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Liu Y, Peng X, Luo S, Zhu J, Xiao W, He L, Zhu K, Wang X. Proton Relative Biological Effectiveness for the Induction of DNA double strand breaks based on Geant4. Biomed Phys Eng Express 2024. [PMID: 38181453 DOI: 10.1088/2057-1976/ad1bb9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Uncertainties in the relative biological effectiveness (RBE) of proton remains a major barrier to the biological optimization of proton therapy. A large amount of experimental data suggest that proton RBE is variable. As an evolving Monte Carlo code toolkit, Geant4-DNA is able to simulate the initial DNA damage caused by particle beams through physical and chemical interactions at the nanometer scale over a short period of time. This contributes to evaluating the radiobiological effects induced by ionizing radiation. Based on the Geant4-DNA toolkit, this study constructed a DNA geometric model containing 6.32Gbp, simulated the relationship between radiochemical yields (G-values) and their corresponding chemical constructors, and calculated a detailed calculation of the sources of damage and the complexity of damage in DNA strand breaks. The damage model constructed in this study can simulate the relative biological effectiveness (RBE) in the proton Bragg peak region. The results indicate that: (1) When the electron energy is below 400 keV, the yield of OH· account for 18.1% to 25.3% of the total water radiolysis yields. (2) Under the influence of histone clearance function, the yield of indirect damage account for over 72.93% of the yield of DNA strand breaks (SBs). When linear energy transfer (LET) increased from 29.79 (keV/µm) to 64.29 (keV/µm), the yield of double strand breaks (DSB) increased from 17.27% to 32.65%. (3) By investigating the effect of proton Bragg peak depth on the yield of direct DSB (DSB_direct) and total DSB (DSB_total), the RBE and RBE levels of cells show that the RBE value of protons reaches 2.2 in the Bragg peak region.
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Affiliation(s)
- Yuchen Liu
- School of Nuclear Science and Technology, University of South China, Hengyang, China, Hengyang, Hunan, 421001, CHINA
| | - Xiaoyu Peng
- School of Nuclear Science and Technology, University of South China, Hengyang, China, Hengyang, Hunan, 421001, CHINA
| | - Siyuan Luo
- School of Nuclear Science and Technology, University of South China, Hengyang, Hengyang, Hunan, 421001, CHINA
| | - Jin Zhu
- School of Nuclear Science and Technology, University of South China, Hengyang, China, Hengyang, Hunan, 421001, CHINA
| | - Wancheng Xiao
- School of Nuclear Science and Technology, University of South China, Hengyang, China, Hengyang, Hunan, 421001, CHINA
| | - Lie He
- School of Nuclear Science and Technology, University of South China, Hengyang, China, Hengyang, Hunan, 421001, CHINA
| | - Kun Zhu
- School of Radiation Medicine and Protection, Soochow University, SuZhou, China, Suzhou, Jiangsu, 215006, CHINA
| | - Xiaodong Wang
- School of Nuclear Science and Technology, University of South China, Hengyang, China, Hengyang, Hunan, 421001, CHINA
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Shamsabadi R, Baghani HR. An inter-comparison between radiobiological characteristics of a commercial low-energy IORT system by Geant4-DNA and MCDS Monte Carlo codes. Int J Radiat Biol 2024:1-10. [PMID: 38166191 DOI: 10.1080/09553002.2023.2295290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/17/2023] [Indexed: 01/04/2024]
Abstract
INTRODUCTION The need for accurate relative biological effectiveness (RBE) estimation for low energy therapeutic X-rays (corresponding to 50 kV nominal energy of a commercial low-energy IORT system (INTRABEAM)) is a crucial issue due to increased radiobiological effects, respect to high energy photons. Modeling of radiation-induced DNA damage through Monte Carlo (MC) simulation approaches can give useful information. Hence, this study aimed to evaluate and compare RBE of low energy therapeutic X-rays using Geant4-DNA toolkit and Monte Carlo damage simulation (MCDS) code. MATERIALS AND METHODS RBE calculations were performed considering the emitted secondary electron spectra through interactions of low energy X-rays inside the medium. In Geant4-DNA, the DNA strand breaks were obtained by employing a B-DNA model in physical stage with 10.79 eV energy-threshold and the probability of hydroxyl radical's chemical reactions of about 0.13%. Furthermore, RBE estimations by MCDS code were performed under fully aerobic conditions. RESULTS Acquired results by two considered MC codes showed that the same trend is found for RBEDSB and RBESSB variations. Totally, a reasonable agreement between the calculated RBE values (both RBESSB and RBEDSB) existed between the two considered MC codes. The mean differences of 9.2% and 1.8% were obtained between the estimated RBESSB and RBEDSB values by two codes, respectively. CONCLUSION Based on the obtained results, it can be concluded that a tolerable accordance is found between the calculated RBEDSB values through MCDS and Geant4-DNA, a fact which appropriates both codes for RBE evaluations of low energy therapeutic X-rays, especially in the case of RBEDSB where lethal damages are regarded.
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Affiliation(s)
- Reza Shamsabadi
- Department of Physics, Hakim Sabzevari University, Sabzeoar, Iran
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Thibaut Y, Gonon G, Martinez JS, Petit M, Babut R, Vaurijoux A, Gruel G, Villagrasa C, Incerti S, Perrot Y. Experimental validation in a neutron exposure frame of the MINAS TIRITH for cell damage simulation. Phys Med Biol 2023; 68:225008. [PMID: 37848039 DOI: 10.1088/1361-6560/ad043d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
In the domains of medicine and space exploration, refining risk assessment models for protecting healthy tissue from ionizing radiation is crucial. Understanding radiation-induced effects requires biological experimentations at the cellular population level and the cellular scale modeling using Monte Carlo track structure codes. We present MINAS TIRITH, a tool using Geant4-DNA Monte Carlo-generated databases to study DNA damage distribution at the cell population scale. It introduces a DNA damage location module and proposes a method to convert double-strand breaks (DSB) into DNA Damage Response foci. We evaluate damage location precision and DSB-foci conversion parameters. MINAS TIRITH's accuracy is validated againstγ-H2AX foci distribution from cell population exposed to monoenergetic neutron beams (2.5 or 15.1 MeV) under different configurations, yielding mixed radiation fields. Strong agreement between simulation and experimental results was found demonstrating MINAS TIRITH's predictive precision in radiation-induced DNA damage topology. Additionally, modeling intercellular damage variability within a population subjected to a specific macroscopic dose identifies subpopulations, enhancing realistic fate models. This approach advances our understanding of radiation-induced effects on cellular systems for risk assessment improvement.
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Affiliation(s)
- Y Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gonon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - J S Martinez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - M Petit
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - R Babut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - A Vaurijoux
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gruel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, LP2i, UMR 5797, F-33170 Gradignan, France
| | - Y Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
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Nicolanti F, Caccia B, Cartoni A, Emfietzoglou D, Faccini R, Incerti S, Kyriakou I, Satta M, Tran HN, Mancini-Terracciano C. Calculation of electron interaction models in N 2 and O 2. Phys Med 2023; 114:102661. [PMID: 37703804 DOI: 10.1016/j.ejmp.2023.102661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/19/2023] [Accepted: 08/05/2023] [Indexed: 09/15/2023] Open
Abstract
Cosmic rays have the potential to significantly affect the atmospheric composition by increasing the rate and changing the types of chemical reactions through ion production. The amount and states of ionization, and the spatial distribution of ions produced are still open questions for atmospheric models. To precisely estimate these quantities, it is necessary to simulate particle-molecule interactions, down to very low energies. Models enabling such simulations require interaction probabilities over a broad energy range and for all energetically allowed scattering processes. In this paper, we focus on electron interaction with the two most abundant molecules in the atmosphere, i.e., N2 and O2, as an initial step. A set of elastic and inelastic cross section models for electron transportation in oxygen and nitrogen molecules valid in the energy range 10 eV - 1 MeV, is presented. Comparison is made with available theoretical and experimental data and a reasonable good agreement is observed. Stopping power is calculated and compared with published data to assess the general consistency and reliability of our results. Good overall agreement is observed, with relative differences lower than 6% with the ESTAR database.
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Affiliation(s)
- F Nicolanti
- Physics Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; INFN, Sec. of Rome, p.le Aldo Moro, 2, 00185, Rome, Italy.
| | - B Caccia
- ISS(Italian National Institute of Health), V. Regina Elena, 299, 00161, Rome, Italy
| | - A Cartoni
- Chemistry Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy
| | - D Emfietzoglou
- Med. Phys. Lab., Dept of Medicine, University of Ioannina, 45110, Ioannina, Greece
| | - R Faccini
- Physics Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; INFN, Sec. of Rome, p.le Aldo Moro, 2, 00185, Rome, Italy
| | - S Incerti
- Université de Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, Chemin du Solarium, 19, 33170, Gradignan, France
| | - I Kyriakou
- Med. Phys. Lab., Dept of Medicine, University of Ioannina, 45110, Ioannina, Greece
| | - M Satta
- Chemistry Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; ISMN-CNR, p. Aldo Moro, 7, 00185, Rome, Italy
| | - H N Tran
- Université de Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, Chemin du Solarium, 19, 33170, Gradignan, France
| | - C Mancini-Terracciano
- Physics Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; INFN, Sec. of Rome, p.le Aldo Moro, 2, 00185, Rome, Italy
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Salas-Ramirez M, Maigne L, Fois G, Scherthan H, Lassmann M, Eberlein U. Radiation-induced double-strand breaks by internal ex vivo irradiation of lymphocytes: Validation of a Monte Carlo simulation model using GATE and Geant4-DNA. Z Med Phys 2023:S0939-3889(23)00089-2. [PMID: 37599196 DOI: 10.1016/j.zemedi.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
This study describes a method to validate a radiation transport model that quantifies the number of DNA double-strand breaks (DSB) produced in the lymphocyte nucleus by internal ex vivo irradiation of whole blood with the radionuclides 90Y, 99mTc, 123I, 131I, 177Lu, 223Ra, and 225Ac in a test vial using the GATE/Geant4 code at the macroscopic level and the Geant4-DNA code at the microscopic level. METHODS The simulation at the macroscopic level reproduces an 8 mL cylindrical water-equivalent medium contained in a vial that mimics the geometry for internal ex vivo blood irradiation. The lymphocytes were simulated as spheres of 3.75 µm radius randomly distributed, with a concentration of 125 spheres/mL. A phase-space actor was attached to each sphere to register all the entering particles. The simulation at the microscopic level for each radionuclide was performed using the Geant4-DNA tool kit, which includes the clustering example centered on a density-based spatial clustering of applications with noise (DBSCAN) algorithm. The irradiation source was constructed by generating a single phase space from the sum of all phase spaces. The lymphocyte nucleus was defined as a water sphere of a 3.1 µm radius. The absorbed dose coefficients for lymphocyte nuclei (dLymph) were calculated and compared with macroscopic whole blood absorbed dose coefficients (dBlood). The DBSCAN algorithm was used to calculate the number of DSBs. Lastly, the number of DSB∙cell-1∙mGy-1 (simulation) was compared with the number of radiation-induced foci per cell and absorbed dose (RIF∙cell-1∙mGy-1) provided by experimental data for gamma and beta emitting radionuclides. For alpha emitters, dLymph and the number of α-tracks∙100 cell-1∙mGy-1 and DBSs∙µm-1 were calculated using experiment-based thresholds for the α-track lengths and DBSs/track values. The results were compared with the results of an ex vivo study with 223Ra. RESULTS The dLymph values differed from the dBlood values by -1.0% (90Y), -5.2% (99mTc), -22.3% (123I), 0.35% (131I), 2.4% (177Lu), -5.6% (223Ra) and -6.1% (225Ac). The number of DSB∙cell-1∙mGy-1 for each radionuclide was 0.015 DSB∙cell-1∙mGy-1 (90Y), 0.012 DSB∙cell-1∙mGy-1 (99mTc), 0.014DSB∙cell-1∙mGy-1 (123I), 0.012 DSB∙cell-1∙mGy-1 (131I), and 0.016 DSB∙cell-1∙mGy-1 (177Lu). These values agree very well with experimental data. The number of α-tracks∙100 cells-1∙mGy-1 for 223Ra and 225Ac where 0.144 α-tracks∙100 cells-1∙mGy-1 and 0.151 α-tracks∙100 cells-1∙mGy-1, respectively. These values agree very well with experimental data. Moreover, the linear density of DSBs per micrometer α-track length were 11.13 ± 0.04 DSB/µm and 10.86 ± 0.06 DSB/µm for 223Ra and 225Ac, respectively. CONCLUSION This study describes a model to simulate the DNA DSB damage in lymphocyte nuclei validated by experimental data obtained from internal ex vivo blood irradiation with radionuclides frequently used in diagnostic and therapeutic procedures in nuclear medicine.
