High-pressure study of thermodynamic parameters of diamond-type structured crystals using interatomic Morse potentials

In this work, we have determined the mean square relative displacement, elastic constant, anharmonic effective potential, correlated function, local force constant, and other thermodynamic parameters of diamond-type structured crystals under high-pressure up to 14 GPa. The parameters are calculated through theoretical interatomic Morse potential parameters, by using the sublimation energy, the compressibility, and the lattice constant in the expanded X-ray absorption fine structure spectrum. Numerical results agree well with the experimental values and other theories.

Combining the Mie-Lennard-Jones and the Morse Potentials in Studying the Elastic Deformation of Interstitial Alloy AGC with FCC Structure under Pressure

In this study, the mean nearest neighbor distance between two atoms, the Helmholtz free energy and characteristic quantities for elastic deformation such as elastic moduli E, G, K and elastic constants C11, C12, C44 for binary interstitial alloys with FCC structure under pressure are derived with the statistical moment method. The numerical calculations for interstitial alloy AGC were performed by combining the Mie-Lennard-Jones potential and the Morse potential. Our calculated results were compared with other calculations and the experimental data.

Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.

Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.

APPLICATION OF MACHINE LEARNING METHODS FOR STUDYING OF CRYSTAL STRUCTURES PROPERTIES

In this work was described a model that allows obtaining the potential energy values of crystal structures using machine learning methods. The developed model was trained on the data obtained with the Tersoff and Morse potentials, using the selected parameters for Si, Ge, C, Al, W, Cu, Fe.

INTERACTION OF HYDROGEN IMPURITY WITH NANOCRYSTALLINE PALLADIUM AND NICKEL

The interaction of hydrogen atoms with nanocrystalline palladium and nickel in the work was studied by the molecular dynamics method. The nanocrystalline structure of palladium and nickel was created in the model by crystallization from the liquid state at the presence of several specially introduced crystalline embryos. After solidification, the calculation blocks, in addition to the crystalline phase, contained grain boundaries and triple junctions of grain boundaries. The interactions of metal atoms with each other were described by the multi-particle Cleri-Rosato potential constructed in the framework of the tight-binding model. Morse potentials were used to describe the interactions of hydrogen atoms with metal atoms and with each other. The parameters of Morse potentials were calculated from the experimental data of theabsorption energy, the activation energy of the above-barrier diffusion of hydrogen in a metal (at normal and high temperatures), the binding energy with a vacancy, dilatation. According to the results obtained in the present work, at a high concentration of hydrogen (the concentration of 10% from the metal atoms was considered), the hydrogen atoms combine into aggregates, which are formed predominantly near the surface of the metal. The aggregates contained, as a rule, several dozen hydrogen atoms and had low diffusion activity. The binding energy of hydrogen atoms with these aggregates was greater than with the metal crystal lattice or grain boundaries in it. In palladium, hydrogen aggregates were formed farther from the surface than in nickel. Apparently, this is due not so much to the relatively low energy of hydrogen absorption by palladium (–0.1 eV) in comparison with nickel (0.16 eV), but rather to the difference in lattice parameters of the metals under consideration: 3.89 Å for Pd and 3.524 Å for Ni. For the same reason, conspicuously, hydrogen aggregates in a pure crystal lattice were more often observed in Pd than in Ni. In Ni, aggregates, as a rule, were formed in defect areas containing an excess free volume: near the free surface, in grain boundaries and in triple junctions.

Atomistic Study of the Copper Cluster Deposition on Si(001) and Si(111) Surface

The deposition of a single Cu cluster on the Si (001) and Si (111) surfaces was studied by molecular dynamics simulations. EAM, SW and Morse potentials were used to describe the interaction of Cu-Cu, Si-Si, and the Cu-Si atoms, respectively. The results show that the crystallographic surface of the substrate had a large effect on film growth. On the Si (111) surface, the cluster structure demonstrate good uniformity and epitaxial relation to the substrate. There is no appreciable intermixing or silicide formation at the film-substrate interface, nor silicon segregation on the surface with incident energy between 0.1 and 1.0eV/atom. However, as the incident energy increases to 3.0eV/atom, intermixing began to appear for Cu13 and Cu19 clusters. For the Cu147 cluster intermixing starts to appear at a lower energy of 1.6eV/atom. In contrast, intermixing appears on the Si (001) surface for a range of incident energy from 0.1 to 3.0eV/atom for all the three clusters studied. Furthermore, the epitaxial relation with the Si substrate result in (001)- or (111)-oriented Cu clusters on Si (001) or Si (111), respectively. This behavior is consistent with experimental observations. We found that the effect of cluster deposition on film property depends not only on the substrate-film material combination and cluster size but also on the substrate crystallographic orientation and incident energy.

Explicit flock solutions for Quasi-Morse potentials

We consider interacting particle systems and their mean-field limits, which are frequently used to model collective aggregation and are known to demonstrate a rich variety of pattern formations. The interaction is based on a pairwise potential combining short-range repulsion and long-range attraction. We study particular solutions, which are referred to as flocks in the second-order models, for the specific choice of the Quasi-Morse interaction potential. Our main result is a rigorous analysis of continuous, compactly supported flock profiles for the biologically relevant parameter regime. Existence and uniqueness are proven for three space dimensions, while existence is shown for the two-dimensional case. Furthermore, we numerically investigate additional Morse-like interactions to complete the understanding of this class of potentials.