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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.

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.

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 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.

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.

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.

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.

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.

In the framework of this paper we have studied the thermal stability of copper clusters in the range of 100 — 150 atoms. The size of the copper nanocluster is determined, which has the greatest thermal stability in the size range under consideration.

In this paper a molecular-dynamics simulation of the structure and thermal stability of the copper clusters size up to 100 atoms has been carried out using many-body tight-binding potential. On the basis of the calculation of a local minimum energy for copper clusters it the «magic» nanoclusters can be found which are more stable. The size dependencies of the thermodynamic and structural characteristics for such clusters demonstrate specific behavior.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease, which affects motor neurons in the brain and spinal cord and leads to patients’ death. One of the causes of motor neuron degeneration and death is the formation of intracellular protein aggregates formed by a mutant SOD1 protein. Recently, it has been shown that the survival time of ALS patients with specific mutation in SOD1 gene inversely correlates with thermodynamic stability of the SOD1 mutant protein. In the present paper, we hypothesize that mutant SOD1 aggregation can be facilitated by not only destabilization due to hydrogen bonds disruption but also by formation of new hydrogen bonds, which can stabilize intermediate “pathogenic” conformations of the mutant SOD1 protein. Molecular dynamics simulations were conducted to estimate frequencies of hydrogen bond occurrence in the protein structure. It was shown that the regression model based on frequencies of hydrogen bond occurrence significantly better correlated with patients’ survival time (R = 0.89, p < 0.00001) than the estimation based on thermodynamic stability analysis of mutant SOD1 proteins.