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Affiliation(s)
| | - Lydia Maigne
- Laboratoire de Physique de Clermont, University of Clermont Auvergne, Clermont, France
| | - Giovanna Fois
- Laboratoire de Physique de Clermont, University of Clermont Auvergne, Clermont, France
| | - Harry Scherthan
- Bundeswehr Institute of Radiobiology affiliated to the University of Ulm, Munich, Germany
| | - Michael Lassmann
- Department of Nuclear Medicine, University of Würzburg, Würzburg, Germany
| | - Uta Eberlein
- Department of Nuclear Medicine, University of Würzburg, Würzburg, Germany
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Chatzipapas K, Dordevic M, Zivkovic S, Tran NH, Lampe N, Sakata D, Petrovic I, Ristic-Fira A, Shin WG, Zein S, Brown JMC, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Geant4-DNA simulation of human cancer cells irradiation with helium ion beams. Phys Med 2023; 112:102613. [PMID: 37356419 DOI: 10.1016/j.ejmp.2023.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/03/2023] [Accepted: 05/30/2023] [Indexed: 06/27/2023] Open
Abstract
PURPOSE This study aimed to develop a computational environment for the accurate simulation of human cancer cell irradiation using Geant4-DNA. New cell geometrical models were developed and irradiated by alpha particle beams to induce DNA damage. The proposed approach may help further investigation of the benefits of external alpha irradiation therapy. METHODS The Geant4-DNA Monte Carlo (MC) toolkit allows the simulation of cancer cell geometries that can be combined with accurate modelling of physical, physicochemical and chemical stages of liquid water irradiation, including radiolytic processes. Geant4-DNA is used to calculate direct and non-direct DNA damage yields, such as single and double strand breaks, produced by the deposition of energy or by the interaction of DNA with free radicals. RESULTS In this study, the "molecularDNA" example application of Geant4-DNA was used to quantify early DNA damage in human cancer cells upon irradiation with alpha particle beams, as a function of linear energy transfer (LET). The MC simulation results are compared to experimental data, as well as previously published simulation data. The simulation results agree well with the experimental data on DSB yields in the lower LET range, while the experimental data on DSB yields are lower than the results obtained with the "molecularDNA" example in the higher LET range. CONCLUSION This study explored and demonstrated the possibilities of the Geant4-DNA toolkit together with the "molecularDNA" example to simulate the helium beam irradiation of cancer cell lines, to quantify the early DNA damage, or even the following DNA damage response.
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Affiliation(s)
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia.
| | - Sara Zivkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia
| | - Ngoc Hoang Tran
- University of Bordeaux, CNRS, LP2i, UMR5797, F-33170 Gradignan, France
| | | | - Dousatsu Sakata
- Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia
| | - Aleksandra Ristic-Fira
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovica Alasa 12-14, 11351 Vinca, Belgrade, Serbia
| | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, 02114 MA, USA
| | - Sara Zein
- University of Bordeaux, CNRS, LP2i, UMR5797, F-33170 Gradignan, France
| | - Jeremy M C Brown
- Optical Sciences Centre, Department of Physics and Astronomy, Swinburne University of Technology, Hawthorn 3122, Australia
| | - Ioanna Kyriakou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Susanna Guatelli
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Sebastien Incerti
- University of Bordeaux, CNRS, LP2i, UMR5797, F-33170 Gradignan, France
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Ballisat L, Beck L, De Sio C, Guatelli S, Sakata D, Incerti S, Tran HN, Duan J, Maclean K, Shi Y, Velthuis J, Rosenfeld A. In-silico calculations of DNA damage induced by α-particles in the 224Ra DaRT decay chain for a better understanding of the radiobiological effectiveness of this treatment. Phys Med 2023; 112:102626. [PMID: 37393861 DOI: 10.1016/j.ejmp.2023.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 07/04/2023] Open
Abstract
Diffusing alpha-emitters radiation Therapy (DaRT) is an interstitial brachytherapy technique using 224Ra seeds. For accurate treatment planning a good understanding of the early DNA damage due to α-particles is required. Geant4-DNA was used to calculate the initial DNA damage and radiobiological effectiveness due to α-particles with linear energy transfer (LET) values in the range 57.5-225.9 keV/μm from the 224Ra decay chain. The impact of DNA base pair density on DNA damage has been modelled, as this parameter varies between human cell lines. Results show that the quantity and complexity of DNA damage changes with LET as expected. Indirect damage, due to water radical reactions with the DNA, decreases and becomes less significant at higher LET values as shown in previous studies. As expected, the yield of complex double strand breaks (DSBs), which are harder for a cell to repair, increases approximately linearly with LET. The level of complexity of DSBs and radiobiological effectiveness have been found to increase with LET as expected. The quantity of DNA damage has been shown to increase for increased DNA density in the expected base pair density range of human cells. The change in damage yield as a function of base pair density is largest for higher LET α-particles, an increase of over 50% for individual strand breaks between 62.7 and 127.4 keV/μm. This change in yield shows that the DNA base pair density is an important parameter for modelling DNA damage particularly at higher LET where the DNA damage is greatest and most complex.
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Affiliation(s)
| | - Lana Beck
- School of Physics, University of Bristol, Bristol, UK
| | - Chiara De Sio
- School of Physics, University of Bristol, Bristol, UK
| | - Susanna Guatelli
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
| | - Dousatsu Sakata
- Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - Hoang Ngoc Tran
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - Jinyan Duan
- School of Physics, University of Bristol, Bristol, UK
| | - Katie Maclean
- School of Physics, University of Bristol, Bristol, UK
| | - Yuyao Shi
- School of Physics, University of Bristol, Bristol, UK
| | - Jaap Velthuis
- School of Physics, University of Bristol, Bristol, UK
| | - Anatoly Rosenfeld
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
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D-Kondo JN, Garcia Garcia OR, LaVerne JA, Faddegon BA, Schuemann J, Shin WG, Ramos-Mendez J. An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry. Phys Med Biol 2023. [PMID: 37201533 DOI: 10.1088/1361-6560/acd6d0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
OBJECTIVE The TOPAS-nBio Monte Carlo track structure simulation code, a wrapper of Geant4-DNA, was extended for its use in pulsed and longtime homogeneous chemistry simulations using the Gillespie algorithm.
Approach: Three different tests were used to assess the reliability of the implementation and its ability to accurately reproduce published experimental results: (1) A simple model with a known analytical solution, (2) the temporal evolution of chemical yields during the homogeneous chemistry stage, and (3) radiolysis simulations conducted in pure water with dissolved oxygen at concentrations ranging from 10 µM to 1 mM with [H2O2] yields calculated for 100 MeV protons at conventional and FLASH dose rates of 0.286 Gy/s and 500 Gy/s, respectively. Simulated chemical yield results were compared closely with data calculated using the Kinetiscope software which also employs the Gillespie algorithm.
Main results: Validation results in the third test agreed with experimental data of similar dose rates and oxygen concentrations within one standard deviation, with a maximum of 1% difference for both conventional and FLASH dose rates. In conclusion, the new implementation of TOPAS-nBio for the homogeneous long time chemistry simulation was capable of recreating the chemical evolution of the reactive intermediates that follow water radiolysis. 
Significance: Thus, TOPAS-nBio provides a reliable all-in-one chemistry simulation of the physical, physico-chemical, non-homogeneous, and homogeneous chemistry and could be of use for the study of FLASH dose rate effects on radiation chemistry.
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Affiliation(s)
- J Naoki D-Kondo
- Department of Radiation Oncology, University of California San Francisco, 1600 Divisadero Street, San Francisco, CA, USA, San Francisco, California, 94115, UNITED STATES
| | - Omar Rodrigo Garcia Garcia
- Facultad de Fisico-Matematicas, Benemerita Universidad Autonoma de Puebla, Av San Claudio, Ciudad Universitaria, La Hacienda, Puebla, Puebla, 72592 , MEXICO
| | - Jay A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, 225 Nieuwland Science Hall, Notre Dame, Indiana, 46556, UNITED STATES
| | - Bruce A Faddegon
- Department of Radiation Oncology, University of California San Francisco, 1600 Divisadero Street, San Francisco, CA, USA, San Francisco, California, 94115, UNITED STATES
| | - Jan Schuemann
- Radiation Oncology, Massachusetts General Hospital, Burr Proton Therapy Center, 30 Fruit Street, Boston, Massachusetts, 02114, UNITED STATES
| | - Wook-Geun Shin
- Department of Radiation Oncology, Massachusetts General Hospital, 30 Fruit Street, Boston, MA, USA 02114, Boston, Massachusetts, 02114-2696, UNITED STATES
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, 1600 Divisadero Street, San Francisco, CA, USA, San Francisco, California, 94115, UNITED STATES
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Chappuis F, Tran HN, Zein SA, Bailat C, Incerti S, Bochud F, Desorgher L. The general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension to investigate mechanisms underlying the FLASH effect in radiotherapy: Current status and challenges. Phys Med 2023; 110:102601. [PMID: 37201453 DOI: 10.1016/j.ejmp.2023.102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023] Open
Abstract
FLASH radiotherapy is a promising approach to cancer treatment that offers several advantages over conventional radiotherapy. With this novel technique, high doses of radiation are delivered in a short period of time, inducing the so-called FLASH effect - a phenomenon characterized by healthy tissue sparing without alteration of tumor control. The mechanisms behind the FLASH effect remain unknown. One way to approach this problem is to gain insight into the initial parameters that can distinguish FLASH from conventional irradiation by simulating particle transport in aqueous media using the general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension. This review article discusses the current status of Geant4 and Geant4-DNA simulations to investigate mechanisms underlying the FLASH effect, as well as the challenges faced in this research field. One of the primary challenges is to accurately simulate the experimental irradiation parameters. Another challenge is the temporal extension of the simulations. This review also focuses on two hypotheses to explain the FLASH effect - namely the oxygen depletion hypothesis and the inter-track interactions hypothesis - and discusses how the Geant4 toolkit can be used to investigate them. The aim of this review is to provide an overview of Geant4 and Geant4-DNA simulations for FLASH radiotherapy and to highlight the challenges that need to be overcome in order to better study the FLASH effect.
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Affiliation(s)
- Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Hoang Ngoc Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Sara A Zein
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Claude Bailat
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Sébastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - François Bochud
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland.
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Margis S, Kyriakou I, Incerti S, Bordage MC, Emfietzoglou D. Sub-keV corrections to binary encounter cross section models for electron ionization of liquid water with application to the Geant4-DNA Monte Carlo code. Appl Radiat Isot 2023; 194:110693. [PMID: 36731390 DOI: 10.1016/j.apradiso.2023.110693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/13/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
INTRODUCTION The electron ionization cross section of water is one of the most important input in Monte Carlo studies of cellular radiobiological effects. Analytical cross section models of the binary-encounter type have the potential of reducing simulation time and facilitate application to a variety of biological materials (other than water). The Binary-Encounter-Bethe (BEB) and Binary-Encounter-Dipole (BED) models of NIST are perhaps the most popular of such models giving reliable results for atoms and molecules in the gas-phase over a wide energy range. However, the use of such models to sub-keV electron energies in liquid water raises concerns due to the neglect of condensed phase effects that leads to a significant overestimation when compared to medium-specific dielectric models. PURPOSE To modify the BEB and BED models towards better agreement with the recommended low-energy dielectric model of Geant4-DNA (Option 4). To implement the new modifications to the existing BEB model of the Option 6 physics constructor of Geant4-DNA and re-evaluate fundamental transport quantities for sub-keV electrons. METHODS In analogy to a Yukawa potential a simple, yet physically-motivated, modification of the Burgess correction term is proposed to account for the reduction of the Coulomb interaction due to the polarizability of the target. The magnitude of the correction is guided by the dielectric-based ionization cross section implemented in Option 4. RESULTS Differential, total and stopping ionization cross sections for low-energy electrons in liquid water are presented. When combined with the Vriens correction (which is not included in Option 6), the proposed modification to the BEB and BED models brings the ionization and stopping cross sections in much better agreement against those used in the Option 4 dielectric model of Geant4-DNA, with up to 30% and 10% deviation, respectively. Implementation of the new correction to the Option 6 constructor of Geant4-DNA and re-evaluation of fundamental transport quantities, such as electron penetration ranges and dose-point-kernels, reduced the discrepancies from Option 4 at sub-keV energies from 20 to 100% (or more) to well below 10% in most cases. CONCLUSIONS A simple modification to the BEB and BED analytic models was found to improve their performance for sub-keV electrons in liquid water medium. Implementation of the new modification to the Option 6 constructor of Geant4-DNA significantly improved the agreement with the recommended low-energy Option 4 constructor for a variety of fundamental quantities related to electron transport.
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Affiliation(s)
- Stefanos Margis
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
| | - Ioanna Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
| | - Sebastien Incerti
- Bordeaux University, CNRS/IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
| | | | - Dimitris Emfietzoglou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece.
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11
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Chappuis F, Grilj V, Tran HN, Zein SA, Bochud F, Bailat C, Incerti S, Desorgher L. Modeling of scavenging systems in water radiolysis with Geant4-DNA. Phys Med 2023; 108:102549. [PMID: 36921424 DOI: 10.1016/j.ejmp.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE This paper presents the capabilities of the Geant4-DNA Monte Carlo toolkit to simulate water radiolysis with scavengers using the step-by-step (SBS) or the independent reaction times (IRT) methods. It features two examples of application areas: (1) computing the escape yield of H2O2 following a 60Co γ-irradiation and (2) computing the oxygen depletion in water irradiated with 1 MeV electrons. METHODS To ease the implementation of the chemical stage in Geant4-DNA, we developed a user interface that helps define the chemical reactions and set the concentration of scavengers. The first application area example required two computational steps to perform water radiolysis using NO2- and NO3- as scavengers and a 60Co irradiation. The oxygen depletion computation technique for the second application area example consisted of simulating track segments of 1 MeV electrons and determining the radio-induced loss and gain of oxygen molecules. RESULTS The production of H2O2 under variable scavenging levels is consistent with the literature; the mean relative difference between the SBS and IRT methods is 7.2 % ± 0.5 %. For the oxygen depletion 1 µs post-irradiation, the mean relative difference between both methods is equal to 9.8 % ± 0.3 %. The results in the microsecond scale depend on the initial partial pressure of oxygen in water. In addition, the computed oxygen depletions agree well with the literature. CONCLUSIONS The Geant4-DNA toolkit makes it possible to simulate water radiolysis in the presence of scavengers. This feature offers perspectives in radiobiology, with the possibility of simulating cell-relevant scavenging mechanisms.
