Soner Ozgen

Accurate determination of the thermodynamic and molecular mechanical properties of amino acids will contribute to a better understanding of their folding mechanisms. In this study, the enthalpy values and molecular mechanics parameters of 17 amino acids were investigated by the classical molecular dynamics method. All calculations were performed using the force-field potential approach. As a result, the calculated solid formation enthalpy for ALA, ASN, ASP, CYS, LYS, and PHE are in good agreement with the experimental data. In addition, molecular mechanics parameters such as Coulomb, bond, angle, dihedral, and Van der Waals were calculated for all amino acids. It is seen that the Coulomb energy is quite low compared to the rest of the molecular mechanical energies. The molecular mechanical energies obtained from the study will contribute to protein-lipid modification studies for electronic interaction, ligand binding to the cell surface, and correct protein localization.

A good understanding of grain formation mechanisms during the solidification of shape memory alloys is an important task for characterization of these alloys. In this study, the grain formation mechanism of the Cu-at.19.9Al shape memory alloy was investigated using molecular dynamics simulations. To realize the simulation study, a cube-shaped model with L12 super-lattice structure and cell size of 5.47 nm was created. Simulation studies in which, the physical interactions between atoms are represented by Cai and Ye version of the embedded atom method (EAM) were performed with LAMMPS software. The model was melted by heating from 300 K to 2500 K and solidified by cooling from 2500 K to 300 K. Melting temperature of the alloy was determined by thermodynamic analysis, bound angle analysis (BAA) and adaptive common neighbor analysis (ACNA). All of these analysing methods were used for structural investigations. As a result, it has determined that the experimental results of the crystal structure of the alloy were in accordance with the simulation results.

There are few theoretical studies on the equation of state (EOS) for amorphous materials while much work has been carried out for crystalline systems. In this study, the EOSs for both crystal- and amorphous-structured nickel are obtained by using an anisotropic molecular dynamics method based on the Voter-Chen formalism of embedded atom method. In order to achieve the EOSs, polynomial curve fitting method has been applied to the data obtained from molecular dynamics simulations carried assuming isothermal and isobaric conditions. Isothermal bulk modulus and their pressure derivatives for both amorphous and crystal structures have also been calculated. The results are compared with the values obtained from well-known Vinet and Davydov EOSs.