This thesis aims to investigate the effects of BAR domain proteins on the shape of cell membranes by the use of molecular dynamics simulations. The curvature of the lipid membranes can be made by different sources. The most important source is proteins. Proteins can change the shape of lipids by various phenomena such as binding to the membrane, local insertion, and scaffolding. Researchers have shown that the BAR domain proteins shift the membrane curvature by scaffolding. In this thesis, the effects of a single I-BAR protein, as well as different patterns of I-BAR proteins on the shape of the membrane, are studied. First, a comprehensive literature survey on the BAR proteins and their roles in the cell mechanisms is carried out. Because of the high computational cost of all-atom simulations, the use of a coarse grain model is inevitable. Next, a coarse grain model of the I-BAR proteins on the membrane is constructed. Finally, the effects of one and a group of proteins on the curvature of the cell membrane are studied. Simulations show that the obtained results depend on many parameters such as protein density, alignment, arrangement on the lipid membrane patch. Finally, the obtained results compared to the available numerical and experimental data in the literature. Keywords: I-BAR Protein; Shape Based Coarse Grain; Molecular Dynamics; Membrane Bending.