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Affiliation(s)
- Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Veljko Grilj
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Hoang Ngoc Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Sara A Zein
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - François Bochud
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Claude Bailat
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Sébastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland.
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12
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Mokari M, Moeini H, Farazmand S. Computational modeling and a Geant4-DNA study of the rejoining of direct and indirect DNA damage induced by low energy electrons and carbon ions. Int J Radiat Biol 2023; 99:1391-1404. [PMID: 36745857 DOI: 10.1080/09553002.2023.2173824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
PURPOSE DNA double-strand breaks (DSBs) created by ionizing radiations are considered as the most detrimental lesion, which could result in the cell death or sterilization. As the empirical evidence gathered from the cellular and molecular radiation biology has demonstrated significant correlations between the initial and lasting levels of DSBs, gaining knowledge into the DSB repair mechanisms proves vital. Much effort has been invested into understanding the mechanisms triggering the repair and processes engaged after irradiation of cells. Given a mechanistic model, we performed - to our knowledge - the first Monte Carlo study of the expected repair kinetics of carbon ions and electrons using on the one hand Geant4-DNA simulations of electrons for benchmarking purposes and on the other hand quantifying the influence of direct and indirect damage. Our objective was to calculate the DSB repair rates using a repair mechanism for G1 and early S phases of the cell cycle in conjunction with simulations of the DNA damage. MATERIALS AND METHODS Based on Geant4-DNA simulations of DSB damage caused by electrons and carbon ions - using a B-DNA model and a water sphere of 3 μm radius resembling the mean size of human cells - we derived the kinetics of various biochemical repair processes. RESULTS The overall repair times of carbon ions increased with the DSB complexity. Comparison of the DSB complexity (DSBc) and repair times as a function of carbon-ion energy suggested that the repair time of no specific fraction of DSBs could solely be explained as a function of DSB complexity. CONCLUSION Analysis of the carbon-ion repair kinetics indicated that, given a fraction of DSBs, decreasing the energy would result in an increase of the repair time. The disagreements of the calculated and experimental repair kinetics for electrons could, among others, be due to larger damage complexity predicted by simulations or created actually by electrons of comparable energies to x-rays. They are also due to the employed repair mechanisms, which introduce no inherent dependence on the radiation type but make direct use of the simulated DSBs.
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Affiliation(s)
- Mojtaba Mokari
- Department of Physics, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran
| | - Hossein Moeini
- Department of Physics, School of Science, Shiraz University, Shiraz, Iran
| | - Shahnaz Farazmand
- Department of Physics, Isfahan University of Technology, Isfahan, Iran
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Sakata D, Hirayama R, Shin WG, Belli M, Tabocchini MA, Stewart RD, Belov O, Bernal MA, Bordage MC, Brown JMC, Dordevic M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Li Z, Meylan S, Michelet C, Nieminen P, Perrot Y, Petrovic I, Ramos-Mendez J, Ristic-Fira A, Santin G, Schuemann J, Tran HN, Villagrasa C, Incerti S. Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA. Phys Med 2023; 105:102508. [PMID: 36549067 DOI: 10.1016/j.ejmp.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell surviving fraction along time after irradiation, for a Chinese hamster V79 cell line, which is one of the most popular and widely investigated cell lines in radiobiology. METHODS We implemented the Two-Lesion Kinetics (TLK) model, originally proposed by Stewart, which allows for simulations to calculate residual DNA damage and surviving fraction along time via the number of initial DNA damage and its complexity as inputs. RESULTS By optimizing the model parameters of the TLK model in accordance to the experimental data on V79, we were able to predict both DNA rejoining kinetics at low linear energy transfers (LET) and cell surviving fraction. CONCLUSION This is the first study to demonstrate the implementation of both the cell surviving fraction and the DNA rejoining kinetics with the estimated initial DNA damage, in a realistic cell geometrical model simulated by full track structure MC simulations at DNA level and for various LET. These simulation and model make the link between mechanistic physical/chemical damage processes and these two specific biological endpoints.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan; Division of Health Sciences, Osaka University, Osaka 565-0871, Japan.
| | - Ryoichi Hirayama
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan
| | - Wook-Geun Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | | | | | - Robert D Stewart
- Department of Radiation Oncology, University of Washington, WA 98195-6043, USA
| | - Oleg Belov
- Veksler and Baldin Laboratory of High Energy Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia; Institute of System Analysis and Management, Dubna State University, 141980 Dubna, Russia
| | - Mario A Bernal
- Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marie-Claude Bordage
- INSERM, Université Paul Sabatier, UMR 1037, CRCT, Toulouse, France; Université Toulouse III-Paul Sabatier, UMR 1037, CRCT, Toulouse, France
| | - Jeremy M C Brown
- Department of Physics and Astronomy, Swinburne University of Technology, Hawthorn, Australia; Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia; Department of Radiation Science and Technology, Delft University of Technology, The Netherlands
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, GR 45110, Ioannina, Greece
| | - Ziad Francis
- Saint Joseph University of Beirut, UR Mathématiques et Modélisation, Beirut, Lebanon
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology (QST), Chiba 263-8555, Japan
| | - Vladimir Ivanchenko
- Geant4 Associates International Ltd, Hebden Bridge, UK; Tomsk State University, Tomsk, Russia
| | | | - Ioanna Kyriakou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, GR 45110, Ioannina, Greece
| | | | - Zhuxin Li
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | | | - Claire Michelet
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | | | - Yann Perrot
- IRSN, Institut de Radioprotection et de Surete Nucleaire, 92262 Fontenay-aux-Roses, France
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, San Francisco 94143, CA, USA
| | - Aleksandra Ristic-Fira
- Vinca Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | | | - Jan Schuemann
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Hoang N Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Surete Nucleaire, 92262 Fontenay-aux-Roses, France
| | - Sebastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
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Seif E, El Bitar Z, Incerti S, Bernal MA, Francis Z. Electron tracks simulation in water: Performance comparison between GPU CPU and the EUMED grid installation. Phys Med 2022; 104:56-66. [PMID: 36368091 DOI: 10.1016/j.ejmp.2022.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 09/27/2022] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
PURPOSE We explored different technologies to minimize simulation time of the Monte-Carlo method for track generation following the Geant4-DNA processes for electrons in water. METHODS A GPU software tool is developed for electron track simulations. A similar CPU version is also developed using the same collision models. CPU simulations were carried out on a single user desktop computer and on the computing grid France Grilles using 10 and 100 computing nodes. Computing time results for CPU, GPU, and grid simulations are compared with those using Geant4-DNA processes. RESULTS The CPU simulations better performs when the number of electrons is less than 104 with 100 eV initial energy, this number decreases as the energy increases. The GPU simulations gives better results when the number of electrons is more than 104 with initial energy of 100 eV, this number decreases to 103 for electrons with 10KeV and increases back with higher energy. The use of the grid introduces an additional queuing time which slows down the overall simulation performance. Thus, the Grid gives better performance when the number of electrons is over 105 with initial energy of 10KeV, and this number decreases as the energy increases. CONCLUSIONS The CPU is best suited for small numbers of primary incident electrons. The GPU is best suited when the number of primary incident particles occupies sufficient resources on GPU card in order to get an important computing power. The grid is best suited for simulations with high number of primary incident electrons with high initial energy.
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Pietrzak M, Nettelbeck H, Perrot Y, Villagrasa C, Bancer A, Bug M, Incerti S. Intercomparison of nanodosimetric distributions in nitrogen simulated with Geant4 and PTra track structure codes. Phys Med 2022; 102:103-109. [PMID: 36162229 DOI: 10.1016/j.ejmp.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/25/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
To facilitate the use of Geant4-DNA for radiation transport simulations in micro- and nanodosimeters, which are physically operated with tissue-equivalent gases such as nitrogen (and propane), this work aims to extend the cross section data available in Geant4-DNA to include those of nitrogen for electron energies ranging from 1 MeV down to the ionisation threshold. To achieve this, interaction cross section data for nitrogen that have been used with the in-house PTB PTra track structure code have been implemented in the current state-of-the-art Geant4-DNA simulation toolkit. An intercomparison has been performed between the two codes to validate this implementation. To quantify the agreement between the cross section models for nitrogen adopted in PTra and those implemented in Geant4-DNA, the simulation results of both codes were analysed using three physical parameters describing the ionisation cluster size distribution (ICSD): mean ionisation cluster size, variance of the cluster size and the probability to obtain a single ionisation within the target. Statistical analysis of the results indicates that the interaction cross section models for nitrogen used in PTra (elastic scattering, impact ionisations and electronic excitations) have been successfully implemented in Geant4-DNA. In addition, simulated ICSDs were compared to those measured with the Jet Counter nanodosimeter for energies between 100 and 2000 eV. For greater energies, the ICRP data for LET and particle range were used as a reference. The modified Geant4-DNA code and data successfully passed all these benchmarks fulfilling the requirement for their public release in the next version of the Geant4 toolkit.
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Affiliation(s)
- Marcin Pietrzak
- National Centre for Nuclear Research (NCBJ), Andrzeja Sołtana 7, 05400 Otwock, Poland; European Radiation Dosimetry Group e.V. (Eurados), Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Heidi Nettelbeck
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116 Braunschweig, Germany; European Radiation Dosimetry Group e.V. (Eurados), Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), 31 Avenue de la Division Leclerc, 92260 Fontenay-Aux-Roses, France; European Radiation Dosimetry Group e.V. (Eurados), Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany; Geant4-DNA Collaboration
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), 31 Avenue de la Division Leclerc, 92260 Fontenay-Aux-Roses, France; European Radiation Dosimetry Group e.V. (Eurados), Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany; Geant4-DNA Collaboration
| | - Aleksandr Bancer
- National Centre for Nuclear Research (NCBJ), Andrzeja Sołtana 7, 05400 Otwock, Poland; European Radiation Dosimetry Group e.V. (Eurados), Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Marion Bug
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116 Braunschweig, Germany; European Radiation Dosimetry Group e.V. (Eurados), Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Sebastien Incerti
- Université de Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, 19 Chemin du Solarium, 33170 Gradignan, France; Geant4-DNA Collaboration
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Salim R, Taherparvar P. Dosimetry assessment of theranostic Auger-emitting radionuclides in a micron-sized multicellular cluster model: A Monte Carlo study using Geant4-DNA simulations. Appl Radiat Isot 2022; 188:110380. [PMID: 35868198 DOI: 10.1016/j.apradiso.2022.110380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/28/2022] [Accepted: 07/07/2022] [Indexed: 11/02/2022]
Abstract
The present work is aimed at improving the multicellular dosimetry of several Auger radionuclides of interest for targeted cancer therapy, including 99mTc, 111In, 123I, 125I, and 201Tl. For this purpose, using the Geant4-DNA Monte Carlo code, a cluster of 13 similar spherical cells with a hexagonal packed arrangement was modeled, and the mean absorbed doses per unit cumulated activity (S-values) were calculated by considering two target←source configurations, cell←cell and nucleus←nucleus. The obtained ratios of cross-dose to self-dose S-value in terms of the distance between the source and target regions were evaluated and also compared to those estimated by the Medical Internal Radiation Dose (MIRD) method. Besides, the contribution of the Coster-Kronig, Auger and internal conversion electrons to the S-values was provided for each radionuclide. According to the results, it can be concluded that in contrast to self-absorption, the cross-absorption due to the Auger-emitters has not a significant role in the total energy deposition within a cell in the cluster.
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Affiliation(s)
- R Salim
- Department of Physics, Faculty of Science, University of Guilan, Rasht, Iran
| | - P Taherparvar
- Department of Physics, Faculty of Science, University of Guilan, Rasht, Iran.
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Thibaut Y, Tang N, Tran HN, Vaurijoux A, Villagrasa C, Incerti S, Perrot Y. Nanodosimetric Calculations of Radiation-Induced DNA Damage in a New Nucleus Geometrical Model Based on the Isochore Theory. Int J Mol Sci 2022; 23:3770. [PMID: 35409128 DOI: 10.3390/ijms23073770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Double-strand breaks (DSBs) in nuclear DNA represents radiation-induced damage that has been identified as particularly deleterious. Calculating this damage using Monte Carlo track structure modeling could be a suitable indicator to better assess and anticipate the side-effects of radiation therapy. However, as already demonstrated in previous work, the geometrical description of the nucleus and the DNA content used in the simulation significantly influence damage calculations. Therefore, in order to obtain accurate results, this geometry must be as realistic as possible. In this study, a new geometrical model of an endothelial cell nucleus and DNA distribution according to the isochore theory are presented and used in a Monte Carlo simulation chain based on the Geant4-DNA toolkit. In this theory, heterochromatin and euchromatin compaction are distributed along the genome according to five different families (L1, L2, H1, H2, and H3). Each of these families is associated with a different hetero/euchromatin rate related to its compaction level. In order to compare the results with those obtained using a previous nuclear geometry, simulations were performed for protons with linear energy transfers (LETs) of 4.29 keV/µm, 19.51 keV/µm, and 43.25 keV/µm. The organization of the chromatin fibers at different compaction levels linked to isochore families increased the DSB yield by 6-10%, and it allowed the most affected part of the genome to be identified. These new results indicate that the genome core is more radiosensitive than the genome desert, with a 3-8% increase in damage depending on the LET. This work highlights the importance of using realistic distributions of chromatin compaction levels to calculate radio-induced damage using Monte Carlo simulation methods.
