Tehran University of Medical Sciences Basic & Clinical Cancer Research 2228-6527 16 4 2025 11 08 196 215 Fatemeh Namdari Department of Physics, Shi.C., Islamic Azad University, Shiraz, Iran Seyedeh Nasrin Hosseinimotlagh faculty member of islamic azad university 2023 01 18 2025 08 14 The aim of this work is a description of quantitatively and qualitatively physical processes for proton therapy when a proton pencil beam passes through a water phantom. Therefore, at first, we determine the absorbed dose with both Maple programming and Geant4 simulation in the suggested water phantom. Then, we used as CSDA method to calculate the proton range and range straggling. Also with the Highland formula the mean scattering angle is calculated and following it we investigate the inelastic cross-section, the ionization, and excitation by protons in the inner and outer shells as well as charge transfer, stripping, and ionization by neutral hydrogen.  Finally, we estimate the probabilities of charge state and stopping cross section and straggling and fragmentation. The height, width, and depth of Bragg's peak are discussed through the investigation of collisions, processing, and random phenomena. https://bccr.tums.ac.ir/index.php/bccrj/article/view/463