%) were synthesized by the wire electric explosion. The experimental intensity distributions obtained from the data of energy-dispersive analysis under the action of an electron beam are presented and analyzed. These distributions correspond to a greater extent to the initial configurations in our molecular dynamics experiments, i.e., they are obviously nonequilibrium. At the same time, it was concluded that the final molecular dynamic configurations are also not entirely equilibrium.

In the paper, a method for analyzing molecular oscillations of the glycine, tryptophan and difenilalanine amino acids in the electric fields of the THz/IR frequency ranges has been implemented with Fourier-frequency spectrum calculation of the integral dipole moment amplitude-time realizations obtained by supercomputer modeling. The achieved results inhibited new possibilities of applying this method, supplemented the understanding of the dynamic properties of biomolecules. The method and the data obtained can be recommended in the development of nanobiotechnologies, bioelectronics, and hetero hybrid microelectronic devices with embedded biomolecular components.

The influence of deposited Al, Pd, Co, Au, Ni atoms on a single-layer graphene substrate is investigated using computer simulations. The computer modelling of spraying nanoparticles on the basis of molecular dynamics method is implemented using the NVIDIA®CUDATM technique. According to the results of model calculations, the general behaviour of the system is investigated. The experiments are performed to study the sputtering of atoms of different metals under different initial conditions of the system. Based on these sprays, the behaviour at the beginning of the interaction of the deposited atoms with the substrate is analysed. The time dependences of the lateral position of nanoparticles’ centre of mass and the substrate force throughout the experiment for different sprayed materials are compared. The behaviour of total and potential energies, temperature and momentum of the system is studied. As shown, there is a jump in total energy and temperature as well as a change in the behaviour of the momentum and the substrate force when carbon atoms of graphene are reached for all depositions.

Amyloid fibrils, dubbed SEVI (semen-derived enhancer of virus infection), contribute to the spread of HIV infection. The main components of SEVI are the fragments of prostatic acid phosphatase (PAP): PAP248-286 and PAP85-120. SEVI captures the viral particles and further stimulates their attachment to the target cells, thereby boosting viral fusion and infection. To study the oligomers of SEVI-forming peptides, we used molecular modeling, which is a powerful tool that has been applied in a great variety of studies on SEVI, and an advanced accelerated sampling method of metadynamics. Based on the obtained molecular dynamics data, it was shown that PAP248-286 has a horseshoe shape with bends in the regions of amino acid residues A274 and N269 in the dimeric state. It was suggested that the horseshoe shape might lead in the fibrillation process to the steric zipper model formation, which is typical of amyloids. It was confirmed that the process of fibril formation of PAP248-286 starts with a pairwise parallel arrangement of the peptide helical regions.

Immunoglobulin and tumor necrosis factor complex formation, which is the basis of immunosuppressive drug etanercept therapeutic action, has been studied using quantum chemical modeling and molecular dynamics. The effect on the possibility of cyanine 7 on hydrogen bonds formation between amino acids from tumor necrosis factor and immunoglobulin has been considered. Analysis of dye effect on tumor necrosis factor and immunoglobulin complexation is caused by need for its use as a fluorescent label of etanercept when studying this drug passing through vessels and tissues of body in vivo. Computer simulation was based on molecular structures and IR spectra calculation using the density functional theory methods, followed by an analysis of formed hydrogen bonds parameters, as well as on the study of tumor necrosis factor protein structure dynamics. It has been found that cyanine 7 has a weak effect on amino acids complexation and, therefore, does not lead to therapeutic effect decrease, which makes it possible to use cyanine 7 for labeling etanercept.

It is of fundamental importance in pharmacology and theoretical biology to analyze the binding of ligands to receptors. A better understanding of this process and its outcomes can help predict the following: how the protein interacts with ligands; whether the ligand acts as an activator, inhibitor, or substrate; in which areas the ligand interacts best with the receptor. This article describes the potential of using a software pipeline for finding the most probable position of the ligand in the receptor. Such a pipeline involves a complex algorithm, from predicting the structure of the receptor to searching and analyzing the interaction of ligands with the receptor. The advantage of the software pipeline is that it allows numerous combinations of ligands and receptors to be analyzed at once. Possible interactions of the receptor–ligand complex are studied based on certain parameters: the energy of the affinity of the ligand for the receptor; the length and energy of the bond between the receptor and the ligand, both in the whole complex and between individual atoms. All characteristics can be automatically calculated by default under the specified optimal parameters. Alternatively, they can be set by the user, depending on the task. To illustrate how the software pipeline works, we analyzed the interaction of ligands with human acetylcholinesterase, a protein with the most studied active center. We confirmed that the software pipeline works correctly by comparing the obtained results with the experimental data on the binding of various ligands to human acetylcholinesterase. The pipeline code was published on GitHub (https://github.com/NastiaKozlova/stabilisation complex-receptor-ligand).