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Ali Y, Auzel L, Monini C, Kriachok K, Létang JM, Testa E, Maigne L, Beuve M. Monte Carlo simulations of nanodosimetry and radiolytic species production for monoenergetic proton and electron beams: Benchmarking of GEANT4-DNA and LPCHEM codes. Med Phys 2022; 49:3457-3469. [PMID: 35318686 DOI: 10.1002/mp.15609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/17/2022] [Accepted: 02/14/2022] [Indexed: 01/10/2023] Open
Abstract
PURPOSE In hadrontherapy, biophysical models can be used to predict the biological effect received by cancerous tissues and organs at risk. The input data of these models generally consist of information on nano/micro dosimetric quantities and, concerning some models, reactive species produced in water radiolysis. In order to fully account for the radiation stochastic effects, these input data have to be provided by Monte Carlo track structure (MCTS) codes allowing to estimate physical, physico-chemical, and chemical effects of radiation at the molecular scale. The objective of this study is to benchmark two MCTS codes, Geant4-DNA and LPCHEM, that are useful codes for estimating the biological effects of ions during radiation therapy treatments. MATERIAL AND METHODS In this study we considered the simulation of specific energy spectra for monoenergetic proton beams (10 MeV) as well as radiolysis species production for both electron (1 MeV) and proton (10 MeV) beams with Geant4-DNA and LPCHEM codes. Options 2, 4, and 6 of the Geant4-DNA physics lists have been benchmarked against LPCHEM. We compared probability distributions of energy transfer points in cylindrical nanometric targets (10 nm) positioned in a liquid water box. Then, radiochemical species (· OH, e aq - ${\rm{e}}_{{\rm{aq}}}^ - $ , H 3 O + , H 2 O 2 ${{\rm{H}}_3}{{\rm{O}}^ + },{\rm{\;}}{{\rm{H}}_2}{{\rm{O}}_2}$ , H2 , and O H - ) ${\rm{O}}{{\rm{H}}^ - }){\rm{\;}}$ yields simulated between 10-12 and 10-6 s after irradiation are compared. RESULTS Overall, the specific energy spectra and the chemical yields obtained by the two codes are in good agreement considering the uncertainties on experimental data used to calibrate the parameters of the MCTS codes. For 10 MeV proton beams, ionization and excitation processes are the major contributors to the specific energy deposition (larger than 90%) while attachment, solvation, and vibration processes are minor contributors. LPCHEM simulates tracks with slightly more concentrated energy depositions than Geant4-DNA which translates into slightly faster recombination than Geant4-DNA. Relative deviations (CEV ) with respect to the average of evolution rates of the radical yields between 10-12 and 10-6 s remain below 10%. When comparing execution times between the codes, we showed that LPCHEM is faster than Geant4-DNA by a factor of about four for 1000 primary particles in all simulation stages (physical, physico-chemical, and chemical). In multi-thread mode (four threads), Geant4-DNA computing times are reduced but remain slower than LPCHEM by ∼20% up to ∼50%. CONCLUSIONS For the first time, the entire physical, physico-chemical, and chemical models of two track structure Monte Carlo codes have been benchmarked along with an extensive analysis on the effects on the water radiolysis simulation. This study opens up new perspectives in using specific energy distributions and radiolytic species yields from monoenergetic ions in biophysical models integrated to Monte Carlo software.
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Affiliation(s)
- Yasmine Ali
- Institut de Physique des 2 Infinis de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3, 4 rue Enrico Fermi, Villeurbanne, 69622, France
| | - Lucas Auzel
- Laboratoire de Physique de Clermont, Université Clermont Auvergne, CNRS/IN2P3, 4 Avenue Blaise Pascal, Aubière cedex, 63178, France
| | - Caterina Monini
- Institut de Physique des 2 Infinis de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3, 4 rue Enrico Fermi, Villeurbanne, 69622, France
| | - Kateryna Kriachok
- Laboratoire de Physique de Clermont, Université Clermont Auvergne, CNRS/IN2P3, 4 Avenue Blaise Pascal, Aubière cedex, 63178, France
| | - Jean Michel Létang
- CREATIS, Université Claude Bernard Lyon 1, CNRS UMR5220, Inserm U1294, INSA-Lyon, Université Lyon 1, Lyon, 69373, France
| | - Etienne Testa
- Institut de Physique des 2 Infinis de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3, 4 rue Enrico Fermi, Villeurbanne, 69622, France
| | - Lydia Maigne
- Laboratoire de Physique de Clermont, Université Clermont Auvergne, CNRS/IN2P3, 4 Avenue Blaise Pascal, Aubière cedex, 63178, France
| | - Michael Beuve
- Institut de Physique des 2 Infinis de Lyon, Université Claude Bernard Lyon 1, CNRS/IN2P3, 4 rue Enrico Fermi, Villeurbanne, 69622, France
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Kyriakou I, Sakata D, Tran HN, Perrot Y, Shin WG, Lampe N, Zein S, Bordage MC, Guatelli S, Villagrasa C, Emfietzoglou D, Incerti S. Review of the Geant4-DNA Simulation Toolkit for Radiobiological Applications at the Cellular and DNA Level. Cancers (Basel) 2021; 14:35. [PMID: 35008196 DOI: 10.3390/cancers14010035] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary A brief description of the methodologies to simulate ionizing radiation transport in biologically relevant matter is presented. Emphasis is given to the physical, chemical, and biological models of Geant4-DNA that enable mechanistic radiobiological modeling at the cellular and DNA level, important to improve the efficacy of existing and novel radiotherapeutic modalities for the treatment of cancer. Abstract The Geant4-DNA low energy extension of the Geant4 Monte Carlo (MC) toolkit is a continuously evolving MC simulation code permitting mechanistic studies of cellular radiobiological effects. Geant4-DNA considers the physical, chemical, and biological stages of the action of ionizing radiation (in the form of x- and γ-ray photons, electrons and β±-rays, hadrons, α-particles, and a set of heavier ions) in living cells towards a variety of applications ranging from predicting radiotherapy outcomes to radiation protection both on earth and in space. In this work, we provide a brief, yet concise, overview of the progress that has been achieved so far concerning the different physical, physicochemical, chemical, and biological models implemented into Geant4-DNA, highlighting the latest developments. Specifically, the “dnadamage1” and “molecularDNA” applications which enable, for the first time within an open-source platform, quantitative predictions of early DNA damage in terms of single-strand-breaks (SSBs), double-strand-breaks (DSBs), and more complex clustered lesions for different DNA structures ranging from the nucleotide level to the entire genome. These developments are critically presented and discussed along with key benchmarking results. The Geant4-DNA toolkit, through its different set of models and functionalities, offers unique capabilities for elucidating the problem of radiation quality or the relative biological effectiveness (RBE) of different ionizing radiations which underlines nearly the whole spectrum of radiotherapeutic modalities, from external high-energy hadron beams to internal low-energy gamma and beta emitters that are used in brachytherapy sources and radiopharmaceuticals, respectively.
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Sakata D, Suzuki M, Hirayama R, Abe Y, Muramatsu M, Sato S, Belov O, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S, Inaniwa T. Performance Evaluation for Repair of HSGc-C5 Carcinoma Cell Using Geant4-DNA. Cancers (Basel) 2021; 13:6046. [PMID: 34885155 DOI: 10.3390/cancers13236046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary To evaluate the repair performance of HSGc-C5 carcinoma cell against radiation-induced DNA damage, a Geant4-DNA application for radiobiological research was extended by using newly measured experimental data acquired in this study. Concerning fast- and slow-DNA rejoining, the two-lesion kinetics (TLK) model parameters were adequately optimized (the repair speeds of each process were reasonably close to the DNA rejoining speed of the nonhomologous end-joining and homologous recombination pathways). The lethality probabilities of the DNA damage induced by complex double strand breaks (DSBs) and binary repair were approximately 3% and 40%, respectively. Using the optimized repair parameters, the Geant4-DNA simulation was able to predict the cell surviving fraction (SF) and the DNA repair kinetics. Abstract Track-structure Monte Carlo simulations are useful tools to evaluate initial DNA damage induced by irradiation. In the previous study, we have developed a Gean4-DNA-based application to estimate the cell surviving fraction of V79 cells after irradiation, bridging the gap between the initial DNA damage and the DNA rejoining kinetics by means of the two-lesion kinetics (TLK) model. However, since the DNA repair performance depends on cell line, the same model parameters cannot be used for different cell lines. Thus, we extended the Geant4-DNA application with a TLK model for the evaluation of DNA damage repair performance in HSGc-C5 carcinoma cells which are typically used for evaluating proton/carbon radiation treatment effects. For this evaluation, we also performed experimental measurements for cell surviving fractions and DNA rejoining kinetics of the HSGc-C5 cells irradiated by 70 MeV protons at the cyclotron facility at the National Institutes for Quantum and Radiological Science and Technology (QST). Concerning fast- and slow-DNA rejoining, the TLK model parameters were adequately optimized with the simulated initial DNA damage. The optimized DNA rejoining speeds were reasonably agreed with the experimental DNA rejoining speeds. Using the optimized TLK model, the Geant4-DNA simulation is now able to predict cell survival and DNA-rejoining kinetics for HSGc-C5 cells.
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Pietrzak M, Mietelska M, Bancer A, Rucinski A, Brzozowska B. Geant4-DNA modeling of nanodosimetric quantities in the Jet Counter for alpha particles. Phys Med Biol 2021; 66. [PMID: 34706345 DOI: 10.1088/1361-6560/ac33eb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/27/2021] [Indexed: 11/11/2022]
Abstract
The purpose of this work was to validate the calculation accuracy of nanodosimetric quantities in Geant4-DNA track structure simulation code. We implemented the Jet Counter (JC) nanodosimeter geometry in the simulation platform and quantified the impact of the Geant4-DNA physics models and JC detector performance on the ionization cluster size distributions (ICSD). ICSD parameters characterize the quality of radiation field and are supposed to be correlated to the complexity of the initial DNA damage in nanoscale and eventually the response of biological systems to radiation. We compared Monte Carlo simulations of ICSD in JC geometry performed using Geant4-DNA and PTra codes with experimental data collected for alpha particles at 3.8 MeV. We investigated the impact of simulation and experimental settings, i.e., three Geant4-DNA physics models, three sizes of a nanometer sensitive volume, gas to water density scaling procedure, JC ion extraction efficiency and the presence of passive components of the detector on the ICSD and their parameters. We found that ICSD in JC geometry obtained from Geant4-DNA simulations in water correspond well to ICSD measurements in nitrogen gas for all investigated settings, while the best agreement is for Geant4-DNA physics option 4. This work also discusses the accuracy and robustness of ICSD parameters in the context of the application of track structure simulation methods for treatment planning in particle therapy.
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Affiliation(s)
| | - Monika Mietelska
- National Centre for Nuclear Research, Świerk, Poland.,Biomedical Physics Division, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | | | | | - Beata Brzozowska
- Biomedical Physics Division, Faculty of Physics, University of Warsaw, Warsaw, Poland
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22
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Zhao X, Liu R, Zhao T, Reynoso FJ. Quantification of gold nanoparticle photon radiosensitization from direct and indirect effects using a complete human genome single cell model based on Geant4. Med Phys 2021; 48:8127-8139. [PMID: 34738643 DOI: 10.1002/mp.15330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 09/22/2021] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To investigate the radiosensitization properties of gold nanoparticles (GNPs) and better understand the intricate deoxyribonucleic acid (DNA) damage induction mechanisms involved in GNP-aided radiotherapy, a single cell model with complete human genome based on the Geant4 Monte Carlo toolkit was applied. MATERIALS AND METHODS A Geant4-DNA model was implemented to simulate direct and indirect DNA damage generated in the physical and chemical stages. In the physical stage, a mixed-physics approach was taken by using Geant4-DNA in water and Livermore in gold. Water radiolysis was created posteriorly in the physicochemical and chemical stages to simulate indirect damage from reactions between DNA molecules and OH• radicals. A mono-energetic photon beam (100 keV) and two clinical photon sources (250-kVp, 6-MV flattening-filter free) were simulated for modeling the irradiation of a single cell with or without GNPs. In order to study the effects of GNP size on radiosensitization, 15, 30, and 100 nm GNPs were simulated. The effects of intracellular distribution were simulated using 90-nm GNPs with different characteristics of distribution within the cell. The time dependence of DNA damage enhancement was also studied with chemistry stage simulation end-time no larger than 10 ns. RESULTS Double strand break (DSB) enhancement due to direct and indirect action was quantified under different scenarios. Under realistic cellular uptake condition, the 100-nm GNPs had the most significant increase in DSBs: 40.9% and 28.5% for 100 keV and 250-kVp photon irradiation, respectively. The intracellular localization showed differing levels of radiosensitization with a maximum of 64%, 27%, and 6% DSB enhancements for 100 keV, 250-kVp, and 6-MV respectively, when 90-nm GNPs congregate around the nucleus. CONCLUSION The results indicate that photon energy, GNP size, and intracellular distribution play an important role in the enhancement of DSB from direct and indirect damage under scenarios close to cell experiments. The radiosensitization effects due to indirect damage are significant and should be considered carefully.
