In this work, we study the heavy-ion collisions in high energy scales. we employ the EMC effect to extract the parton distribution functions (PDF s) inside the Lead (Pb) and Gold (Au) nuclei. Calculated PDFs are used to achieve the transverse momentum dependent (TMD) ones, using the Pythia 8 and MCFM-10 codes. Through this procedure TMDPDFs for charm and bottom quarks in Au at $\sqrt{S_{NN}} = 200$ GeV, Pb at $\sqrt{S_{NN}} = 2.76$ TeV and $\sqrt{S_{NN}} = 5.02$ TeV are calculated. To evaluate the validity of results and investigate the influence of nuclear EMC effects, achieved TMDs are used as input to calculate the heavy quark modification factor $R_{AA}$ at transverse plane $P_T$. This observable is calculated through numerical solution of the Fokker-Planck equation by extracting the drag and diffusion coefficients, using the hard thermal loop correction in the frame work of the relativistic hydrodynamics up to the third order approximation of gradient expansion. The results are compared with same solution when the input PDFs are considered inside the unbounded protons. Some predictions for future experiments are also presented.