Liposomal preparations have a number of advantages: they protect the cells of the body from the toxic effects of drugs; prolong the action of the drug introduced into the body; protect medicinal substances from degradation; promote the manifestation of targeted specificity due to selective penetration from blood into tissues; change the pharmacokinetics of drugs, increasing their pharmacological effectiveness; make it possible to create a water-soluble form of a number of medicinal substances, thereby increasing their bioavailability. In this work, studies were carried out for the development of the method for determining the degree of inclusion of cinnarizine used as a corrector of cerebrovascular accidents into liposomes from soy lecithin. The aim of this study was to determine the distance between the membranes of endotheliocytes, which is critical for the passage of a liposome through the blood-brain barrier. A simulation of changes in the structure of a liposome with cinnarizine located between two cell membranes was carried out using the molecular dynamics method at various distances between the membranes. A square planar fragment of a bilayer phospholipid membrane was assembled using the Internet service Charmm-GUI->Input Generator->Martini Maker‑>BilayerBuilder (http://www.charmm-gui.org/?doc=input/mbilayer). Geometry optimization and molecular dynamics simulation were performed in Gromacs 2019 using Martini 2.2 force field. According to the results of the simulation of coarse-grained molecular dynamics, a liposome from purified soy lecithin with cinnarizine adsorbed on its inner and outer surface is able to maintain integrity, being between the membranes of endotheliocytes at a distance between membranes of more than 8 nm. When the distance between the membranes of endothelial cells is less than 8 nm, the liposome with cinnarizine located between the endotheliocytes can lose its structural integrity due to fusion with the endothelial cell membrane. As a result of the studies, the distance between the membranes of endotheliocytes was established, at which point the liposome with cinnarizine, located between endotheliocytes, can lose its structural integrity due to fusion with the endothelial cell membrane.

The aim of this work is to carry out molecular dynamics simulation of the uniaxial stretching of a cooled Al/Cu composition. The LAMMPS software package has been used for calculations, which includes the classic molecular dynamics code with an emphasis on modeling materials. The Ovito program has been used for visualization, which has a large number of functions, so that the user can thoroughly investigate the results obtained. When describing the interatomic interaction in the Al/Cu nanocomposite, we used the potential of the embedded EAM atom. The choice of potential is due to the fact that it adequately describes and reproduces the properties of a wide class of materials, including metals, semiconductors and alloys. The simulation has been carried out in two stages. At the first stage, a sample consisting of two crystallites of aluminum and copper in the form of parallelepipeds, connected along one of the joint boundaries, was placed in the computational domain and cooled at constant pressure. Cooling was carried out to stabilize the nanosystem. At the second stage, corresponding to the deformation, the temperature and pressure were changed in accordance with the ongoing physical processes. The algorithm of the thermostat and the Nose – Hoover barostat has been used to control the temperature and pressure at the initial stage of cooling. The paper demonstrates the nature of the distribution of longitudinal stresses over the entire volume of the crystal in the process of stretching. When the sample reached the elastic limit, the nucleation of crystal lattice defects and their distribution over the crystal in the form of shifts and rotations of atoms in crystal planes were observed. Areas of plastic deformation origin have been determined. The maximum destruction of the material occurred along the interface. The parameters of the Al/Cu composition (deformation, temperature, mechanical stress) have been dynamically investigated using molecular dynamics simulation. Comparison of the characteristics of the sample in the deformation process has been carried. Under loading conditions, a variety of processes are implemented in the material, including generation of defects, elastic and plastic deformation, generation of damage, and mechanical mixing.

