A novel simplified structure model for accurate and flexible simulation of radiation-induced DNA damage

This study aims to propose and validate a simplified and flexible DNA model for accurate calculations of double strand break (DSB) yields induced by ionizing radiation.

By decoupling the macro- and micro-DNA spatial structures, a novel nuclear DNA model was integrated into the GPU-based gMicroMC code framework. A series of DNA models with varying dihedral angles between nucleotide pairs were uniformly distributed in the cell nucleus. The dihedral angle was optimized based on a cubic polynomial fit to the simulated DSB yield irradiated by Aluminum K-shell X-rays. The optimized model was validated using 4.5 keV monoenergetic electrons and proton beams with energies ranging from 1 MeV to 20 MeV, by comparing the simulated DSB yields with published data derived from experiments or calculations based on other models.

An optimal dihedral angle of 49° was determined from DSB yield induced by Aluminum K-shell X-rays in the V79 cell line. For 4.5 keV electrons, the simulated DSB yield based on the structure-optimized model differed by 1.6% from the experimental data, which was lower than that of other dihedral angles. The DSB yields for protons with initial energies ranging from 1 MeV to 20 MeV were also highly consistent with various calculated or experimental results in the other works.

The proposed DNA model enabled more flexible simulation of radiation-induced DNA damage under various radiation conditions without sacrificing accuracy, potentially applicable to radiobiological research.