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By studying change of ion concentrations in animal cells, researchers have reach to important information about cell cycles such as cell growth, muscle cell contraction and cell migration. Manner and amount of passage of ions through cell membrane are basic information that for studying the cell cycle is required. In this thesis, by using two methods, Forward-Reverse constant velocity Steered Molecular Dynamics (FR-cv-SMD) and classical Equilibrium Molecular Dynamics (EMD), diffusion coefficient and Potential of Mean Force (PMF) of sodium and potassium permeation through their protein channels are obtained. For verification the molecular dynamics (MD) methods, diffusion coefficient of K+...