The introduction provides a brief critical review of the available definitions and interpretations of the Tamman temperature, usually defined as Т(∞)T=0,5T(∞)m, and of the Hüttig temperature Т(∞)H=0,3T(∞)m where T(∞)m is the macroscopic value of the melting point of the material. For a nanoparticle we propose to replace in the above relations T(∞)m by the melting temperature of the small object Tm, i.e. to define TT as 0,5Tm and TH as 0,3Tm. In our molecular dynamics experiments on Au nanoparticles, carried out using the LAMMPS program, we found that at the temperature T=TT, in both the central part of the fcc nanoparticle (the core) and in its surface layer (the shell), some local species of a quasicrystalline structure appear which are alternately identified either as crystalline or as non-crystalline by the OVITO program. However, contrary to opinion of E. Rukenstein (1984), at T=TT, a liquid layer on the surface of the crystalline nanoparticle is not formed yet. However, a liquid-like layer was gradually developed in the course of the further temperature elevation. At the same time, in our molecular dynamics experiments we did not reveal any manifestation of the Hüttig temperature TH in the structure of crystalline Au nanoparticles reproduced in our molecular dynamics experiments. It is also of interest that in our molecular dynamics experiments the nanoparticle sintering took place not only above the Tammann temperature but below it as well.

The geometric instability of nanoscale island films is interpreted as a manifestation of the solid state wetting phenomenon, and instability of continuous extended films with nanosized thickness as a consequence of the solid state dewetting. Using molecular dynamics experiment, regularities and mechanisms are investigated of spreading of Pb solid nanoparticles on different Cu faces at a temperature 10 K below the melting temperature of nanoparticles of the chosen size ( 10 nm). The results obtained in molecular dynamics experiments are compared with experimental data for Pb microparticles of 5 - 10 μm in size. It has been also established that in the same «island – substrate» system both solid state wetting and solid state dewetting phenomena can simultaneously take place.

A series of molecular dynamics experiments on cooling disordered Au, Cu, Al, Ti metal nanoparticles and Au — Cu, Ti — Al bimetallic nanoalloys using the tight-binding potential have been performed. The size dependences of the temperature coefficient of linear expansion and the elasticity modulus for mono- and bimetallic particles are obtained. In the first approximation, the size dependence of the linear expansion coefficient is inversely proportional to the corresponding dependence for the melting temperature of a nanoparticle, which correlates with an analytical model. Molecular dynamics results predict a more moderate relative increase in the linear expansion coefficient compared to the analytical model. It was found that the modulus of elasticity increases with decreasing the nanoparticle size.

Algorithms for generating the initial configurations of icosahedral, decahedral and cuboctahedral nanoclusters have been developed and verified. Algorithms and corresponding computer programs have been approbated on the gold nanocluster isomers. Molecular dynamics was also employed to study the regularities of the thermally induced structural transformations in gold nanoparticles with the initial cuboctahedral configuration. It was found that the melting of cuboctahedra is preceded by their transition into icosahedral isomers.

Silver particles smaller than the wavelength of visible light are capable of absorbing light to a large extent due to the surface plasmon resonance, the frequency and intensity of which depend on the shape and structure of nanoparticles. In other words, control of the structure of Ag nanoclusters, widely used in plasmonics, makes it possible to control the wavelengths of light that they scatter and absorb. This article discusses the issue of thermal stability of small Ag clusters with the number of atoms corresponding to the «magic» numbers of the fcc structure, with the initial amorphous configuration of the clusters. It has been shown that the initial amorphous morphology of particles can significantly change the nature of the structure formation of Ag nanoclusters: the formation of a stable fcc structure is replaced by a transition to Dh - and Ih - configurations.

The kinetics of hydrogen permeability and diffusion in hydrogenated membrane alloys based on Fe and Ni have been investigated, which have functional characteristics, structural strength and thermal stability, and are a promising alternative to expensive palladium alloys. The strength characteristics, thermal stability and resistance to hydrogen embrittlement have been studied. The mechanisms of structuring, diffusion and permeability of hydrogen in crystalline, amorphous, nanocrystalline states are considered. For membrane alloys, a particularly important aspect is the combination in open structures (amorphous and bcc), while for hydrogen accumulation, in addition to transport channels (diffusion and permeability), high-density intermetallic clusters are also required. It is noted that, during long-term operation, due to the appearance of dense cluster configurations of intermediate ordering, which shorten the diffusion channels, the transport of hydrogen through them begins to decrease.

In this work, molecular dynamics simulation is carried out of crystallization of bimetallic Co — Au nanoparticles from the melt with various compositions. The effects of the dimensional mismatch between the atomic radii and external pressure on the final configurations cooled up to the temperature 100 K was studied. It was found that the specific potential energy for the bimetallic Co — Au nanoparticle increases with an increase in external pressure. Besides, as the external pressure increases, structural changes occur, namely, the average number of icosahedral atoms inside the cluster changes in a nonlinear character. The dependence of the specific potential energy of bimetallic Co — Au nanoparticles of various compositions on the coefficient of the dimensional mismatch ξ is more complex. The minimum for the gold-enriched composition and equiatomic composition is observed at the values ξ = 1,09 and ξ = 1,15, respectively.

