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Gardner LL, Thompson SJ, O'Connor JD, McMahon SJ. Modelling radiobiology. Phys Med Biol 2024; 69:18TR01. [PMID: 39159658 DOI: 10.1088/1361-6560/ad70f0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/19/2024] [Indexed: 08/21/2024]
Abstract
Radiotherapy has played an essential role in cancer treatment for over a century, and remains one of the best-studied methods of cancer treatment. Because of its close links with the physical sciences, it has been the subject of extensive quantitative mathematical modelling, but a complete understanding of the mechanisms of radiotherapy has remained elusive. In part this is because of the complexity and range of scales involved in radiotherapy-from physical radiation interactions occurring over nanometres to evolution of patient responses over months and years. This review presents the current status and ongoing research in modelling radiotherapy responses across these scales, including basic physical mechanisms of DNA damage, the immediate biological responses this triggers, and genetic- and patient-level determinants of response. Finally, some of the major challenges in this field and potential avenues for future improvements are also discussed.
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Affiliation(s)
- Lydia L Gardner
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - Shannon J Thompson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - John D O'Connor
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
- Ulster University School of Engineering, York Street, Belfast BT15 1AP, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
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2
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Rafiepour P, Sina S, Amoli ZA, Shekarforoush SS, Farajzadeh E, Mortazavi SMJ. A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study. Phys Eng Sci Med 2024; 47:1015-1035. [PMID: 38652348 DOI: 10.1007/s13246-024-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Sedigheh Sina
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
- Radiation research center, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
| | - Zahra Alizadeh Amoli
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ebrahim Farajzadeh
- Secondary Standard Dosimetry Laboratory (SSDL), Pars Isotope Co, Karaj, Iran
| | - Seyed Mohammad Javad Mortazavi
- Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Tuan Anh L, Ngoc Hoang T, Thibaut Y, Chatzipapas K, Sakata D, Incerti S, Villagrasa C, Perrot Y. "dsbandrepair" - An updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair. Phys Med 2024; 124:103422. [PMID: 38981169 DOI: 10.1016/j.ejmp.2024.103422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/07/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024] Open
Abstract
PURPOSE Interdisciplinary scientific communities have shown large interest to achieve a mechanistic description of radiation-induced biological damage, aiming to predict biological results produced by different radiation quality exposures. Monte Carlo track-structure simulations are suitable and reliable for the study of early DNA damage induction used as input for assessing DNA damage. This study presents the most recent improvements of a Geant4-DNA simulation tool named "dsbandrepair". METHODS "dsbandrepair" is a Monte Carlo simulation tool based on a previous code (FullSim) that estimates the induction of early DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). It uses DNA geometries generated by the DNAFabric computational tool for simulating the induction of early single-strand breaks (SSBs) and double-strand breaks (DSBs). Moreover, the new tool includes some published radiobiological models for survival fraction and un-rejoined DSB. Its application for a human fibroblast cell and human umbilical vein endothelial cell containing both heterochromatin and euchromatin was conducted. In addition, this new version offers the possibility of using the new IRT-syn method for computing the chemical stage. RESULTS The direct and indirect strand breaks, SSBs, DSBs, and damage complexity obtained in this work are equivalent to those obtained with the previously published simulation tool when using the same configuration in the physical and chemical stages. Simulation results on survival fraction and un-rejoined DSB are in reasonable agreement with experimental data. CONCLUSIONS "dsbandrepair" is a tool for simulating DNA damage and repair, benchmarked against experimental data. It has been released as an advanced example in Geant4.11.2.
