Iranian Journal of Medical Physics

Iranian Journal of Medical Physics

Monte Carlo Simulation of DNA Break Prediction Following Electron Irradiation Using Geant4-DNA Toolkit

Document Type : Original Paper

Authors
1 Department of Physics, College of Science, University of Kirkuk, Kirkuk, Iraq
2 Physics Dept., College of Science,kirkuk University ,Kirkuk, IRAQ
3 Department of Biology, College of Education for Women, University of Kirkuk, Kirkuk, Iraq
10.22038/ijmp.2026.92994.2655
Abstract
Introduction: The interaction of ionizing radiation with cells involves complex physical and chemical processes that can cause single-strand breaks (SSB) and double-strand breaks (DSB). DSB is one of the most deleterious forms of DNA damage caused by radiation exposure and is also poorly repaired. Misrepaired or unrepaired damage can finally lead to genomic mutations, which may initiate cancer or cell death.
Material and Methods: The Monte Carlo simulation toolkit Geant4-DNA is used in this study to simulate the physical and chemical processes that can damage the DNA of human fibroblast cells resulting from an incident electron on the DNA.
Results: Electrons are classified as low-Linear Energy Transfer (LET) radiation, typically depositing energy at a rate of approximately 0.2 to 15 keV µm-1 in water or soft tissue; therefore, we examined the occurrence of SSB and DSB vs. electron energy of 0.5, 0.8, 1, 10, and 100 keV. Since there are no published data for human fibroblast cells, our simulation results were compared with available experimental data and findings from other simulation models of other cell types. Our results demonstrated consistent agreement with previously published studies.
Conclusion: The outcomes of our simulation, using the Monte Carlo simulation Geant4-DNA code with the “molecular DNA” based on G4EmDNAPhysics_option6 and G4EmDNAChemistry_option3, are in line with experimental data and simulation results of other cells that have already been published. The maximum DSB value was about 1 keV, with an LET value of about 10 keV μm-1.
Keywords
Subjects