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Affiliation(s)
- Xiandong Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Ruirui Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tianyu Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Francisco J Reynoso
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri, USA
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Shin WG, Sakata D, Lampe N, Belov O, Tran NH, Petrovic I, Ristic-Fira A, Dordevic M, Bernal MA, Bordage MC, Francis Z, Kyriakou I, Perrot Y, Sasaki T, Villagrasa C, Guatelli S, Breton V, Emfietzoglou D, Incerti S. A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. Cancers (Basel) 2021; 13:4940. [PMID: 34638425 DOI: 10.3390/cancers13194940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary DNA damage caused by ionizing radiation in a human fibroblast cell evaluated by the Geant4-DNA Monte Carlo toolkit is presented. A validation study using a computational geometric human DNA model was then carried out, and the calculated DNA damage as a function of particle type and energy is presented. The results of this work showed a significant improvement on past work and were consistent with recent radiobiological experimental data, such as damage yields. This work and the developed methodology could impact a broad number of research fields in which the understanding of radiation effects is crucial, such as cancer radiotherapy, space science, and medical physics. Abstract Accurately modeling the radiobiological mechanisms responsible for the induction of DNA damage remains a major scientific challenge, particularly for understanding the effects of low doses of ionizing radiation on living beings, such as the induction of carcinogenesis. A computational approach based on the Monte Carlo technique to simulate track structures in a biological medium is currently the most reliable method for calculating the early effects induced by ionizing radiation on DNA, the primary cellular target of such effects. The Geant4-DNA Monte Carlo toolkit can simulate not only the physical, but also the physico-chemical and chemical stages of water radiolysis. These stages can be combined with simplified geometric models of biological targets, such as DNA, to assess direct and indirect early DNA damage. In this study, DNA damage induced in a human fibroblast cell was evaluated using Geant4-DNA as a function of incident particle type (gammas, protons, and alphas) and energy. The resulting double-strand break yields as a function of linear energy transfer closely reproduced recent experimental data. Other quantities, such as fragment length distribution, scavengeable damage fraction, and time evolution of damage within an analytical repair model also supported the plausibility of predicting DNA damage using Geant4-DNA.The complete simulation chain application “molecularDNA”, an example for users of Geant4-DNA, will soon be distributed through Geant4.
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Tamborino G, Perrot Y, De Saint-Hubert M, Struelens L, Nonnekens J, de Jong M, Konijnenberg MW, Villagrasa C. Modeling early radiation DNA damage occurring during [ 177Lu]Lu-DOTA-[Tyr 3]octreotate radionuclide therapy. J Nucl Med 2021; 63:761-769. [PMID: 34503959 PMCID: PMC9051596 DOI: 10.2967/jnumed.121.262610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/05/2021] [Indexed: 12/01/2022] Open
Abstract
The aim of this study was to build a simulation framework to evaluate the number of DNA double-strand breaks (DSBs) induced by in vitro targeted radionuclide therapy (TRT). This work represents the first step toward exploring underlying biologic mechanisms and the influence of physical and chemical parameters to enable a better response prediction in patients. We used this tool to characterize early DSB induction by 177Lu-DOTATATE, a commonly used TRT for neuroendocrine tumors. Methods: A multiscale approach was implemented to simulate the number of DSBs produced over 4 h by the cumulated decays of 177Lu distributed according to the somatostatin receptor binding. The approach involves 2 sequential simulations performed with Geant4/Geant4-DNA. The radioactive source is sampled according to uptake experiments on the distribution of activities within the medium and the planar cellular cluster, assuming instant and permanent internalization. A phase space is scored around the nucleus of the central cell. Then, the phase space is used to generate particles entering the nucleus containing a multiscale description of the DNA in order to score the number of DSBs per particle source. The final DSB computations are compared with experimental data, measured by immunofluorescent detection of p53-binding protein 1 foci. Results: The probability of electrons reaching the nucleus was significantly influenced by the shape of the cell compartment, causing a large variance in the induction pattern of DSBs. A significant difference was found in the DSBs induced by activity distributions in cell and medium, as is explained by the specific energy (z¯) distributions. The average number of simulated DSBs was 14 DSBs per cell (range, 7–24 DSBs per cell), compared with 13 DSBs per cell (range, 2–30 DSBs per cell) experimentally determined. We found a linear correlation between the mean absorbed dose to the nucleus and the number of DSBs per cell: 0.014 DSBs per cell mGy−1 for internalization in the Golgi apparatus and 0.017 DSBs per cell mGy−1 for internalization in the cytoplasm. Conclusion: This simulation tool can lead to a more reliable absorbed-dose–to–DNA correlation and help in prediction of biologic response.
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Affiliation(s)
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, France
| | | | - Lara Struelens
- Research in Dosimetric Applications, Belgian Nuclear Research Centre (SCK CEN), Belgium
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Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štěpán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol 2021; 66. [PMID: 34412044 DOI: 10.1088/1361-6560/ac1f39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022]
Abstract
The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for·OH, e-aq, and H2with published experimental data. For H2O2and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by137Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - J A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - N Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - J Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, United States of America
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - W-G Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - S Incerti
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - A McNamara
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - H Paganetti
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - J Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, United States of America
| | - J Schuemann
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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Tran HN, Chappuis F, Incerti S, Bochud F, Desorgher L. Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach. Int J Mol Sci 2021; 22:6023. [PMID: 34199598 DOI: 10.3390/ijms22116023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/18/2023] Open
Abstract
In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based (“on-lattice”) model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volume (“mesh”), which is divided into sub-volumes (or “voxels”). We then discuss the choice of voxel size and merging technique of a given mesh, along with the evolution of the system using the hierarchical algorithm for the RDME (“hRDME”). Since the compartment-based model cannot describe high concentration species of early radiation-induced spurs, we propose a combination of the particle-based step-by-step (“SBS”) Brownian dynamics model and the compartment-based model (“SBS-RDME model”) for the simulation. We, finally, use the particle-based SBS Brownian dynamics model of Geant4-DNA as a reference to test the model implementation through several benchmarks. We find that the compartment-based model can efficiently simulate the system with a large number of species and for longer timescales, beyond the microsecond, with a reasonable computing time. Our aim in developing this model is to study the production and evolution of reactive oxygen species generated under irradiation with different dose rate conditions, such as in FLASH and conventional radiotherapy.
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Moradi MS, Bidabadi BS. Assessment of Single-and Double-Strand Breaks in DNA Induced by Auger Electrons of Radioisotopes Used in Diagnostic and Therapeutic Applications. J Med Phys 2021; 45:240-248. [PMID: 33953500 PMCID: PMC8074716 DOI: 10.4103/jmp.jmp_79_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 11/30/2022] Open
Abstract
Introduction: Most of the radionuclides that are used for diagnostic purposes emit Auger electrons and can thus cause damage to the DNA molecule on a nanometer scale. Therefore, the nanodosimetric calculation of these radioisotopes is necessary to achieve better understanding on their effects. Aim: The aim of this study was to calculate the mean number of DNA strand breaks (single-strand breaks and double-strand breaks) caused by direct and indirect effects for six widely used Auger electron-emitting diagnostic radioisotopes, including 123I, 125I, 99mTc, 67Ga, 201Tl, 111In and two therapeutic radioisotopes of 131I(beta + Auger + CK emitter) and 211At(alpha + Auger + CK emitter). Materials and Methods: Geant4-DNA simulation tool was used to evaluate the effects of Auger electrons, beta and alpha particles of these radioisotopes on DNA molecules. Two different DNA molecule geometric models were simulated and the results of these two models were compared with each other as well as with the results of previous studies. Results and Conclusion: The results showed that the geometric shape of the sugar-phosphate groups may have a significant effect on the number of single-strand breaks (SSBs) and double-strand breaks (DSBs) of the DNA molecule. Among the most widely used diagnostic radioisotopes, 201Tl and 125I, had the greatest impact on the number of SSBs and DSBs, respectively, while therapeutic radioisotope of 131I almost had no effect, therapeutic radioisotope of 211At had the moderate effect on the number of breaks in the DNA chain.
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Affiliation(s)
- Mahdi Seifi Moradi
- Department of Nuclear Engineering, Faculty of Physics, University of Isfahan, Isfahan, Iran
| | - Babak Shirani Bidabadi
- Department of Nuclear Engineering, Faculty of Physics, University of Isfahan, Isfahan, Iran
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Chatzipapas KP, Papadimitroulas P, Loudos G, Papanikolaou N, Kagadis GC. IDDRRA: A novel platform, based on Geant4-DNA to quantify DNA damage by ionizing radiation. Med Phys 2021; 48:2624-2636. [PMID: 33657650 DOI: 10.1002/mp.14817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 01/23/2023] Open
Abstract
PURPOSE This study proposes a novel computational platform that we refer to as IDDRRA (DNA Damage Response to Ionizing RAdiation), which uses Monte Carlo (MC) simulations to score radiation induced DNA damage. MC simulations provide results of high accuracy on the interaction of radiation with matter while scoring the energy deposition based on state-of-the-art physics and chemistry models and probabilistic methods. METHODS The IDDRRA software is based on the Geant4-DNA toolkit together with new tools that were developed for the purpose of this study, including a new algorithm that was developed in Python for the design of the DNA molecules. New classes were developed in C++ to integrate the GUI and produce the simulation's output in text format. An algorithm was also developed to analyze the simulation's output in terms of energy deposition, Single Strand Breaks (SSB), Double Strand Breaks (DSB) and Cluster Damage Sites (CDS). Finally, a new tool was developed to implement probabilistic SSB and DSB repair models using MC techniques. RESULTS This article provides the first benchmarks that the user of the IDDRRA tool can use to validate the functionality of the software as well as to provide a starting point to produce different types of DNA simulations. These benchmarks incorporate different kind of particles (e-, e+, protons, electron spectrum) and DNA molecules. CONCLUSION We have developed the IDDRRA tool and demonstrated its use to study various aspects of the modeling and simulation of a DNA irradiation experiment. The tool is expandable and can be expanded by other users with new benchmarks and applications based on the user's needs and experience. New functionality will be added over time, including the quantification of the indirect damage.
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Affiliation(s)
- Konstantinos P Chatzipapas
- 3dmi Research Group, Department of Medical Physics, School of Medicine, University of Patras, Rion, 26504, Greece
| | | | - George Loudos
- Bioemission Technology Solutions (BIOEMTECH), Athens, 11472, Greece
| | - Niko Papanikolaou
- Health Science Center, University of Texas, San Antonio, TX, 78229, USA
| | - George C Kagadis
- 3dmi Research Group, Department of Medical Physics, School of Medicine, University of Patras, Rion, 26504, Greece
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Kyriakou I, Tremi I, Georgakilas AG, Emfietzoglou D. Microdosimetric investigation of the radiation quality of low-medium energy electrons using Geant4-DNA. Appl Radiat Isot 2021; 172:109654. [PMID: 33676082 DOI: 10.1016/j.apradiso.2021.109654] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
The increasing clinical use of low-energy photon and electron sources (below few tens of keV) has raised concerns on the adequacy of the existing approximation of an energy-independent radiobiological effectiveness. In this work, the variation of the quality factor (Q) and relative biological effectiveness (RBE) of electrons over the low-medium energy range (0.1 keV-1 MeV) is examined using several microdosimetry-based Monte Carlo methodologies with input data obtained from Geant4-DNA track-structure simulations. The sensitivity of the results to the different methodologies, Geant4-DNA physics models, and target sizes is examined. Calculations of Q and RBE are based on the ICRU Report 40 recommendations, the Kellerer-Hahn approximation, the site version of the theory of dual radiation action (TDRA), the microdosimetric kinetic model (MKM) of cell survival, and the calculated yield of DNA double strand breaks (DSB). The stochastic energy deposition spectra needed as input in the above approaches have been calculated for nanometer spherical volumes using the different electron physics models of Geant4-DNA. Results are normalized at 100 keV electrons which is here considered the reference radiation. It is shown that in the energy range ~50 keV-1 MeV, the calculated Q and RBE are approximately unity (to within 1-2%) irrespective of the methodology, Geant4-DNA physics model, and target size. At lower energies, Q and RBE become energy-dependent reaching a maximum value of ~1.5-2.5 between ~200 and 700 eV. The detailed variation of Q and RBE at low energies depends mostly upon the adopted methodology and target size, and less so upon the Geant4-DNA physics model. Overall, the DSB yield predicts the highest RBE values (with RBEmax≈2.5) whereas the MKM the lowest RBE values (with RBEmax≈1.5). The ICRU Report 40, Kellerer-Hahn, and TDRA methods are in excellent agreement (to within 1-2%) over the whole energy range predicting a Qmax≈2. In conclusion, the approximation Q=RBE=1 was found to be valid only above ~50 keV whereas at lower energies both Q and RBE become strongly energy-dependent. It is envisioned that the present work will contribute towards establishing robust methodologies to determine theoretically the energy-dependence of radiation quality of individual electrons which may then be used in subsequent calculations involving practical electron and photon radiation sources.
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Affiliation(s)
- Ioanna Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece.
| | - Ioanna Tremi
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, Athens, Greece
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, Athens, Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
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Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S, Villagrasa C. Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber. Med Phys 2020; 48:890-901. [PMID: 33232522 PMCID: PMC7986154 DOI: 10.1002/mp.14612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Purpose Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA. Methods This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT. Results Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA. Conclusion Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.
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Affiliation(s)
- Hoang Ngoc Tran
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
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Bertolet A, Grilj V, Guardiola C, Harken AD, Cortés-Giraldo MA, Baratto-Roldán A, Carabe A. Experimental validation of an analytical microdosimetric model based on Geant4-DNA simulations by using a silicon-based microdosimeter. Radiat Phys Chem Oxf Engl 1993 2020; 176:109060. [PMID: 33100611 PMCID: PMC7583143 DOI: 10.1016/j.radphyschem.2020.109060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
PURPOSE To study the agreement between proton microdosimetric distributions measured with a silicon-based cylindrical microdosimeter and a previously published analytical microdosimetric model based on Geant4-DNA in-water Monte Carlo simulations for low energy proton beams. METHODS AND MATERIAL Distributions for lineal energy (y) are measured for four proton monoenergetic beams with nominal energies from 2.0 MeV to 4.5 MeV, with a tissue equivalent proportional counter (TEPC) and a silicon-based microdosimeter. The actual energy for protons traversing the silicon-based microdosimeter is simulated with SRIM. Monoenergetic beams with these energies are simulated with Geant4-DNA code by simulating a water cylinder site of dimensions equal to those of the microdosimeter. The microdosimeter response is calibrated by using the distribution peaks obtained from the TEPC. Analytical calculations fory ¯ F andy ¯ D using our methodology based on spherical sites are also performed choosing the equivalent sphere to be checked against experimental results. RESULTS Distributions for y at silicon are converted into tissue equivalent and compared to the Geant4-DNA simulated, yielding maximum deviations of 1.03% fory ¯ F and 1.17% fory ¯ D . Our analytical method generates maximum deviations of 1.29% and 3.33%, respectively, with respect to experimental results. CONCLUSION Simulations in Geant4-DNA with ideal cylindrical sites in liquid water produce similar results to the measurements in an actual silicon-based cylindrical microdosimeter properly calibrated. The found agreement suggests the possibility to experimentally verify the calculated clinicaly ¯ D with our analytical method.
