Purpose
This study proposes a novel computational platform that we refer to as IDDRRA (DNA Damage Response to Ionizing RAdiation), which uses Monte Carlo (MC) simulations to score radiation induced DNA damage. MC simulations provide results of high accuracy on the interaction of radiation with matter while scoring the energy deposition based on state-of-the-art physics and chemistry models and probabilistic methods.

Methods
The IDDRRA software is based on the Geant4-DNA toolkit together with new tools that were developed for the purpose of this study, including a new algorithm that was developed in Python for the design of the DNA molecules. New classes were developed in C++ to integrate the GUI and produce the simulation’s output in text format. An algorithm was also developed to analyze the simulation’s output in terms of energy deposition, Single Strand Breaks (SSB), Double Strand Breaks (DSB) and Cluster Damage Sites (CDS). Finally, a new tool was developed to implement probabilistic SSB and DSB repair models using MC techniques.

Results
This article provides the first benchmarks that the user of the IDDRRA tool can use to validate the functionality of the software as well as to provide a starting point to produce different types of DNA simulations. These benchmarks incorporate different kind of particles (e-, e+, protons, electron spectrum) and DNA molecules.

Conclusion
We have developed the IDDRRA tool and demonstrated its use to study various aspects of the modeling and simulation of a DNA irradiation experiment. The tool is expandable and can be expanded by other users with new benchmarks and applications based on the user’s needs and experience. New functionality will be added over time, including the quantification of the indirect damage.

Optical Monte Carlo simulations have been extensively used for the accurate modeling of light transport in scintillators for the improvement of detector designs. In the present work, a GATE Monte Carlo toolkit was used to study the effect of scintillator thicknesses and septa materials in the performance parameters evaluation of a commercially available small animal gamma-optical camera, named “γ-eye”. Firstly, the simulated γ-eye system was validated against experimental data. Then, part of the validated camera was modeled defining all of the optical properties by means of the UNIFIED model of GATE. Different CsI:Na scintillator crystals with varying thicknesses (from 4 mm up to 6 mm) and different reflector (septa) materials were simulated and compared in terms of sensitivity, light output and spatial resolution. Results have demonstrated the reliability of the model and indicate that the thicker crystal array presents higher sensitivity values, but degraded spatial resolution properties. Moreover, the use of black tape around crystals leads to an improvement in spatial resolution values compared to a standard white reflector material.

Purpose
This study aims to standardize the simulation procedure in measuring DNA double-strand breaks (DSBs), by using advanced Monte Carlo toolkits, and newly introduced experimental methods for DNA DSB measurement.

Methods
For the experimental quantification of DNA DSB, an innovative DNA dosimeter was used to produce experimental data. GATE in combination with Geant4-DNA toolkit were exploited to simulate the experimental environment. The PDB4DNA example of Geant4-DNA was upgraded and investigated. Parameters of the simulation such energy threshold (ET) for a strand break and base pair threshold (BPT) for a DSB were evaluated, depending on the dose.

Results
Simulations resulted to minimum differentiation in comparison to experimental data for ET = 19 ± 1 eV and BPT = 10 bp, and high differentiation for ET<17.5 eV or ET>22.5 eV and BPT = 10 bp. There was also small differentiation for ET = 17.5 eV and BPT = 6 bp. Uncertainty has been kept lower than 3%.

Conclusions
This study includes first results on the quantification of DNA double-strand breaks. The energy spectrum of a LINAC was simulated and used for the first time to irradiate DNA molecules. Simulation outcome was validated on experimental data that were produced by a prototype DNA dosimeter.