论文标题

使用Geant4-DNA对DNA损伤的模拟:“分子”示例应用的概述

Simulation of DNA damage using Geant4-DNA: an overview of the "molecularDNA" example application

论文作者

Chatzipapas, Konstantinos P., Tran, Ngoc Hoang, Dordevic, Milos, Zivkovic, Sara, Zein, Sara, Shin, Wook Geun, Sakata, Dousatsu, Lampe, Nathanael, Brown, Jeremy M. C., Ristic-Fira, Aleksandra, Petrovic, Ivan, Kyriakou, Ioanna, Emfietzoglou, Dimitris, Guatelli, Susanna, Incerti, Sébastien

论文摘要

科学界对研究DNA损伤诱导,DNA损伤修复以及暴露于电离辐射后对细胞和细胞系统的生物学影响表现出极大的兴趣。到目前为止,已经提出了几种使用Monte Carlo模拟来研究这些机制的方法。这项研究概述了一个名为“ Moleculardna”的Geant4-DNA示例应用程序,该应用程序在Geant4的11.1版(2022年12月)中公开发行。它是为新手Geant4用户开发的,仅需要对脚本语言的基本理解才能开始。该示例当前提出了生物学靶标的两个不同的DNA尺度几何形状,即“圆柱体”和“人类细胞”。该公共版本基于以前的原型,包括:采用:采用新方法进行化学阶段(IRT-Sync),使用标准DNA损伤(SDD)格式来描述辐射诱导的DNA损伤和升级计算工具以估算DNA损伤响应。使用这些几何形状中的每一种都产生了单链断裂(SSB)和双链断裂(DSB)的仿真数据。将结果与文献进行了比较,以验证该示例,在所有情况下产生的差异不到5%。

The scientific community shows a great interest in the study of DNA damage induction, DNA damage repair and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in-silico methods have been proposed so far to study these mechanisms using Monte Carlo simulations. This study outlines a Geant4-DNA example application, named "molecularDNA", publicly released in the 11.1 version of Geant4 (December 2022). It was developed for novice Geant4 users and requires only a basic understanding of scripting languages to get started. The example currently proposes two different DNA-scale geometries of biological targets, namely "cylinders", and the "human cell". This public version is based on a previous prototype and includes new features such as: the adoption of a new approach for the modeling of the chemical stage (IRT-sync), the use of the Standard DNA Damage (SDD) format to describe radiation-induced DNA damage and upgraded computational tools to estimate DNA damage response. Simulation data in terms of single strand break (SSB) and double strand break (DSB) yields were produced using each of these geometries. The results were compared to the literature, to validate the example, producing less than 5 % difference in all cases.

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