In this work, we studied the diversity of silicic acid oligomers with Sin=(3−8) obtained during molecular dynamics in a reaction Feston–Garofalini force field that describes the process of oligomerization of silicic acids in an aqueous solution at the atomic level. Two systems with different concentrations of silicic acids, including 576 and 729 monomers Si(OH)4 , were studied. According to the calculation results, the highest frequency isomers were represented by linear and branched forms. Throughout the simulation, a high level of dimers was constantly observed. The silicic acids oligomers size increased over time up to 27 Si atoms. The distribution of oligomers by the frequency of permeability for Si n=(3−5) was almost completely comparable with the NMR 29Si and quantum-chemical calculations. A previously undescribed new low-frequency isomer presented in both studied systems was identified among the pentamers. For oligomers with Si n=(6−8) , a wide variety of spatial isomers were observed; some of them have been partially or completely detected experimentally. Analysis of the Si average coordination number during MD simulation showed that 98% of Si atoms have a degree of coordination IV.

Phase diagrams for Au-Si nanoparticles were constructed by using molecular dynamics and thermodynamic simulation, based on the CALPHAD methodology extended to nanoscale objects. It was established that the eutectic temperature of nanoparticles decreases by about 200 K compared to the bulk eutectic temperature, and the position of the eutectic point slightly shifts to a lower value of the molar fraction of Si.

In this paper a molecular-dynamic study of melting of binary metal nanowires with different initial composition and mesoscopic structure is carried out. For the Ni – Cu system it is shown that the melting temperature is significantly affected not only by the percentage of components, but also by their location in the particle, i.e. by the mesoscopic structure. Thus, the Ni nanowire coated with Cu atoms retains its stability at much higher temperatures than the Cu nanowire coated with Ni atoms, ceteris paribus.

In this paper the process of the structure formation in the bimetallic nanosystem Au – Ag of the equiatomic type at different external pressures has been investigated. It has been found that the external pressure affects the process of formation of the bcc phase only slightly, as does the size factor as well. At the same time, the ratios between fcc, hcp and icosahedral phases can vary significantly, under influence of both the external pressure and thesize effect.

On the basis of the molecular dynamics results obtained by using the tight binding potential, the heats of melting, crystallization, and also the sublimation and evaporation heats of platinum and palladium nanoclusters were found. The obtained size dependences are linear if the inverse radius is chosen as an argument, which allows extrapolating the dependencies to the corresponding bulk phases and comparing with the tabulated values.

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.

Molecules were proposed to block the functional cycles of the influenza virus A and SARS-CoV- 2. The blocker molecules efficiently bind inside the M2 and E channels of influenza A and SARS-CoV-2 viruses and block diffusion of H^(+)/K^(+) ions, thus distorting the virus functional cycle. A family of positively charged (+2 e.u.) molecular blockers of H^(+)/K^(+) ion diffusion through the M2 and E channels was proposed. The blocker molecules were diazabicyclooctane (DABCO) derivatives and were investigated for affinity for the M2 and E channels. Thermal dynamics of native and mutant channel structures and blocker binding were modeled by exhaustive docking. Binding energy calculations revealed within-channel, blocking, and extrachannel binding sites in the M2 and E channel proteins. Blocker molecules with higher affinity for the blocking sites were proposed. The most probable amino acid mutations the M2 and E channels were considered, the efficiency of channel blocking was analyzed, and optimal structures were assumed for the blocker molecules.

The mutants of human lysozyme are capable of fibril formation implicated in the etiology of familial systemic or renal amyloidosis. A series of 100 ns thermal unfolding molecular dynamics (MD) simulations with WT human lysozyme and its seven amyloidogenic variants (I56T, D67H, F57I, W64R, Y54N, F57I/T70N and T70N/W112R) have been performed at 500 K. The molecular dynamics simulations were performed with GROMACS software (version 5.1) using the CHARMM36m force field. The MD results have been analysed in terms of the parameters characterizing both the global and local protein structure, such as the backbone root mean-square deviation, gyration radius, solvent accessible surface area, the root mean-square fluctuations and the secondary structure content. Depending on the observed effects, the examined variants of human lysozyme have been roughly divided into three groups comprising of mutants with faster (Y54N and F57I/T70N), similar (D67H and I56T) or slower (W64, F57I and T70N/W112R) unfolding rate compared to the wild-type counterpart. The analysis of the protein fluctuational behavior revealed that in most mutants the β-domain displays stronger fluctuations (except the W64R and F57I) and higher flexibility of the C- and D-helices relative to the native lysozyme with the exception of W64R and Y54N which show marked decrease (W64R) or increase (Y54N) in mobility of almost all residues. The analysis of secondary structure evolution provided evidence for higher stability of α-domain compared to β-domain. The results obtained reinforce the idea that mutation-induced global structural destabilization is not the only factor contributing to protein misfolding, the modifications in conformation and dynamics of selected protein regions may also play significant role in amyloid fibril formation.

