Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application
Abstract 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 M...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-03-01
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| Series: | Precision Radiation Oncology |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/pro6.1186 |
| _version_ | 1797858382815690752 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Konstantinos P. Chatzipapas |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-09T21:12:30Z |
| format | Article |
| id | doaj.art-e57040ab957f497c8eb60c8adf205695 |
| institution | Directory Open Access Journal |
| issn | 2398-7324 |
| language | English |
| last_indexed | 2024-04-09T21:12:30Z |
| publishDate | 2023-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Precision Radiation Oncology |
| spelling | doaj.art-e57040ab957f497c8eb60c8adf2056952023-03-28T14:57:03ZengWileyPrecision Radiation Oncology2398-73242023-03-017141410.1002/pro6.1186Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example applicationKonstantinos P. Chatzipapas0Ngoc Hoang Tran1Milos Dordevic2Sara Zivkovic3Sara Zein4Wook‐Geun Shin5Dousatsu Sakata6Nathanael Lampe7Jeremy M. C. Brown8Aleksandra Ristic‐Fira9Ivan Petrovic10Ioanna Kyriakou11Dimitris Emfietzoglou12Susanna Guatelli13Sébastien Incerti14University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan FranceUniversity of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan FranceVinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade SerbiaVinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade SerbiaUniversity of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan FrancePhysics Division, Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School Boston Massachusetts USADivision of Health Science Osaka University Osaka JapanUnaffiliated Melbourne Victoria AustraliaDepartment of Physics and Astronomy Swinburne University of Technology Melbourne AustraliaVinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade SerbiaVinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade SerbiaMedical Physics Laboratory Department of Medicine University of Ioannina Ioannina GreeceMedical Physics Laboratory Department of Medicine University of Ioannina Ioannina GreeceCentre for Medical Radiation Physics University of Wollongong Wollongong New South Wales AustraliaUniversity of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan FranceAbstract 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.https://doi.org/10.1002/pro6.1186DNA damagedouble strand breaksGeant4‐DNAmolecularDNAMonte Carlo simulations |
| spellingShingle | 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 Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application Precision Radiation Oncology DNA damage double strand breaks Geant4‐DNA molecularDNA Monte Carlo simulations |
| title | Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application |
| title_full | Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application |
| title_fullStr | Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application |
| title_full_unstemmed | Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application |
| title_short | Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application |
| title_sort | simulation of dna damage using geant4 dna an overview of the moleculardna example application |
| topic | DNA damage double strand breaks Geant4‐DNA molecularDNA Monte Carlo simulations |
| url | https://doi.org/10.1002/pro6.1186 |
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