1.        Taqi Ali H., Faraj K. A., Zaynal S. A., Said J. J., Hameed A. M. Effects of high doses of X-ray on hematological parameters and morphology of red blood cells in human blood. Iranian Journal of Medical Physics 2019; 16:112–9. https://doi.org/10.22038/ijmp.2018.31184.1366.
2.        Al-Salihi A, Al-Saedi A, Abdullah K, Safaa M, Sikhi B, Alaa T. Review: Dosimetry in Dental Radiology. Kirkuk University Journal-Scientific Studies 2021; 16:1–12. https://doi.org/10.32894/kujss.2021.170449.
3.        Mohammed Amin Soma, Faraj K. A. Review: Influence of Radiation on Female Fertility and Pregnancy. Kirkuk University Journal-Scientific Studies 2021; 16:1–23. https://doi.org/10.32894/kujss.2021.168660.
4.        Taqi Ali H, Faraj K. A., Zaynal S. A. The effect of long-term X-ray exposure on human lymphocyte. J Biomed Phys Eng 2019; 9:127–32. https://doi.org/10.31661/jbpe.v0i0.935.
5.        Taqi Ali H., Faraj KA, Zaynal S. A, Hameed AM, Mahmood AAA. Effects of occupational exposure of X-Ray on hematological parameters of diagnostic technicians. Radiation Physics and Chemistry 2018; 147:45–52. https://doi.org/10.1016/j.radphyschem.2018.01.027.
6.        Tang N, Bueno M, Meylan S, Incerti S, Clairand I, Villagrasa C. Simulation of Early Radiation-Induced Dna Damage On Different Types of Cell Nuclei. Radiat Prot Dosimetry 2019; 183:26–31. https://doi.org/10.1093/rpd/ncy237.
7.        Chatzipapas KP, Tran HN, Dordevic M, Sakata D, Incerti S, Visvikis D, Bert J. Development of a novel computational technique to create DNA and cell geometrical models for Geant4-DNA. Physica Medica 2024;127. https://doi.org/10.1016/j.ejmp.2024.104839.
8.        Sakata D, Lampe N, Karamitros M, Kyriakou I, Belov O, Bernal MA, Bolst D, Bordage MC, Breton V, Brown JMC, Francis Z, Ivanchenko V, Meylan S, Murakami K, Okada S, Petrovic I, Ristic-Fira A, Santin G, Sarramia D, Sasaki T, Shin WG, Tang N, Tran HN, Villagrasa C, Emfietzoglou D, Nieminen P, Guatelli S, Incerti S. Evaluation of early radiation DNA damage in a fractal cell nucleus model using Geant4-DNA. Physica Medica 2019; 62:152–7. https://doi.org/10.1016/j.ejmp.2019.04.010.
9.        Liamsuwan T, Emfietzoglou D, Uehara S, Nikjoo H. Microdosimetry of low-energy electrons. Int. J. Radiat. Biol., vol. 88, 2012, p. 899–907. https://doi.org/10.3109/09553002.2012.699136.
10.     Friedland W, Dingfelder M, Kundrát P, Jacob P. Track structures, DNA targets and radiation effects in the biophysical Monte Carlo simulation code PARTRAC. Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis 2011; 711:28–40. https://doi.org/10.1016/j.mrfmmm.2011.01.003.
11.     Incerti S, Kyriakou I, Bernal MA, Bordage MC, Francis Z, Guatelli S, Ivanchenko V, Karamitros M, Lampe N, Lee SB, Meylan S, Min CH, Shin WG, Nieminen P, Sakata D, Tang N, Villagrasa C, Tran HN, Brown JMC. Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project. Med Phys 2018;45:e722–39. https://doi.org/10.1002/mp.13048.
12.     Lai Y, Tsai MY, Tian Z, Qin N, Yan C, Hung SH, Chi Y, Jia X. A new open-source GPU-based microscopic Monte Carlo simulation tool for the calculations of DNA damages caused by ionizing radiation — Part II: sensitivity and uncertainty analysis. Med Phys 2020; 47:1971–82. https://doi.org/10.1002/mp.14036.
13.     Okada S, Murakami K, Incerti S, Amako K, Sasaki T. MPEXS-DNA, a new GPU-based Monte Carlo simulator for track structures and radiation chemistry at subcellular scale. Med Phys 2019;46:1483–500. https://doi.org/10.1002/mp.13370.
14.     Folkard M, Prise KM, Vojnovic B, Davies S, Roper MJ, Michael BD. Measurement of DNA Damage by Electrons with Energies between 25 and 4000 EV. Int J Radiat Biol 1993;64:651–8. https://doi.org/10.1080/09553009314551891.
15.     de Lara CM, Hill MA, Jenner TJ, Papworth D, O’Neill P. Dependence of the yield of DNA double-strand breaks in Chinese hamster V79-4 cells on the photon energy of ultrasoft X rays. Radiat Res 2001;155:440–8. https://doi.org/10.1667/0033-7587(2001)155[0440:dotyod]2.0.co;2.
16.     Fulford J, Nikjoo H, Goodhead DT, O’Neill P. Yields of SSB and DSB induced in DNA by Al K ultrasoft X-rays and α-particles: comparison of experimental and simulated yields. Int J Radiat Biol 2001;77:1053–66. https://doi.org/10.1080/09553000110069308.
17.     Semenenko VA, Stewart RD. A fast Monte Carlo algorithm to simulate the spectrum of DNA damages formed by ionizing radiation. Radiat Res 2004;161:451–7. https://doi.org/10.1667/rr3140.
18.     Lampe N, Karamitros M, Breton V, Brown JMC, Kyriakou I, Sakata D, Sarramia D, Incerti S. Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry. Physica Medica 2018;48:135–45. https://doi.org/10.1016/j.ejmp.2018.02.011.
