A molecular dynamics simulation of DNA damage induction by ionizing radiation

Abstract

Purpose: We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl (•OH) free radicals generated by electrons and protons. Methods: The computational method comprises of interfacing the Geant4-DNA Monte Carlo with the ReaxFF molecular dynamics software. A clustering method was employed to map the coor-dinates of •OH-radicals extracted from the ionization track-structures onto nano-meter simulation voxels filled with DNA and water molecules. Results: The molecular dynamics simulation provides the time evolution and chemical reactions in individual simulation voxels as well as the energy-landscape accounted for the DNA-•OH chemical reaction that is essential for the first principle enumeration of hydrogen abstractions, chemical bond breaks, and DNA-lesions induced by collection of ions in clusters less than the critical dimension which is approximately 2-3 Å. We show that the formation of broken bonds leads to DNA base and backbone damages that collectively propagate to DNA single and double strand breaks. For illustration of the methodology, we focused on particles with initial energy of 1 MeV. Our stud-ies reveal a qualitative difference in DNA damage induced by low energy electrons and protons. Electrons mainly generate small pockets of •OH-radicals, randomly dispersed in the cell volume.