3dmi Research Group, Department of Medical Physics, School of Medicine, University of Patras, Rion, 26504, Greece.
Bioemission Technology Solutions (BIOEMTECH), Athens, 11472, Greece.
Med Phys. 2021 May;48(5):2624-2636. doi: 10.1002/mp.14817. Epub 2021 Mar 30.
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.
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.
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.
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.
本研究提出了一种新颖的计算平台，我们称之为 IDDRRA（电离辐射导致的 DNA 损伤的 DNA 损伤反应），它使用蒙特卡罗（MC）模拟来对辐射诱导的 DNA 损伤进行评分。MC 模拟在基于最先进的物理和化学模型和概率方法对辐射与物质的相互作用提供高精度的结果的同时，根据能量沉积对其进行评分。
IDDRRA 软件基于 Geant4-DNA 工具包以及为本研究目的开发的新工具，包括用于设计 DNA 分子的新的 Python 算法。在 C++中开发了新的类来集成 GUI 并以文本格式生成模拟的输出。还开发了一种算法来根据能量沉积、单链断裂（SSB）、双链断裂（DSB）和簇损伤位点（CDS）分析模拟的输出。最后，开发了一种新工具来使用 MC 技术实现概率性 SSB 和 DSB 修复模型。
本文提供了用户可以用来验证 IDDRRA 工具的功能的第一个基准，以及提供产生不同类型 DNA 模拟的起点。这些基准包含不同种类的粒子（电子、正电子、质子、电子能谱）和 DNA 分子。
我们已经开发了 IDDRRA 工具，并展示了它在研究 DNA 辐照实验的建模和模拟的各个方面的应用。该工具具有可扩展性，并且可以根据用户的需求和经验，由其他用户使用新的基准和应用程序进行扩展。随着时间的推移，将添加新的功能，包括间接损伤的量化。