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Affiliation(s)
- Le Tuan Anh
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Tran Ngoc Hoang
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Yann Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | | | | | - Sébastien Incerti
- CNRS/IN2P3, CENBG, UMR 5797, Bordeaux University, 33170 Gradignan, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), BP 17, 92262 Fontenay-aux-Roses, France
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4
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Fois GR, Tran HN, Fiegel V, Blain G, Chiavassa S, Craff E, Delpon G, Evin M, Haddad F, Incerti S, Koumeir C, Métivier V, Mouchard Q, Poirier F, Potiron V, Servagent N, Vandenborre J, Maigne L. Monte Carlo simulations of microdosimetry and radiolytic species production at long time post proton irradiation using GATE and Geant4-DNA. Med Phys 2024. [PMID: 38976841 DOI: 10.1002/mp.17281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/29/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Radiobiological effectiveness of radiation in cancer treatment can be studied at different scales (molecular till organ scale) and different time post irradiation. The production of free radicals and reactive oxygen species during water radiolysis is particularly relevant to understand the fundamental mechanisms playing a role in observed biological outcomes. The development and validation of Monte Carlo tools integrating the simulation of physical, physico-chemical and chemical stages after radiation is very important to maintain with experiments. PURPOSE Therefore, in this study, we propose to validate a new Geant4-DNA chemistry module through the simulation of water radiolysis and Fricke dosimetry experiments on a proton preclinical beam line. MATERIAL AND METHODS In this study, we used the GATE Monte Carlo simulation platform (version 9.3) to simulate a 67.5 MeV proton beam produced with the ARRONAX isochronous cyclotron (IBA Cyclone 70XP) at conventional dose rate (0.2 Gy/s) to simulate the irradiation of ultra-pure liquid water samples and Fricke dosimeter. We compared the depth dose profile with measurements performed with a plane parallel Advanced PTW 34045 Markus ionization chamber. Then, a new Geant4-DNA chemistry application proposed from Geant4 version 11.2 has been used to assess the evolution ofHO • ${\mathrm{HO}}^ \bullet $ ,e aq - ${\mathrm{e}}_{{\mathrm{aq}}}^ - $ ,H 3 O + ${{\mathrm{H}}}_3{{\mathrm{O}}}^ + $ ,H 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ ,H 2 ${{\mathrm{H}}}_2$ ,HO 2 • ${\mathrm{HO}}_2^ \bullet $ ,HO 2 - , O 2 • - ${\mathrm{HO}}_2^ - ,{\mathrm{\ O}}_2^{ \bullet - }$ andHO - ${\mathrm{HO}}^ - $ reactive species along time until 1-h post-irradiation. In particular, the effect of oxygen and pH has been investigated through comparisons with experimental measurements of radiolytic yields forH 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ and Fe3+. RESULTS GATE simulations reproduced, within 4%, the depth dose profile in liquid water. With Geant4-DNA, we were able to reproduce experimentalH 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ radiolytic yields 1-h post-irradiation in aerated and deaerated conditions, showing the impact of small changes in oxygen concentrations on species evolution along time. For the Fricke dosimeter, simulated G(Fe3+) is 15.97 ± 0.2 molecules/100 eV which is 11% higher than the measured value (14.4 ± 04 molecules/100 eV). CONCLUSIONS These results aim to be consolidated by new comparisons involving other radiolytic species, such ase aq - ${\mathrm{e}}_{{\mathrm{aq}}}^ - $ or, O 2 • - $,{\mathrm{\ O}}_2^{ \bullet - }$ to further study the mechanisms underlying the FLASH effect observed at ultra-high dose rates (UHDR).