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Affiliation(s)
- A Bertolet
- Department of Radiation Oncology, Hospital of The University of Pennsylvania, Philadelphia, PA, USA
- Department of Atomic, Molecular and Nuclear Physics, Universidad de Sevilla, Seville, Spain
| | - V Grilj
- Radiological Research Accelerator Facility, Columbia University, Irvington, NY, USA
| | - C Guardiola
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France; Université de Paris, IJCLab, 91405 Orsay France
| | - A D Harken
- Radiological Research Accelerator Facility, Columbia University, Irvington, NY, USA
| | - M A Cortés-Giraldo
- Department of Atomic, Molecular and Nuclear Physics, Universidad de Sevilla, Seville, Spain
| | - A Baratto-Roldán
- Department of Atomic, Molecular and Nuclear Physics, Universidad de Sevilla, Seville, Spain
| | - A Carabe
- Department of Radiation Oncology, Hospital of The University of Pennsylvania, Philadelphia, PA, USA
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Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štěpán V, Okada S, Moreno-Barbosa E, Faddegon B. Independent reaction times method in Geant4-DNA: Implementation and performance. Med Phys 2020; 47:5919-5930. [PMID: 32970844 DOI: 10.1002/mp.14490] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 11/10/2022] Open
Abstract
PURPOSE The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico-chemical contribution to the biological effect of ionizing radiation. However, the step-by-step simulation of the reaction kinetics of radiolytic species is the most time-consuming task in Monte Carlo track-structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4-DNA Monte Carlo toolkit to improve the computational efficiency of calculating G-values, defined as the number of chemical species created or lost per 100 eV of deposited energy. METHODS The computational efficiency of IRT, as implemented, is compared to that from available Geant4-DNA step-by-step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for • OH and e aq - for time-dependent G-values. For IRT, simulations in the presence of scavengers irradiated by cobalt-60 γ-ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET-dependent G-values with Geant4-DNA calculations in pure liquid water is presented. RESULTS The IRT improved the computational efficiency by three orders of magnitude relative to the step-by-step method while differences in G-values by 3.9% at 1 μs were found. At 7 ps, • OH and e aq - yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for • OH and e aq - , respectively. Uncertainties are one standard deviation. Finally, G-values at different scavenging capacities and LET-dependent G-values reproduced the behavior of measurements for all radiation qualities. CONCLUSION The comprehensive validation of the Geant4-DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.
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Affiliation(s)
- José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jorge Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Ngoc Hoang Tran
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Sebastien Incerti
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Eduardo Moreno-Barbosa
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
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Zhao X, Liu R, Zhao T, Reynoso FJ. Modeling double-strand breaks from direct and indirect action in a complete human genome single cell Geant4 model. Biomed Phys Eng Express 2020; 6. [PMID: 34035191 DOI: 10.1088/2057-1976/abb4bd] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022]
Abstract
The aim of this work is to develop and validate a computational model to investigate direct and indirect DNA damage by directly quantifying DNA strand breaks. A detailed geometrical target model was created in the Monte Carlo toolkit Geant4 to represent the nucleus of a single human cell with complete human genome. A calculation framework to simulate double-strand breaks (DSBs) was implemented using this single cell model in the Geant4-DNA extension. A detailed ellipsoidal single cell model was implemented using a compacted DNA structure representing the fibroblast cell in the G0/G1 phase of the cycle using a total of 6 Gbp within the nucleus to represent the complete human genome. This geometry was developed from the publicly available Geant4-DNA example (wholeNuclearDNA), and modified to record DNA damage for both the physical and chemical stages. A clustering algorithm was implemented in the analysis process in order to quantify direct, indirect, and mixed DSBs. The model was validated against published experimental and computational results for DSB Gy-1Gbp-1and the relative biological effectiveness (RBE) values for 250 kVp and Co-60 photons, as well as 2-100 MeV mono-energetic protons. A general agreement was observed over the whole simulated proton energy range, Co-60 beam, and 250 kVp in terms of the yield of DSB Gy-1Gbp-1and RBE. The DSB yield was 8.0 ± 0.3 DSB Gy-1Gbp-1for Co-60, and 9.2 ± 0.2 DSB Gy-1Gbp-1for 250 kVp, and between 11.1 ± 0.9 and 8.1 ± 0.5 DSB Gy-1Gbp-1for 2-100 MeV protons. The results also show mixed DSBs composed of direct and indirect SSBs make up more than half of the total DSBs. The results presented indicate that the current model reliably predicts the DSB yield and RBE for proton and photon irradiations, and allows for the detailed computational investigation of direct and indirect effects in DNA damage.
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Affiliation(s)
- Xiandong Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
| | - Ruirui Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
| | - Tianyu Zhao
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
| | - Francisco J Reynoso
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, United States of America
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Chegeni N, Kouhkan E, Hussain A, Hassanvand M. The effect of the nucleus random location on the cellular S-values - Based on Geant4-DNA. Appl Radiat Isot 2020; 168:109427. [PMID: 33097380 DOI: 10.1016/j.apradiso.2020.109427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/23/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
INTRODUCTION The nucleus is the most crucial target in cell micro-dosimetry. At cell division time, cells do not have concentric geometry synchronously. This issue will be more essential for the low-energy electron emitters. This study investigates the variety of mean absorbed dose (S-value) in the non-concentric cell-nucleus model and random nucleus location within the cell. METHODS The S-values were calculated by Geant4-DNA for the cell and nucleus with different radius (with the RC/RN ratio = 1.2, 2, 3) and the cell geometry contains nuclei with varying positions inside the cell. Two important components, cytoplasm to the nucleus (N←Cy) and the cell surface to the nucleus (N←Cs) are considered in this work for mono energetic electrons (10-100 keV). To eliminate the effect of the nucleus position (during cell division) on the S-value, the nucleus location in each run was randomly selected inside the cell to represent the cell in a floating state. RESULTS As the nucleus becomes closer to the cell membrane the differences are more noticeable especially for electrons with energy less than 20 keV as for RN/RC = 1.2, 2, and 3 about 18, 70, and 200%, respectively. CONCLUSION Due to the variable position of the nucleus in cell division, using a random place defined in Geant4, the calculations are getting closer to the reality while there is not such possibility for analytical method used by MIRD.
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Affiliation(s)
- N Chegeni
- Departments of Medical Physics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - E Kouhkan
- Departments of Medical Physics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - A Hussain
- MCCPM, Medical Physics Department, 675 McDermott Ave, Winnipeg, MB, R3E 0V9, Cancer Care Manitoba, MB, Canada.
| | - M Hassanvand
- Department of Physics, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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Kouhkan E, Chegeni N, Hussain A. The Effect of Nucleus Size on the Cell Dose in Targeted Radionuclide Therapy - A Monte Carlo Study. J Med Signals Sens 2020; 10:113-118. [PMID: 32676447 PMCID: PMC7359958 DOI: 10.4103/jmss.jmss_21_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/04/2019] [Accepted: 12/25/2019] [Indexed: 11/04/2022]
Abstract
Background: Nowadays, the use of radiopharmaceuticals in medicine is unavoidable. Depending on the distribution of the radiopharmaceutical in the cells, the nucleus absorbed dose changes by the variations in their geometry size. Therefore, this study aims to investigate the S-value by the variation of nucleus size using Geant4 toolkit. Methods: Two spherical cells with a variety of nucleus size have been considered as the cancerous cell. Monoenergetic electrons ranging from 5 to 300 keV are distributed uniformly. The S-value for four target-source components (including Nucleus←Cytoplasm, Nucleus←Cell surface, Nucleus←Nucleus, and Nucleus←Nucleus surface) is computed and plotted. Then, the obtained data are compared with analytical Medical Internal Radiation Dose (MIRD) data. Results: In Nucleus←Cytoplasm compartment for electrons below 10 keV, obtained S-values show a slight decrease for the nucleus in the radii of around half of the cell radius and then S-values increase with the increase in the nucleus radii. In the S-value of Nucleus←Cell surface, for all electron energy levels, a slight decrease observed with the increase of nucleus radii. For Nucleus←Nucleus and Nucleus←Nucleus surface cases, with an increase in the size of the cell nucleus, a sharp reduction in the S-values is detected. Conclusion: It can be concluded that for the beta emitters with low-energy radiation (<40 keV), the S-value is heavily dependent on the nucleus size which may affect the treatment of small tumors. While for the beta emitters with higher-energy radiation (>100 keV), the size of the nucleus is not very noticeable in the induced S-value.
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Affiliation(s)
- Ebrahim Kouhkan
- Department of Medical Physics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nahid Chegeni
- Department of Medical Physics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amjad Hussain
- Department of Medical Physics, Cancer Care Manitoba, Winnipeg, MB, Canada
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Salim R, Taherparvar P. Cellular S values in spindle-shaped cells: a dosimetry study on more realistic cell geometries using Geant4-DNA Monte Carlo simulation toolkit. Ann Nucl Med 2020; 34:742-56. [PMID: 32632563 DOI: 10.1007/s12149-020-01498-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/01/2020] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Cellular dosimetry plays a crucial role in radiobiology and evaluation of the relative merits of radiopharmaceuticals used for targeted radionuclide therapy. The present study aims to investigate the effects of various cell geometries on dosimetric characteristics of several Auger emitters distributed in different subcellular compartments using Monte Carlo simulation. METHODS The Geant4-DNA extension of the Geant4 Monte Carlo simulation toolkit was employed to calculate the mean absorbed dose per unit cumulated activity (S value) for different subcellular distributions of several Auger electron-emitting theranostic radionuclides including 99mTc, 111In, 123I, 125I, and 201Tl. The simulations were carried out in various single-cell models of liquid water including spherical, ellipsoidal, spherical spindle, and ellipsoidal spindle cell models. The latter two models which are generalized from the first two models were inspired by the morphologies of spindle-shaped (fusiform) cells, and were developed to provide more realistic modeling of this common geometry observed in many healthy and cancerous cells. RESULTS Evaluation of the S values calculated for the examined cell models reveals that the differences are small (less than 9%) for the cell ← cell, cell ← cell surface, and nucleus ← nucleus source-target combinations. However, moderate discrepancies are seen (up to 28%) when the nucleus is considered as the target, as well as the radioactivity is either internalized into the cytoplasm or bound to the cell membrane. CONCLUSIONS The findings of the present work suggest that the assumption of spherical cell geometry may provide reasonably accurate estimates of the cellular/nuclear dose for the considered Auger emitters, even for spindle-shaped cells. Of course, this approximation should be used with caution for the nucleus ← cytoplasm and nucleus ← cell surface configurations, since the S-value sensitivity to the cell geometry is somewhat significant in these cases.
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Wang Y, Li Z, Zhang S, Tang W, Li X, Chen D, Sun L. The influence of Geant4-DNA toolkit parameters on electron microdosimetric track structure. J Radiat Res 2020; 61:58-67. [PMID: 31846034 PMCID: PMC6977597 DOI: 10.1093/jrr/rrz076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/19/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
The influence of different physical process factors on tracks of low-energy electrons in liquid water was analyzed and evaluated based on the Geant4-DNA toolkit of Geant4 version 10.4, and it provides theoretical support for obtaining the basic parameters of microdosimetry concerned with radiotherapy and radiation protection. According to the characteristics of different models, five physics constructors of Geant4-DNA toolkit were selected to simulate monoenergetic electrons in microscopic scale. Details of track structure of different Geant4-DNA physics constructors were compared, including total number of interaction processes, number and energy percentage of excitation and ionization; analyzing the impacts of mean lineal energy of several factors, including Geant4-DNA physics constructors, initial energy, radius of scoring spheres, interaction processes and cut-off energy. Firstly, 'G4EmDNAPhysics' (hereinafter referred to as 'dna') is well consistent with 'G4EmDNAPhysics_option 2' (hereinafter referred to as 'option 2'), and 'G4EmDNAPhysics_option 4' (hereinafter referred to as 'option 4') is well consistent with 'G4EmDNAPhysics_option 5' (hereinafter referred to as 'option 5'); secondly, there are differences for the information of track structure and mean lineal energy between 'option 2' 'option 4' and 'G4EmDNAPhysics_option 6' (hereinafter referred to as 'option 6'); thirdly, the influence of the model on the mean lineal energy decreases with the increase of the radius of the scoring spheres, whereas mean lineal energy increases as the tracking cut increases. Several alternative discrete physics constructors of Geant4-DNA are comprehensively discussed overlaying multiple perspectives under different conditions in this work.
