we have studied the phase transitions in atomic clusters by molecular dynamics simulation, assuming lennard-jones interatomic pair potential. calculations are performed by dap parallel computer. the results are analyzed by simulating their orientational distribution plots (dot-plot), and neutron diffraction patterns. it is shown that all the main features of the bulk phase transitions are essen...

Interactions of 3,3',4,4'-tetrahydroxybiphenyl (BPT) and three isomeric 3,3",4,4"-tetrahydroxyterphenyls (OTT, MTT, PTT) with Alzheimer’s amyloid-β peptide (Aβ) were studied by molecular dynamics simulation and molecular docking. Structural parameters such as Root-mean-square derivations (RMSD), radial distribution function (RDF), helix percentage and other physical parameters were obtained. Th...

Because of participation in many aspects of human life, and due to oxidation-sensitive characteristics of dopamine (DA) and arachidonoyl dopamine (AA-DA), the necessity of biocompatible carrier to keep them against oxidation is of importance. In this work, we explored the putative binding sites of DA and AA-DA to -lactoglobulin (BLG) as potent carrier. Docking results identified the binding si...

We have developed atomic-scale material models capable of melting, crystallization and amorphization. These models feature molecular dynamics governed by Langevin equations of motion in which particle interact through attractive covalent forces and short-range repulsion forces. Also, we present an interactive virtual visualization tool for the simulation of atomic scale material behavior. An ap...

How the results obtained by computer simulation of molecular systems can be validated is considered. The overall quality of the simulated properties of a molecular system will depend on ~i! the quality of the theory or model, ~ii! the accuracy of the interatomic interaction function or force field, ~iii! the degree of sampling, statistics and convergence reached in the simulation, ~iv! the qual...