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Affiliation(s)
| | | | | | - Guillaume Blain
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | | | | | - Grégory Delpon
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Manon Evin
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Ferid Haddad
- GIP ARRONAX, Saint-Herblain, France
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | | | | | - Vincent Métivier
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Quentin Mouchard
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | | | - Vincent Potiron
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
- Université de Nantes, CNRS, US2B, Saint-Herblain, France
| | - Noël Servagent
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Johan Vandenborre
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Lydia Maigne
- Université Clermont-Auvergne, CNRS, LPCA, Clermont-Ferrand, France
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5
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Tran HN, Archer J, Baldacchino G, Brown JMC, Chappuis F, Cirrone GAP, Desorgher L, Dominguez N, Fattori S, Guatelli S, Ivantchenko V, Méndez JR, Nieminen P, Perrot Y, Sakata D, Santin G, Shin WG, Villagrasa C, Zein S, Incerti S. Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project. Med Phys 2024. [PMID: 38889367 DOI: 10.1002/mp.17256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024] Open
Abstract
A chemistry module has been implemented in Geant4-DNA since Geant4 version 10.1 to simulate the radiolysis of water after irradiation. It has been used in a number of applications, including the calculation of G-values and early DNA damage, allowing the comparison with experimental data. Since the first version, numerous modifications have been made to the module to improve the computational efficiency and extend the simulation to homogeneous kinetics in bulk solution. With these new developments, new applications have been proposed and released as Geant4 examples, showing how to use chemical processes and models. This work reviews the models implemented and application developments for modeling water radiolysis in Geant4-DNA as reported in the ESA BioRad III Project.
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Affiliation(s)
| | - Jay Archer
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, LIDYL, Gif-sur-Yvette, France
- CY Cergy Paris Université, CEA, LIDYL, Gif-sur-Yvette, France
| | - Jeremy M C Brown
- Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, Australia
| | - Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Antonio Pablo Cirrone
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud (LNS), Catania, Italy
- Centro Siciliano di Fisica Nucleare e Struttura della Materia, Catania, Italy
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Naoki Dominguez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Serena Fattori
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud (LNS), Catania, Italy
| | - Susanna Guatelli
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - José-Ramos Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | | | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Dousatsu Sakata
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
- Division of Health Sciences, Osaka University, Osaka, Japan
- School of Physics, University of Bristol, Bristol, UK
| | | | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts, USA
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Sara Zein
- Univ. Bordeaux, CNRS, LP2I, UMR 5797, Gradignan, France
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Toigawa T, Kai T, Kumagai Y, Yokoya A. Consideration of the dielectric response for radiation chemistry simulations. J Chem Phys 2024; 160:214119. [PMID: 38836449 DOI: 10.1063/5.0211089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
The spur reaction, a spatially nonhomogeneous chemical reaction following ionization, is crucial in radiolysis or photolysis in liquids, but the spur expansion process has yet to be elucidated. One reason is the need to understand the role of the dielectric response of the solvating molecules surrounding the charged species generated by ionization. The dielectric response corresponds to the time evolution of the permittivity and might affect the chemical reaction-diffusion of the species in a spur expansion process. This study examined the competitive relationship between reaction-diffusion kinetics and the dielectric response by solving the Debye-Smoluchowski equation while considering the dielectric response. The Coulomb force between the charged species gradually decreases with the dielectric response. Our calculation results found a condition where fast recombination occurs before the dielectric response is complete. Although it has been reported that the primary G-values of free electrons depend on the static dielectric constant under low-linear-energy transfer radiation-induced ionization, we propose that considering the dielectric response can provide a deeper insight into fast recombination reactions under high-linear-energy transfer radiation- or photo-induced ionization. Our simulation method enables the understanding of fast radiation-induced phenomena in liquids.
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Affiliation(s)
- Tomohiro Toigawa
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Takeshi Kai
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Yuta Kumagai
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi 263-8555, Japan
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7
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Ballisat L, De Sio C, Beck L, Guatelli S, Sakata D, Shi Y, Duan J, Velthuis J, Rosenfeld A. Dose and DNA damage modelling of diffusing alpha-emitters radiation therapy using Geant4. Phys Med 2024; 121:103367. [PMID: 38701625 DOI: 10.1016/j.ejmp.2024.103367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
PURPOSE Diffusing alpha-emitters radiation therapy (DaRT) is a brachytherapy technique using α-particles to treat solid tumours. The high linear energy transfer (LET) and short range of α-particles make them good candidates for the targeted treatment of cancer. Treatment planning of DaRT requires a good understanding of the dose from α-particles and the other particles released in the 224Ra decay chain. METHODS The Geant4 Monte Carlo toolkit has been used to simulate a DaRT seed to better understand the dose contribution from all particles and simulate the DNA damage due to this treatment. RESULTS Close to the seed α-particles deliver the majority of dose, however at radial distances greater than 4 mm, the contribution of β-particles is greater. The RBE has been estimated as a function of number of double strand breaks (DSBs) and complex DSBs. A maximum seed spacing of 5.5 mm and 6.5 mm was found to deliver at least 20 Gy RBE weighted dose between the seeds for RBEDSB and RBEcDSB respectively. CONCLUSIONS The DNA damage changes with radial distance from the seed and has been found to become less complex with distance, which is potentially easier for the cell to repair. Close to the seed α-particles contribute the majority of dose, however the contribution from other particles cannot be neglected and may influence the choice of seed spacing.