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Affiliation(s)
- Yidi Wang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Zhanpeng Li
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Shuyuan Zhang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Wei Tang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Xiang Li
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Dandan Chen
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Liang Sun
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China
- State Key Laboratory of Radiation Medicine and Protection, Suzhou 215123, China
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
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Mehnaz, Yang LH, Zou YB, Da B, Mao SF, Li HM, Zhao YF, Ding ZJ. A comparative study on Monte Carlo simulations of electron emission from liquid water. Med Phys 2019; 47:759-771. [PMID: 31702062 DOI: 10.1002/mp.13913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/06/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Liquid water being the major constituent of the human body, is of fundamental importance in radiobiological research. Hence, the knowledge of electron-water interaction physics and particularly the secondary electron yield is essential. However, to date, only very little is known experimentally on the low energy electron interaction with liquid water because of certain practical limitations. The purpose of this study was to gain some useful information about electron emission from water using a Monte Carlo (MC) simulation technique that can numerically model electron transport trajectories in water. METHODS In this study, we have performed MC simulations of electron emission from liquid water in the primary energy range of 50 eV-30 keV by using two different codes, i.e., a classical trajectory MC (CMC) code developed in our laboratory and the Geant4-DNA (G4DNA) code. The calculated secondary electron yield and electron backscattering coefficient are compared with experimental results wherever applicable to verify the validity of physical models for the electron-water interaction. RESULTS The secondary electron yield vs. primary energy curves calculated using the two codes present the same generic curve shape as that of metals but in rather different absolute values. G4DNA underestimates the secondary electron yield due to the application of one step thermalization model by setting a cutoff energy at 10 eV so that the low energy losses due to phonon excitations are omitted. Our CMC code, using a full energy loss spectrum to model electron inelastic scattering, allows the simulation of individual phonon scattering events for very low energy losses down to 10 meV, which then enables the calculated secondary electron yields much closer to the experimental data and also gives quite reasonable energy distribution curve of secondary electrons. CONCLUSIONS It is concluded that full dielectric function data at low energy loss values below 10 eV are recommended for modeling of low energy electrons in liquid water.
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Affiliation(s)
- Mehnaz
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - L H Yang
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - Y B Zou
- School of Physics & Electronic Engineering, Xinjiang Normal University, Urumqi, Xinjiang, 830054, P.R. China
| | - B Da
- Center for Materials Research by Information Integration (CMI2), Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - S F Mao
- Department of Engineering and Applied Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - H M Li
- Supercomputing Center, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - Y F Zhao
- Radiotherapy Department, Anhui Provincial Hospital, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
| | - Z J Ding
- Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China
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Salado-Leza D, Traore A, Porcel E, Dragoe D, Muñoz A, Remita H, García G, Lacombe S. Radio-Enhancing Properties of Bimetallic Au:Pt Nanoparticles: Experimental and Theoretical Evidence. Int J Mol Sci 2019; 20:ijms20225648. [PMID: 31718091 PMCID: PMC6888691 DOI: 10.3390/ijms20225648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/28/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022] Open
Abstract
The use of nanoparticles, in combination with ionizing radiation, is considered a promising method to improve the performance of radiation therapies. In this work, we engineered mono- and bimetallic core-shell gold–platinum nanoparticles (NPs) grafted with poly (ethylene glycol) (PEG). Their radio-enhancing properties were investigated using plasmids as bio-nanomolecular probes and gamma radiation. We found that the presence of bimetallic Au:Pt-PEG NPs increased by 90% the induction of double-strand breaks, the signature of nanosize biodamage, and the most difficult cell lesion to repair. The radio-enhancement of Au:Pt-PEG NPs were found three times higher than that of Au-PEG NPs. This effect was scavenged by 80% in the presence of dimethyl sulfoxide, demonstrating the major role of hydroxyl radicals in the damage induction. Geant4-DNA Monte Carlo simulations were used to elucidate the physical processes involved in the radio-enhancement. We predicted enhancement factors of 40% and 45% for the induction of nanosize damage, respectively, for mono- and bimetallic nanoparticles, which is attributed to secondary electron impact processes. This work contributed to a better understanding of the interplay between energy deposition and the induction of nanosize biomolecular damage, being Monte Carlo simulations a simple method to guide the synthesis of new radio-enhancing agents.
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Affiliation(s)
- Daniela Salado-Leza
- Institut des Sciences Moléculaires d’Orsay (UMR 8214) CNRS, Université Paris-Saclay, Université Paris Sud, 91405 Orsay, France; (D.S.-L.); (E.P.)
- Cátedras CONACyT, Universidad Autónoma de San Luis Potosí, Facultad de Ciencias Químicas, Av. Dr. Manuel Nava 6, Zona Universitaria, San Luis Potosí 78210, S.L.P., Mexico
| | - Ali Traore
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain; (A.T.); (G.G.)
| | - Erika Porcel
- Institut des Sciences Moléculaires d’Orsay (UMR 8214) CNRS, Université Paris-Saclay, Université Paris Sud, 91405 Orsay, France; (D.S.-L.); (E.P.)
| | - Diana Dragoe
- Institut de Chimie Moléculaire et des Matériaux d’Orsay (UMR 8182) CNRS, Université Paris Saclay, Université Paris Sud, 91405 Orsay, France;
| | - Antonio Muñoz
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Avda. Complutense 22, 28040 Madrid, Spain;
| | - Hynd Remita
- Laboratoire de Chimie Physique (UMR 8000) CNRS, Université Paris Saclay, Université Paris Sud, 91405 Orsay, France;
| | - Gustavo García
- Instituto de Física Fundamental, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 113-bis, 28006 Madrid, Spain; (A.T.); (G.G.)
| | - Sandrine Lacombe
- Institut des Sciences Moléculaires d’Orsay (UMR 8214) CNRS, Université Paris-Saclay, Université Paris Sud, 91405 Orsay, France; (D.S.-L.); (E.P.)
- Correspondence: ; Tel.: +33-(1)-6915-8263
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Salim R, Taherparvar P. Monte Carlo single-cell dosimetry using Geant4-DNA: the effects of cell nucleus displacement and rotation on cellular S values. Radiat Environ Biophys 2019; 58:353-371. [PMID: 30927051 DOI: 10.1007/s00411-019-00788-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Investigation of biological effects of low-dose ionizing radiation at the (sub-) cellular level, which is referred to as microdosimetry, remains a major challenge of today's radiobiology research. Monte Carlo simulation of radiation tracks can provide a detailed description of the physical processes involved in dimensions as small as the critical substructures of the cell. Hereby, in the present study, microdosimetric calculations of cellular S values for mono-energetic electrons and six Auger-emitting radionuclides were performed in single-cell models of liquid water using Geant4-DNA. The effects of displacement and rotation of the nucleus within the cell on the cellular S values were studied in spherical and ellipsoidal geometries. It was found that for the examined electron energies and radionuclides, in the case of nucleus cross-absorption where the radioactivity is either localized in the cytoplasm of the cell or distributed on the cell surface, rotation of the nucleus within the cell affects cellular S values less than displacement of the nucleus. Especially, the considerable differences observed in S(nucleus ← cell surface) values between an eccentric and a concentric cell-nucleus configuration in spherical and ellipsoidal geometries (up to 63% and up to 44%, respectively) suggests that the approximation of concentricity should be used with caution, at least for localized irradiation of the cell membrane by an Auger-emitter in targeted radionuclide cancer therapy. The obtained results, which are based on a more realistic modeling of the cell than was done before, provide more accurate information about nuclear dose. This can be useful for theranostic applications.
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Affiliation(s)
- Ramak Salim
- Department of Physics, Faculty of Science, University of Guilan, Namjoo Avenue, P.O. Box 41335-19141, Rasht, 4193833697, Iran
| | - Payvand Taherparvar
- Department of Physics, Faculty of Science, University of Guilan, Namjoo Avenue, P.O. Box 41335-19141, Rasht, 4193833697, Iran.
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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; 46:1483-1500. [PMID: 30593679 PMCID: PMC6850505 DOI: 10.1002/mp.13370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 11/23/2022] Open
Abstract
Purpose Track structure simulation codes can accurately reproduce the stochastic nature of particle–matter interactions in order to evaluate quantitatively radiation damage in biological cells such as DNA strand breaks and base damage. Such simulations handle large numbers of secondary charged particles and molecular species created in the irradiated medium. Every particle and molecular species are tracked step‐by‐step using a Monte Carlo method to calculate energy loss patterns and spatial distributions of molecular species inside a cell nucleus with high spatial accuracy. The Geant4‐DNA extension of the Geant4 general‐purpose Monte Carlo simulation toolkit allows for such track structure simulations and can be run on CPUs. However, long execution times have been observed for the simulation of DNA damage in cells. We present in this work an improvement of the computing performance of such simulations using ultraparallel processing on a graphical processing unit (GPU). Methods A new Monte Carlo simulator named MPEXS‐DNA, allowing high computing performance by using a GPU, has been developed for track structure and radiolysis simulations at the subcellular scale. MPEXS‐DNA physics and chemical processes are based on Geant4‐DNA processes available in Geant4 version 10.02 p03. We have reimplemented the Geant4‐DNA process codes of the physics stage (electromagnetic processes of charged particles) and the chemical stage (diffusion and chemical reactions for molecular species) for microdosimetry simulation by using the CUDA language. MPEXS‐DNA can calculate a distribution of energy loss in the irradiated medium caused by charged particles and also simulate production, diffusion, and chemical interactions of molecular species from water radiolysis to quantitatively assess initial damage to DNA. The validation of MPEXS‐DNA physics and chemical simulations was performed by comparing various types of distributions, namely the radial dose distributions for the physics stage, and the G‐value profiles for each chemical product and their linear energy transfer dependency for the chemical stage, to existing experimental data and simulation results obtained by other simulation codes, including PARTRAC. Results For physics validation, radial dose distributions calculated by MPEXS‐DNA are consistent with experimental data and numerical simulations. For chemistry validation, MPEXS‐DNA can also reproduce G‐value profiles for each molecular species with the same tendency as existing experimental data. MPEXS‐DNA also agrees with simulations by PARTRAC reasonably well. However, we have confirmed that there are slight discrepancies in G‐value profiles calculated by MPEXS‐DNA for molecular species such as H2 and H2O2 when compared to experimental data and PARTRAC simulations. The differences in G‐value profiles between MPEXS‐DNA and PARTRAC are caused by the different chemical reactions considered. MPEXS‐DNA can drastically boost the computing performance of track structure and radiolysis simulations. By using NVIDIA's GPU devices adopting the Volta architecture, MPEXS‐DNA has achieved speedup factors up to 2900 against Geant4‐DNA simulations with a single CPU core. Conclusion The MPEXS‐DNA Monte Carlo simulation achieves similar accuracy to Monte Carlo simulations performed using other codes such as Geant4‐DNA and PARTRAC, and its predictions are consistent with experimental data. Notably, MPEXS‐DNA allows calculations that are, at maximum, 2900 times faster than conventional simulations using a CPU.
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Affiliation(s)
- Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | | | - Sebastien Incerti
- University of Bordeaux, CENBG, UMR 5797, Gradignan, F-33170, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, F-33170, France
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Chatzipapas KP, Papadimitroulas P, Obeidat M, McConnell KA, Kirby N, Loudos G, Papanikolaou N, Kagadis GC. Quantification of DNA double-strand breaks using Geant4-DNA. Med Phys 2018; 46:405-413. [PMID: 30418675 PMCID: PMC7379675 DOI: 10.1002/mp.13290] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/30/2018] [Accepted: 11/06/2018] [Indexed: 01/24/2023] Open
Abstract
Purpose This study aims to standardize the simulation procedure in measuring DNA double‐strand breaks (DSBs), by using advanced Monte Carlo toolkits, and newly introduced experimental methods for DNA DSB measurement. Methods For the experimental quantification of DNA DSB, an innovative DNA dosimeter was used to produce experimental data. GATE in combination with Geant4‐DNA toolkit were exploited to simulate the experimental environment. The PDB4DNA example of Geant4‐DNA was upgraded and investigated. Parameters of the simulation such energy threshold (ET) for a strand break and base pair threshold (BPT) for a DSB were evaluated, depending on the dose. Results Simulations resulted to minimum differentiation in comparison to experimental data for ET = 19 ± 1 eV and BPT = 10 bp, and high differentiation for ET<17.5 eV or ET>22.5 eV and BPT = 10 bp. There was also small differentiation for ET = 17.5 eV and BPT = 6 bp. Uncertainty has been kept lower than 3%. Conclusions This study includes first results on the quantification of DNA double‐strand breaks. The energy spectrum of a LINAC was simulated and used for the first time to irradiate DNA molecules. Simulation outcome was validated on experimental data that were produced by a prototype DNA dosimeter.
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Affiliation(s)
| | | | - Mohammad Obeidat
- University of Texas, Health Science Center, San Antonio, TX, 78229, USA
| | | | - Neil Kirby
- University of Texas, Health Science Center, San Antonio, TX, 78229, USA
| | - George Loudos
- University of West Attica, Department of Biomedical Engineering, Egaleo, GR, 12243, Greece
| | - Niko Papanikolaou
- University of Texas, Health Science Center, San Antonio, TX, 78229, USA
| | - George C Kagadis
- Department of Medical Physics, University of Patras, Rion, GR, 26504, Greece
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43
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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. [PMID: 29901835 DOI: 10.1002/mp.13048] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/03/2018] [Accepted: 06/04/2018] [Indexed: 01/11/2023] Open
Abstract
This Special Report presents a description of Geant4-DNA user applications dedicated to the simulation of track structures (TS) in liquid water and associated physical quantities (e.g., range, stopping power, mean free path…). These example applications are included in the Geant4 Monte Carlo toolkit and are available in open access. Each application is described and comparisons to recent international recommendations are shown (e.g., ICRU, MIRD), when available. The influence of physics models available in Geant4-DNA for the simulation of electron interactions in liquid water is discussed. Thanks to these applications, the authors show that the most recent sets of physics models available in Geant4-DNA (the so-called "option4" and "option 6" sets) enable more accurate simulation of stopping powers, dose point kernels, and W-values in liquid water, than the default set of models ("option 2") initially provided in Geant4-DNA. They also serve as reference applications for Geant4-DNA users interested in TS simulations.