The process of desorption of vinpocetine on the surface of crystalline silicon and silicon oxide in various media has been studied by molecular dynamics modeling. The desorption of vinpocetine in water has been established both from the surface of silicon and from the surface of silicon oxide. The character of the desorption of vinpocetine from silicon and silicon oxide at pH 6.8 and pH 7 differs insignificantly (within the error of the simulation results). The desorption of vinpocetine in acidic medium (pH 2) from silicon and silicon oxide occurs more efficiently and at a higher rate, compared to pH 6.8 and pH 7.

The simulation was carried out using two alternative Monte Carlo and molecular dynamics methods of the coalescence process with gradual thermal action for metallic nanoparticles based on nickel, aluminum, copper, silver and gold. The following types of mono- and bimetallic systems were considered: in the form of a sphere and in the form of two perpendicular blocks. It is established that the evolution of the coalescence process for monometallic nanoparticles differs significantly from that for bimetallic nanoparticles. Characteristics such as the coalescence temperature, the structure and shape of the neck, the dihedral angle between the nanoparticles can differ significantly. It is argued that it is impossible to accurately predict the behavior of a bimetallic system in the process of coalescence, knowing the evolution of the process of coalescence for monometallic systems consisting of the same metals.

Using molecular dynamics solid state wetting in the Cu (nanoparticle) / Cu (substrate) system was studied. It has been found that the solid state spreading mechanism corresponds, first of all, to the surface diffusion that was confirmed by the linear dependence of square radii of the first monolayer on the spreading time. A hypophysis was put forward and justified that the degradation of nanorelief of the solid surface occurs by means of the solid state wetting mechanism.

In this work computer simulation of the condensation processes of Cu-Si core-shell nanoparticles was performed by the molecular dynamics method. It was shown that simultaneous cooling of atomic vapors of copper and silicon leads to the formation of disordered CuSi alloy particles. A possible mechanism for the formation of nanoparticles (Cu – core, Si – shell) is associated with deposition of small silicon clusters onto a pre-formed copper core.

A comparative molecular dynamics study has been carried out of the melting of infinite metallic nanowires and free spherical metallic nanoparticles of the same diameter. It was found that the nanowire is melted at a higher temperature than its spherical analogue as the shape of the nanowire is non-equilibrium. As a result, the melting of the nanowire leads to the loss of its stability, i.e. to the break of the nanowire.

Size dependence of the melting temperature of Si nanoparticles has been investigated combining molecular dynamics and thermodynamic simulations. The results of the atomistic simulation obtained using the Stillinger-Weber potential agree with the results of other authors and with the thermodynamic simulation results based on Thomson’s formula. These results predict that the melting temperature Tm of Si nanoparticles diminishes with increasing their reciprocal radius R-1 following to the linear law. The available experimental data predict much lower values of Tm, including underestimated values of the limiting value Tm(∞) found by means of the linear extrapolation of experimental dots to R-1 → 0 (i.e. to the particle radius R → ∞), and the underestimation of Tm(∞) ranges from 200 to 300 K in comparison with the melting point 1688 K of the bulk crystalline Si. Taking into account the obtained results and their comparison with available results of other authors, a conclusion is made that molecular dynamics results, obtained by using the Stillinger-Weber potential, should be more adequate than the available experimental data on the melting temperature of Si nanoparticles.

There have been considered the characteristics and structure forming of amorphous and nanocrystalline binary and ternary alloys based on Pd, as well as high-entropy Zr − Cu (Ni, Ti) compositions based on binary Ni − Ti, Ni − V and ternary Zr − Cu − Ti systems, which are difficult to manufacture, however, can significantly improve the economic efficiency of the processes of separation, purification of hydrogen and its safe storage. The analysis of the formation specificities of stable functional structures of membrane amorphous and nanocrystalline alloys in depending on their ability to hydride formation was also carried out.

