In this work, the thermal reaction of aluminum (Al) and nickel oxide (NiO) was investigated by molecular dynamics simulations. Some effective features of reaction such as reaction temperature, the reaction mechanism, and diffusion rate of oxygen into aluminum structure were studied. ReaxFF force field was performed to study the Al/NiO thermite reaction behavior at five different temperatures (5...

Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible. Simulations aid our understanding of biochemical processe...

Large biological molecules are frequently represented by a single three-dimensional structure, but in reality, under physiological conditions, they are dynamic entities in constant motion. One important theoretical technique for analyzing both motions and energetics and the roles they play in macromolecular structure and function is a form of simulation termed molecular dynamics. The field of o...

A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T , pressure p) in runs carried out in the microcanonical (NV...

Special-purpose parallel machines that are plugged into a workstation to accelerate molecular dynamics (MD) simulations are attracting a considerable amount of interest. These machines comprise scalable homogeneous multiprocessors for calculating nonbonded forces (Coulombic and van der Waals forces), which consume more than 99% of the central processing unit (CPU) time in standard MD simulation...

Scorpion venom is a rich source of toxins which have great potential to develop new therapeutic agents. Scorpion chloride channel toxins (ClTxs), such as Chlorotoxin selectively inhibit human Matrix Methaloproteinase-2 (hMMP-2). The inhibitors of hMMP-2 have potential use in cancer therapy. Three new ClTxs, meuCl14, meuCl15 and meuCl16, derived from the venom transcriptome of Iranian scorpion, ...