A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast

Shin, Wook; Sakata, D.; Lampe, Nathanael; Belov, Oleg; Tran, Ngoc Hoang; Petrović, Ivan; Ristić-Fira, Aleksandra; Dordevic, M.; Bernal, Mario A.; Bordage, M.C.; Francis, Z.; Kyriakou, Ioanna; Perrot, Y.; Sasaki, Takashi; Villagrasa, C.; Guatelli, Susanna; Breton, Vincent; Emfietzoglou, Dimitris; Incerti, S.

doi:10.3390/cancers13194940

Cited by 22 publications

(13 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…37 Molecules produced during the pre-chemical phase react with the sugar-phosphate group and get scavenged by histone or by one another. 38 Using the chemistry model G4EmDNAChemistry, the energydeposition locations of all particles were extracted for further analysis at the end of the physical-simulation stage (10 −15 -10 −12 s after generating a carbon ion). The electrons would now be thermalized and capable of chemical reactions.…”

Section: Methodsmentioning

confidence: 99%

DNA damage and microdosimetry for carbon ions: Track structure simulations as the key to quantitative modeling of radiation‐induced damage

Moeini

Mokari²

2022

Medical Physics

View full text Add to dashboard Cite

Purpose Dose distribution in carbon‐ion irradiations is generally envisaged to have therapeutic advantages over protons, primarily due to the carbon ion's comparatively higher relative biological effectiveness in the tumor than in the encompassing healthy tissues. The objective of this work was to simulate the overall physical and chemical reactions of primary carbon ions impinging on liquid water and, as such, to investigate the DNA‐damage yields in the form of strand breaks (SBs) and in connection with the expected microdosimetric quantities. Materials and methods Using a B‐DNA model and Geant4‐DNA, we simulated the primary and secondary interactions in a spherical medium of water. Subsequently, we categorized DNA damages based on their complexity utilizing the concept of μ‐randomness. We assumed a threshold of 17.5 eV for a direct SB and a probability of 0.13 for an indirect SB triggered by chemical reactions of hydroxyl radicals. Microdosimetric quantities were extracted for three cylindrical volumes representing typical subcellular organisms. Results For fully ionized carbons of 8–256 MeV/u, the yield results appeared to be considerably influenced by the chemical reactions—indicating the important role of secondary electrons in inflicting damage. However, it was mostly the direct‐damage spectrum that determined the overall shape of the damage spectrum. At all primary energies, it was more probable to break each DNA strand at one point—the two points being less than 10 bp apart—than to break only one strand at two random points. Unlike proton's mean‐specific‐energy results, which showed more sensitivity to the volume increase of the smallest cylinder than of the larger ones, carbon‐ion results showed no such sensitivity. Conclusion The growth of the yield ratio of the single‐ and double‐strand breaks (DSB) with the particle energy was estimated for protons to be about 2 times that of alphas and 92 times that of carbon ions. Unlike the proton results, which suggested significant correlations between the DSB yields and mean‐specific (and lineal) energies, carbon ions exhibited no such correlations.

show abstract

Section: Methodsmentioning

confidence: 99%

DNA damage and microdosimetry for carbon ions: Track structure simulations as the key to quantitative modeling of radiation‐induced damage

Moeini

Mokari²

2022

Medical Physics

View full text Add to dashboard Cite

show abstract

“…This public version of "molecularDNA", based on a non-public prototype by Lampe et al, 26,27 has been significantly upgraded from its previous development iterations. [28][29][30][31][32][33][34] In particular, it includes the new chemistry model (Synchronous Independent Reaction Time model, socalled "IRT-sync"), 35 the "G4EmDNAChemistry_option3" Geant4-DNA chemistry list based on Plante and Devroye, 36 as well as an upgrade of computational tools to estimate DNA damage response (DDR), such as repair kinetics and survival probability of cells. In addition, in this study, simulation results are benchmarked against results available in the literature.…”

Section: Introductionmentioning

confidence: 99%

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

Chatzipapas

Tran

Dordevic³

et al. 2023

Precision Radiation Oncology

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…This therapy is receiving increasing attention in clinical cancer treatment. DNA is considered the most sensitive target for most the biological effects of ionizing radiation [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA

Ke-di

Chun

Peng

et al. 2022

IJMS

View full text Add to dashboard Cite

Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fiber model and new physics constructors with the ELastic Scattering of Electrons and Positrons by neutral Atoms (ELSEPA) model were used to describe the DNA geometry and the physical stage of water radiolysis with the Geant4-DNA toolkit, respectively. Three key parameters (the energy threshold model for strand breaks, the physics model and the maximum distance to distinguish DSB clusters) of scoring DNA damage were studied to investigate the impact on the uncertainties of DNA damage. On the basis of comparison of our results with experimental data and published findings, we were able to accurately predict the yield of various types of DNA damage. Our results indicated that the difference in physics constructor can cause up to 56.4% in the DNA double-strand break (DSB) yields. The DSB yields were quite sensitive to the energy threshold for strand breaks (SB) and the maximum distance to classify the DSB clusters, which were even more than 100 times and four times than the default configurations, respectively.

show abstract

A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast

Cited by 22 publications

References 66 publications

DNA damage and microdosimetry for carbon ions: Track structure simulations as the key to quantitative modeling of radiation‐induced damage

DNA damage and microdosimetry for carbon ions: Track structure simulations as the key to quantitative modeling of radiation‐induced damage

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

Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA

Contact Info

Product

Resources

About