19.     Mokari M, Alamatsaz MH, Moeini H, Babaei-Brojeny AA, Taleei R. Track structure simulation of low energy electron damage to DNA using Geant4-DNA. Biomed Phys Eng Express 2018;4:065009. https://doi.org/10.1088/2057-1976/aae02e.
20.     Matsuya Y, Kai T, Yoshii Y, Yachi Y, Naijo S, Date H, Sato T. Modeling of yield estimation for DNA strand breaks based on Monte Carlo simulations of electron track structure in liquid water. J Appl Phys 2019;126. https://doi.org/10.1063/1.5115519.
21.     Mokari M, Moeini H, Soleimani M, Fereidouni E. Calculation and comparison of the direct and indirect DNA damage induced by low energy electrons using default and CPA100 cross section models within Geant4-DNA. Nucl Instrum Methods Phys Res B 2020;480:56–66. https://doi.org/10.1016/j.nimb.2020.08.011.
22.     Margis S, Magouni M, Kyriakou I, Georgakilas AG, Incerti S, Emfietzoglou D. Microdosimetric calculations of the direct DNA damage induced by low energy electrons using the Geant4-DNA Monte Carlo code. Phys Med Biol 2020;65:045007. https://doi.org/10.1088/1361-6560/ab6b47.
23.     Matsuya Y, Nakano T, Kai T, Shikazono N, Akamatsu K, Yoshii Y, Sato T. A simplified cluster analysis of electron track structure for estimating complex dna damage yields. Int J Mol Sci 2020;21. https://doi.org/10.3390/ijms21051701.
24.     Lampe N. The long term impact of ionising radiation on living systems. n.d.
25.     Watson JD, Crick FH. The structure of DNA. Cold Spring Harb Symp Quant Biol 1953;18:123–31. https://doi.org/10.1101/SQB.1953.018.01.020.
26.     Travers A, Muskhelishvili G. DNA structure and function. FEBS Journal 2015;282:2279–95. https://doi.org/10.1111/febs.13307.
27.     Shi Y. Title: Verification of GEANT4-DNA and a simplified DNA model. n.d.
28.     Dos Santos M, Villagrasa C, Clairand I, Incerti S. Influence of the DNA density on the number of clustered damages created by protons of different energies. Nucl Instrum Methods Phys Res B 2013;298:47–54. https://doi.org/10.1016/j.nimb.2013.01.009.
29.     Hemnani T, Parihar MS. Reactive Oxygen Species And Oxidative Dna Damage. vol. 42. 1998.
30.     Fachbereich Physik V, Dirk Müssig aus Miltenberg Referent D-P, Durante M, Korreferent PD, Bert C. Re-scanning in scanned ion beam therapy in the presence of organ motion Re-scanning in scanned ion beam therapy in the presence of organ motion Mehrfachbestrahlung in der Ionentherapie in der Gegenwart von Organbewegung. 2014.
31.     Sakata D, Belov O, Bordage MC, Emfietzoglou D, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Petrovic I, Ristic-Fira A, Shin WG, Incerti S. Fully integrated Monte Carlo simulation for evaluating radiation induced DNA damage and subsequent repair using Geant4-DNA. Sci Rep 2020;10. https://doi.org/10.1038/s41598-020-75982-x.
32.     Lampe N, Karamitros M, Breton V, Brown JMC, Sakata D, Sarramia D, Incerti S. Mechanistic DNA damage simulations in Geant4-DNA Part 2: Electron and proton damage in a bacterial cell. Physica Medica 2018;48:146–55. https://doi.org/10.1016/j.ejmp.2017.12.008.
33.     Ghosh SK, Jost D. How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes. PLoS Comput Biol 2018;14. https://doi.org/10.1371/journal.pcbi.1006159.
34.     Nikjoo H, O’Neill P, Wilson WE, Goodhead DT. Computational approach for determining the spectrum of DNA damage induced by ionizing radiation. Radiat Res 2001;156:577–83. https://doi.org/10.1667/0033-7587(2001)156[0577:cafdts]2.0.co;2.
35.     Nikjoo H, O’Neill P, Goodhead DT, Terrissol M. Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events. Int J Radiat Biol 1997;71:467–83. https://doi.org/10.1080/095530097143798.
36.     Bernal MA, Liendo JA. An investigation on the capabilities of the PENELOPE MC code in nanodosimetry. Med Phys 2009;36:620–5. https://doi.org/10.1118/1.3056457.
37.     Folkard M, Prise KM, Vojnovic B, Davies S, Roper MJ, Michael BD. Measurement of DNA Damage by Electrons with Energies between 25 and 4000 EV. Int J Radiat Biol 1993;64:651–8. https://doi.org/10.1080/09553009314551891.
38.     Botchway SW, Stevens DL, Hill MA, Jenner TJ, O’Neill P. Induction and rejoining of DNA double-strand breaks in Chinese hamster V79-4 cells irradiated with characteristic aluminum K and copper L ultrasoft X rays. Radiat Res 1997;148:317–24.
39.     Francis Z, Incerti S, Karamitros M, Tran HN, Villagrasa C. Stopping power and ranges of electrons, protons and alpha particles in liquid water using the Geant4-DNA package. Nucl Instrum Methods Phys Res B 2011;269:2307–11. https://doi.org/10.1016/j.nimb.2011.02.031.
 
 
Volume 23, Issue 2 - Serial Number 2
March and April 2026
Pages 117-123

  • Receive Date 25 November 2025
  • Revise Date 11 May 2026
  • Accept Date 13 May 2026