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Affiliation(s)
- S Incerti
- University of Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
| | - I Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
| | - M A Bernal
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - M C Bordage
- Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse, France
- Inserm, UMR1037 CRCT, Toulouse, France
| | - Z Francis
- Department of Physics, Faculty of Sciences, Université Saint Joseph, Beirut, Lebanon
| | - S Guatelli
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
- Illawarra Health & Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - V Ivanchenko
- Geant4 Associates International Ltd., Hebden Bridge, UK
- Tomsk State University, Tomsk, Russia
| | - M Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - N Lampe
- Vicinity Centres, Data Science & Insights, Office Tower One, 1341 Dandenong Rd, Chadstone, Victoria, 3148, Australia
| | - S B Lee
- Proton Therapy Center, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Korea
| | - S Meylan
- SymAlgo Technologies, 75 rue Léon Frot, 75011, Paris, France
| | - C H Min
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Korea
| | - W G Shin
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Korea
| | | | - D Sakata
- University of Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - N Tang
- IRSN, Institut de Radioprotection et de Sureté Nucléaire, 92262, Fontenay-aux-Roses, France
| | - C Villagrasa
- IRSN, Institut de Radioprotection et de Sureté Nucléaire, 92262, Fontenay-aux-Roses, France
| | - H N Tran
- Division of Nuclear Physics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - J M C Brown
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
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Sakata D, Kyriakou I, Okada S, Tran HN, Lampe N, Guatelli S, Bordage MC, Ivanchenko V, Murakami K, Sasaki T, Emfietzoglou D, Incerti S. Geant4-DNA track-structure simulations for gold nanoparticles: The importance of electron discrete models in nanometer volumes. Med Phys 2018; 45:2230-2242. [PMID: 29480947 DOI: 10.1002/mp.12827] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 01/17/2018] [Accepted: 02/03/2018] [Indexed: 01/15/2023] Open
Abstract
PURPOSE Gold nanoparticles (GNPs) are known to enhance the absorbed dose in their vicinity following photon-based irradiation. To investigate the therapeutic effectiveness of GNPs, previous Monte Carlo simulation studies have explored GNP dose enhancement using mostly condensed-history models. However, in general, such models are suitable for macroscopic volumes and for electron energies above a few hundred electron volts. We have recently developed, for the Geant4-DNA extension of the Geant4 Monte Carlo simulation toolkit, discrete physics models for electron transport in gold which include the description of the full atomic de-excitation cascade. These models allow event-by-event simulation of electron tracks in gold down to 10 eV. The present work describes how such specialized physics models impact simulation-based studies on GNP-radioenhancement in a context of x-ray radiotherapy. METHODS The new discrete physics models are compared to the Geant4 Penelope and Livermore condensed-history models, which are being widely used for simulation-based NP radioenhancement studies. An ad hoc Geant4 simulation application has been developed to calculate the absorbed dose in liquid water around a GNP and its radioenhancement, caused by secondary particles emitted from the GNP itself, when irradiated with a monoenergetic electron beam. The effect of the new physics models is also quantified in the calculation of secondary particle spectra, when originating in the GNP and when exiting from it. RESULTS The new physics models show similar backscattering coefficients with the existing Geant4 Livermore and Penelope models in large volumes for 100 keV incident electrons. However, in submicron sized volumes, only the discrete models describe the high backscattering that should still be present around GNPs at these length scales. Sizeable differences (mostly above a factor of 2) are also found in the radial distribution of absorbed dose and secondary particles between the new and the existing Geant4 models. The degree to which these differences are due to intrinsic limitations of the condensed-history models or to differences in the underling scattering cross sections requires further investigation. CONCLUSIONS Improved physics models for gold are necessary to better model the impact of GNPs in radiotherapy via Monte Carlo simulations. We implemented discrete electron transport models for gold in Geant4 that is applicable down to 10 eV including the modeling of the full de-excitation cascade. It is demonstrated that the new model has a significant positive impact on particle transport simulations in gold volumes with submicron dimensions compared to the existing Livermore and Penelope condensed-history models of Geant4.
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Affiliation(s)
- Dousatsu Sakata
- Univ. Bordeaux, CENBG, UMR 5797, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
| | - Ioanna Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, Ioannina, Greece
| | - Shogo Okada
- Organization for Advanced and Integrated Research, Kobe University, Kobe, Japan
| | - Hoang N Tran
- Irfu, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Susanna Guatelli
- University of Wollongong, Centre For Medical Radiation Physics, Wollongong, Australia
| | - Marie-Claude Bordage
- INSERM, UMR1037 CRCT, Toulouse, France.,Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse, France
| | - Vladimir Ivanchenko
- Geant4 Associates International Ltd, Hebden Bridge, UK.,Tomsk State University, Tomsk, Russia
| | | | | | | | - Sebastien Incerti
- Univ. Bordeaux, CENBG, UMR 5797, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, France
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45
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Belov OV, Batmunkh M, Incerti S, Lkhagva O. Radiation damage to neuronal cells: Simulating the energy deposition and water radiolysis in a small neural network. Phys Med 2016; 32:1510-1520. [PMID: 27865670 DOI: 10.1016/j.ejmp.2016.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/21/2023] Open
Abstract
Radiation damage to the central nervous system (CNS) has been an on-going challenge for the last decades primarily due to the issues of brain radiotherapy and radiation protection for astronauts during space travel. Although recent findings revealed a number of molecular mechanisms associated with radiation-induced impairments in behaviour and cognition, some uncertainties exist in the initial neuronal cell injury leading to the further development of CNS malfunction. The present study is focused on the investigation of early biological damage induced by ionizing radiations in a sample neural network by means of modelling physico-chemical processes occurring in the medium after exposure. For this purpose, the stochastic simulation of incident particle tracks and water radiation chemistry was performed in realistic neuron phantoms constructed using experimental data on cell morphology. The applied simulation technique is based on using Monte-Carlo processes of the Geant4-DNA toolkit. The calculations were made for proton, 12C, and 56Fe particles of different energy within a relatively wide range of linear energy transfer values from a few to hundreds of keV/μm. The results indicate that the neuron morphology is an important factor determining the accumulation of microscopic radiation dose and water radiolysis products in neurons. The estimation of the radiolytic yields in neuronal cells suggests that the observed enhancement in the levels of reactive oxygen species may potentially lead to oxidative damage to neuronal components disrupting the normal communication between cells of the neural network.
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Affiliation(s)
- Oleg V Belov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia.
| | - Munkhbaatar Batmunkh
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia
| | - Sébastien Incerti
- Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France; CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Oidov Lkhagva
- Natural Science Division, National University of Mongolia, 1 University St., 210646 Ulaanbaatar, Mongolia
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Bordage MC, Bordes J, Edel S, Terrissol M, Franceries X, Bardiès M, Lampe N, Incerti S. Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA. Phys Med 2016; 32:1833-40. [PMID: 27773539 DOI: 10.1016/j.ejmp.2016.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/26/2016] [Accepted: 10/05/2016] [Indexed: 11/23/2022] Open
Abstract
A new alternative set of elastic and inelastic cross sections has been added to the very low energy extension of the Geant4 Monte Carlo simulation toolkit, Geant4-DNA, for the simulation of electron interactions in liquid water. These cross sections have been obtained from the CPA100 Monte Carlo track structure code, which has been a reference in the microdosimetry community for many years. They are compared to the default Geant4-DNA cross sections and show better agreement with published data. In order to verify the correct implementation of the CPA100 cross section models in Geant4-DNA, simulations of the number of interactions and ranges were performed using Geant4-DNA with this new set of models, and the results were compared with corresponding results from the original CPA100 code. Good agreement is observed between the implementations, with relative differences lower than 1% regardless of the incident electron energy. Useful quantities related to the deposited energy at the scale of the cell or the organ of interest for internal dosimetry, like dose point kernels, are also calculated using these new physics models. They are compared with results obtained using the well-known Penelope Monte Carlo code.
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Incerti S, Douglass M, Penfold S, Guatelli S, Bezak E. Review of Geant4-DNA applications for micro and nanoscale simulations. Phys Med 2016; 32:1187-200. [PMID: 27659007 DOI: 10.1016/j.ejmp.2016.09.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/01/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022] Open
Abstract
Emerging radiotherapy treatments including targeted particle therapy, hadron therapy or radiosensitisation of cells by high-Z nanoparticles demand the theoretical determination of radiation track structure at the nanoscale. This is essential in order to evaluate radiation damage at the cellular and DNA level. Since 2007, Geant4 offers physics models to describe particle interactions in liquid water at the nanometre level through the Geant4-DNA Package. This package currently provides a complete set of models describing the event-by-event electromagnetic interactions of particles with liquid water, as well as developments for the modelling of water radiolysis. Since its release, Geant4-DNA has been adopted as an investigational tool in kV and MV external beam radiotherapy, hadron therapies using protons and heavy ions, targeted therapies and radiobiology studies. It has been benchmarked with respect to other track structure Monte Carlo codes and, where available, against reference experimental measurements. While Geant4-DNA physics models and radiolysis modelling functionalities have already been described in detail in the literature, this review paper summarises and discusses a selection of representative papers with the aim of providing an overview of a) geometrical descriptions of biological targets down to the DNA size, and b) the full spectrum of current micro- and nano-scale applications of Geant4-DNA.
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48
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Wanek J, Rühli FJ. Risk to fragmented DNA in dry, wet, and frozen states from computed tomography: a comparative theoretical study. Radiat Environ Biophys 2016; 55:229-241. [PMID: 26883247 DOI: 10.1007/s00411-016-0637-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Computed tomography represents the gold standard in forensic and palaeopathological diagnosis. However, the X-rays used may affect the DNA quality through fragmentation and loss of genetic information. Previous work showed that the effects of ionizing radiation on dry DNA are non-significant with P < 10(-8), which cannot be detected by means of polymerase chain reaction methods. In the present paper, complete analytical model that characterizes radiation effects on fragmented DNA in dry, wet, and frozen states is described. Simulation of radiation tracks in water phantom cells was performed using the Geant4-DNA toolkit. Cell hits by electrons with energies between 5 and 20 keV were simulated, and the formation of radiolytic products was assessed at a temperature of 298 K. The diffusion coefficient and the mean square displacement of reactive species were calculated by Stokes-Einstein-Smoluchowski relations at 273 K. Finally, DNA fragment damage was estimated using the density distribution of fragments calculated from atomic force microscopy images. The lowest probability of radiation-induced DNA damage was observed for dry state, with a range from 2.5 × 10(-9) to 7.8 × 10(-12) at 298 K, followed by that for frozen state, with a range from 0.9 to 4 × 10(-7) at 273 K. The highest probability of radiation-induced DNA damage was demonstrated for fragmented DNA in wet state with a range from 2 to 9 × 10(-7) at 298 K. These results significantly improve the interpretation of CT imaging in future studies in forensic and palaeopathological science.
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Affiliation(s)
- Johann Wanek
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Frank Jakobus Rühli
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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Semsarha F, Raisali G, Goliaei B, Khalafi H. Microdosimetry of DNA conformations: relation between direct effect of (60)Co gamma rays and topology of DNA geometrical models in the calculation of A-, B- and Z-DNA radiation-induced damage yields. Radiat Environ Biophys 2016; 55:243-254. [PMID: 26984469 DOI: 10.1007/s00411-016-0644-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
In order to obtain the energy deposition pattern of ionizing radiation in the nanometric scale of genetic material and to investigate the different sensitivities of the DNA conformations, direct effects of (60)Co gamma rays on the three A, B and Z conformations of DNA have been studied. For this purpose, single-strand breaks (SSB), double-strand breaks (DSB), base damage (BD), hit probabilities and three microdosimetry quantities (imparted energy, mean chord length and lineal energy) in the mentioned DNA conformations have been calculated and compared by using GEometry ANd Tracking 4 (Geant4) toolkit. The results show that A-, B- and Z-DNA conformations have the highest yields of DSB (1.2 Gy(-1) Gbp(-1)), SSB (25.2 Gy(-1) Gbp(-1)) and BD (4.81 Gy(-1) Gbp(-1)), respectively. Based on the investigation of direct effects of radiation, it can be concluded that the DSB yield is largely correlated to the topological characteristics of DNA models, although the SSB yield is not. Moreover, according to the comparative results of the present study, a reliable candidate parameter for describing the relationship between DNA damage yields and geometry of DNA models in the theoretical radiation biology research studies would be the mean chord length (4 V/S) of the models.
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Affiliation(s)
- Farid Semsarha
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box: 11365-3486, Tehran, Iran
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, P.O. Box: 13145-1384, Tehran, Iran
| | - Gholamreza Raisali
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box: 11365-3486, Tehran, Iran.
| | - Bahram Goliaei
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, P.O. Box: 13145-1384, Tehran, Iran
| | - Hossein Khalafi
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, P.O. Box: 11365-3486, Tehran, Iran
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Bernal MA, Bordage MC, Brown JMC, Davídková M, Delage E, El Bitar Z, Enger SA, Francis Z, Guatelli S, Ivanchenko VN, Karamitros M, Kyriakou I, Maigne L, Meylan S, Murakami K, Okada S, Payno H, Perrot Y, Petrovic I, Pham QT, Ristic-Fira A, Sasaki T, Štěpán V, Tran HN, Villagrasa C, Incerti S. Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit. Phys Med 2015; 31:861-74. [PMID: 26653251 DOI: 10.1016/j.ejmp.2015.10.087] [Citation(s) in RCA: 275] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/28/2015] [Accepted: 10/07/2015] [Indexed: 11/24/2022] Open
Abstract
Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of today's radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described.
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