Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fiber model and new physics constructors with the ELastic Scattering of Electrons and Positrons by neutral Atoms (ELSEPA) model were used to describe the DNA geometry and the physical stage of water radiolysis with the Geant4-DNA toolkit, respectively. Three key parameters (the energy threshold model for strand breaks, the physics model and the maximum distance to distinguish DSB clusters) of scoring DNA damage were studied to investigate the impact on the uncertainties of DNA damage. On the basis of comparison of our results with experimental data and published findings, we were able to accurately predict the yield of various types of DNA damage. Our results indicated that the difference in physics constructor can cause up to 56.4% in the DNA double-strand break (DSB) yields. The DSB yields were quite sensitive to the energy threshold for strand breaks (SB) and the maximum distance to classify the DSB clusters, which were even more than 100 times and four times than the default configurations, respectively.

FLASH radiotherapy delivers therapeutic doses at ultra-high dose rates and may reduce normal tissue injury while preserving tumor control, but its mechanisms remain unclear. Radiolytic oxygen depletion has been proposed as one contributor, yet the combined effects of initial oxygen conditions and the spatial distribution of protons on oxygen depletion remain insufficiently understood. Geant4-DNA was used to simulate water radiolysis induced by 100 MeV protons in oxygenated water. All primary protons were introduced simultaneously, representing an idealized limiting case of zero pulse duration. Initial dissolved oxygen concentration and source radius were varied to evaluate oxygen depletion coefficients and the temporal evolution of chemical species. Relative changes in oxygen enhancement ratio were estimated using the Grimes model. Oxygen depletion coefficients increased with initial dissolved oxygen concentration, whereas reducing the source radius and increasing proton spatial aggregation decreased net oxygen depletion per unit dose. Species evolution supported enhanced radical recombination or termination at the smaller source radius and competition with oxygen scavenging pathways. The relative change in OER was jointly determined by initial oxygen conditions, oxygen depletion coefficients, and absorbed dose, with greater sensitivity under hypoxic conditions. These findings show that initial oxygen conditions and proton spatial distribution jointly regulate microsecond-scale oxygen depletion and the associated relative change in OER.