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Affiliation(s)
| | - Chiara De Sio
- School of Physics, University of Bristol, Bristol, UK
| | - Lana Beck
- 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
| | - Yuyao Shi
- School of Physics, University of Bristol, Bristol, UK
| | - Jinyan Duan
- 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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8
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Mortazavi SMJ, Rafiepour P, Mortazavi SAR, Razavi Toosi SMT, Shomal PR, Sihver L. Radium deposition in human brain tissue: A Geant4-DNA Monte Carlo toolkit study. Z Med Phys 2024; 34:166-174. [PMID: 38420703 PMCID: PMC10919964 DOI: 10.1016/j.zemedi.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/09/2023] [Accepted: 09/28/2023] [Indexed: 03/02/2024]
Abstract
NASA has encouraged studies on 226Ra deposition in the human brain to investigate the effects of exposure to alpha particles with high linear energy transfer, which could mimic some of the exposure astronauts face during space travel. However, this approach was criticized, noting that radium is a bone-seeker and accumulates in the skull, which means that the radiation dose from alpha particles emitted by 226Ra would be heavily concentrated in areas close to cranial bones rather than uniformly distributed throughout the brain. In the high background radiation areas of Ramsar, Iran, extremely high levels of 226Ra in soil contribute to a large proportion of the inhabitants' radiation exposure. A prospective study on Ramsar residents with a calcium-rich diet was conducted to improve the dose uniformity due to 226Ra throughout the cerebral and cerebellar parenchyma. The study found that exposure of the human brain to alpha particles did not significantly affect working memory but was significantly associated with increased reaction times. This finding is crucial because astronauts on deep space missions may face similar cognitive impairments due to exposure to high charge and energy particles. The current study was aimed to evaluate the validity of the terrestrial model using the Geant4 Monte Carlo toolkit to simulate the interactions of alpha particles and representative cosmic ray particles, acknowledging that these radiation types are only a subset of the complete space radiation environment.
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Affiliation(s)
- S M J Mortazavi
- Ionizing and Non-Ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
| | - Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - S A R Mortazavi
- MVLS College, The University of Glasgow, Glasgow Scotland, UK
| | - S M T Razavi Toosi
- Physiology Department, School of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | - Parya Roshan Shomal
- Physiology Department, School of Medicine, Guilan University of Medical Sciences, Guilan, Iran
| | - Lembit Sihver
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czechia; Technische Universität Wien, Atominstitut, Vienna, Austria.
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9
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Derksen L, Adeberg S, Zink K, Baumann KS. Comparison of two methods simulating inter-track interactions using the radiobiological Monte Carlo toolkit TOPAS-nBio. Phys Med Biol 2024; 69:03NT01. [PMID: 38198700 DOI: 10.1088/1361-6560/ad1cf4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/10/2024] [Indexed: 01/12/2024]
Abstract
Objective.To compare two independently developed methods that enable modelling inter-track interactions in TOPAS-nBio by examining the yield of radiolytic species in radiobiological Monte Carlo track structure simulations. One method uses a phase space file to assign more than one primary to one event, allowing for inter-track interaction between these primary particles. This method has previously been developed by this working group and published earlier. Using the other method, chemical reactions are simulated based on a new version of the independent reaction time approach to allow inter-track interactions.Approach.G-values were calculated and compared using both methods for different numbers of tracks able to undergo inter-track interactions.Main results.Differences in theG-values simulated with the two methods strongly depend on the molecule type, and deviations can range up to 3.9% (H2O2), although, on average, the deviations are smaller than 1.5%.Significance.Both methods seem to be suitable for simulating inter-track interactions, as they provide comparableG-values even though both techniques were developed independently of each other.