Copyright of Metallophysics & Advanced Technologies / Metallofizika i Novejsie Tehnologii is the property of G.V. Kurdyumov Institute for Metal Physics, N.A.S.U and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Metallophysics & Advanced Technologies / Metallofizika i Novejsie Tehnologii is the property of G.V. Kurdyumov Institute for Metal Physics, N.A.S.U and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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 didnt 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 doesnt 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.

In various areas of science, technology, environment protection, construction, it is very important to study processes of porous materials interaction with different substances in different aggregation states. From the point of view of ecology and environmental protection it is particularly actual to investigate processes of porous materials interaction with water in liquid and gaseous phases. Since one mole of water contains 6.022140857 · 1023 molecules of H2O, macroscopic approaches considering the water vapor as continuum media in the framework of classical aerodynamics are mainly used to describe properties, for example properties of water vapor in the pore. In this paper we construct and use for simulation the macroscopic two-dimensional diffusion model [Bitsadze, Kalinichenko, 1980] describing the behavior of water vapor inside the isolated pore. Together with the macroscopic model it is proposed microscopic model of the behavior of water vapor inside the isolated pores. This microscopic model is built within the molecular dynamics approach [Gould et al., 2005]. In the microscopic model a description of each water molecule motion is based on Newton classical mechanics considering interactions with other molecules and pore walls. Time evolution of "water vapor - pore" system is explored. Depending on the external to the pore conditions the system evolves to various states of equilibrium, characterized by different values of the macroscopic characteristics such as temperature, density, pressure. Comparisons of results of molecular dynamic simulations with the results of calculations based on the macroscopic diffusion model and experimental data allow to conclude that the combination of macroscopic and microscopic approach could produce more adequate and more accurate description of processes of water vapor interaction with porous materials.

Molecular dynamics method was applied to simulate processes of melting of disordered CuAg alloy particles in the D = 3 — 5 nm size range. It is shown that for small nanoparticles (diameter D = 3 nm) melting process is associated with formation of an outer layer consisting of Ag atoms and further transition of the particle to an amorphous state. With increasing the particle size to D = 5 nm, this effect was not observed.

In this work computer simulation of the cluster condensation from a high-temperature gas phase containing pairs of copper and gold atoms was carried out by the molecular dynamics method. The average growth rates of clusters and the stoichiometric composition of the emerging particles are determined. It is shown that for particles with diameter of 3 nm or more the molar composition tends to Cu0,75Au0,25.

Using molecular dynamics method, the solid state wetting in the system Pb (nanoparticle) / Cu (substrate) has been observed and studied. It has been found that the solid state spreading mechanism corresponds to the surface diffusion developed via the linear dependence of the square first monolayer radius on the spreading time. From the dependence in question, the surface diffusion coefficient was evaluated.

Amyloid fibrils are highly ordered insoluble protein aggregates that are involved in molecular etiology of a number of severe disorders, including Alzheimer's, Parkinson’s and prion’s diseases, some types of systemic amyloidosis, etc. One of the most effective approaches to detecting the amyloid fibrils is based on monitoring the spectral behavior of specific fluorescent dye Thioflavin T (ThT). Using the molecular docking and molecular dynamics tools, such as PatchDock, FireDock, CreateFibril and GROMACS, the model of twisted K-peptide fibril that supposedly represent the core region of lysozyme amyloid fibrils, has been constructed and analyzed. The effect of fibril twisting angle on the binding characteristics of ThT has been evaluated. The results obtained strongly suggest that ThT specificity for the twisted ribbon fibril polymorphs is primarily determined by the curvature effects rather than amino acid composition of fibril grooveswhich accomodate ThT molecule.

In this work the processes of an internal structure formation in copper-bearing nanoalloys of silver, cobalt and palladium were studied using molecular dynamics with a modified tight-binding potential. For each bimetallic system, five chemical compositions with different proportions of copper atoms were investigated. Non-structural clusters, obtained by melting the primary fcc nanoparticles, were then subjected to freezing procedure at room temperature with a fixed cooling rate. It is shown that upon cooling from the liquid superheated phase it is possible to form structural domains of different internal structure, including multiple nuclei of icosahedral symmetry. Some criteria for obtaining the ordered structure of the nano-melting core with a dense packing of atoms are determined.

The melting and crystallization temperatures of platinum nanoclusters have been found by using results of molecular dynamics modeling, obtained employing two different computer programs and different interatomic interaction potentials. The size dependences found in computer experiments are compared with molecular dynamics data of other authors and with estimations of the melting temperature using Thomson’s formula.