Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application

• Published in: Precision radiation oncology 2023-03, Vol.7 (1), p.4-14
• Main Authors: 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
• Format: Article
• Language: English
• Subjects: Chemistry; Collaboration; Computer Science; DNA damage; double strand breaks; Geant4‐DNA; Geometry; Medical Physics; molecularDNA; Monte Carlo simulations; Physics; Radiation; Simulation
• ISSN: 2398-7324; 2398-7324
• DOI: 10.1002/pro6.1186

Purpose The scientific community shows 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). Methods It was developed for novice Geant4 users and requires only a basic understanding of scripting languages to get started. The example includes two different DNA‐scale geometries of biological targets, namely “cylinders” and “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, the use of the standard DNA damage format to describe radiation‐induced DNA damage, and upgraded computational tools to estimate DNA damage response. Results Simulation data in terms of single‐strand break and double‐strand break yields were produced using each of the available geometries. The results were compared with the literature, to validate the example, producing less than 5% difference in all cases. Conclusion: “molecularDNA” is a prototype tool that can be applied in a wide variety of radiobiology studies, providing the scientific community with an open‐access base for DNA damage quantification calculations. New DNA and cell geometries for the “molecularDNA” example will be included in future versions of Geant4‐DNA. This study outlines a Geant4‐DNA example application, named “molecularDNA”, publicly released in the 11.1 version of the Geant4 toolkit (December 2022). It was developed for novice Geant4 users and requires only a basic understanding of scripting languages to get started. “molecularDNA” , includes two different DNA‐scale geometries of biological targets, namely “cylinders” and “human cell”. This multiscale example includes the “IRT‐sync”, the implementation of the standard DNA damage file format, and computational tools to estimate the DNA damage response of cells.