A Review on Molecular Dynamics Simulations in Understanding the Mechanism of Biological Phenomena at the nanoscale

Molecular dynamics (MD) simulation is a well-known subject in the field of bioinformatics. MD simulations study the complexity of biological processes in the aqueous dynamic environment similar to the cellular world at the nanoscale. Over the last five decades since the first molecular dynamics simulations were performed on a protein, the biological understanding of the mechanism of molecular processes has been transformed from several perspectives by these simulations. In this review article, the most important molecular dynamics simulation studies on the biological systems are discussed. While reviewing the most important studies, the focus would be on the three main breakthroughs in this field. These Three turning points include: protein folding, the role of the cell membrane in the function of the cell receptors and the effect of water molecules in MD simulations. Finally, the means of determining the simulation time and the number of atoms in the system are discussed.