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

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

doi:10.1002/pro6.1186

arXiv · 2210.01564

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

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

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Abstract

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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Konstantinos P. Chatzipapas, Ngoc Hoang Tran, Milos Dordevic, Sara Zivkovic, Sara Zein, Wook Geun Shin, Dousatsu Sakata, Nathanael Lampe, Jeremy M. C. Brown, Aleksandra Ristic-Fira, Ivan Petrovic, Ioanna Kyriakou, Dimitris Emfietzoglou, Susanna Guatelli, Sébastien Incerti. 2022-10-04. Simulation of DNA damage using Geant4-DNA: an overview of the "molecularDNA" example application. https://doi.org/10.1002/pro6.1186

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