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Affiliation(s)
- Larissa Derksen
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
| | - Sebastian Adeberg
- Marburg University Hospital, Department of Radiotherapy and Radiation Oncology, Marburg, Germany
- Marburg Ion-Beam Therapy Center (MIT), Department of Radiotherapy and Radiation Oncology, Marburg University Hospital, Marburg, Germany
- University Cancer Center, Frankfurt-Marburg, Germany
| | - Klemens Zink
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
- Marburg University Hospital, Department of Radiotherapy and Radiation Oncology, Marburg, Germany
- Marburg Ion-Beam Therapy Center (MIT), Department of Radiotherapy and Radiation Oncology, Marburg University Hospital, Marburg, Germany
| | - Kilian-Simon Baumann
- University of Applied Sciences, Institute of Medical Physics and Radiation Protection, Giessen, Germany
- Marburg University Hospital, Department of Radiotherapy and Radiation Oncology, Marburg, Germany
- Marburg Ion-Beam Therapy Center (MIT), Department of Radiotherapy and Radiation Oncology, Marburg University Hospital, Marburg, Germany
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10
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Gobet F, Barberet P, Delville MH, Devès G, Guérin T, Liénard R, Tran HN, Vecco-Garda C, Würger A, Zein S, Seznec H. Electric Fields in Liquid Water Irradiated with Protons at Ultrahigh Dose Rates. PHYSICAL REVIEW LETTERS 2023; 131:178001. [PMID: 37955497 DOI: 10.1103/physrevlett.131.178001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/21/2023] [Indexed: 11/14/2023]
Abstract
We study the effects of irradiating water with 3 MeV protons at high doses by observing the motion of charged polystyrene beads outside the proton beam. By single-particle tracking, we measure a radial velocity of the order of microns per second. Combining electrokinetic theory with simulations of the beam-generated reaction products and their outward diffusion, we find that the bead motion is due to electrophoresis in the electric field induced by the mobility contrast of cations and anions. This work sheds light on the perturbation of biological systems by high-dose radiations and paves the way for the manipulation of colloid or macromolecular dispersions by radiation-induced diffusiophoresis.
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Affiliation(s)
- F Gobet
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - P Barberet
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - M-H Delville
- University of Bordeaux, CNRS, ICMCB, UMR 5026, F-33608 Pessac, France
| | - G Devès
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - T Guérin
- University of Bordeaux, CNRS, LOMA, UMR 5798, F-33400 Talence, France
| | - R Liénard
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - H N Tran
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - C Vecco-Garda
- University of Bordeaux, CNRS, ICMCB, UMR 5026, F-33608 Pessac, France
| | - A Würger
- University of Bordeaux, CNRS, LOMA, UMR 5798, F-33400 Talence, France
| | - S Zein
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - H Seznec
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
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11
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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] [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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12
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Bian J, Duran J, Shin WG, Ramos-Méndez J, Sankey JC, Childress L, Seuntjens J, Enger SA. GEANT4-DNA simulation of temperature-dependent and pH-dependent yields of chemical radiolytic species. Phys Med Biol 2023; 68:124002. [PMID: 37230081 DOI: 10.1088/1361-6560/acd90d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/25/2023] [Indexed: 05/27/2023]
Abstract
Objective.GEANT4-DNA can simulate radiation chemical yield (G-value) for radiolytic species such as the hydrated electron (eaq-) with the independent reaction times (IRT) method, however, only at room temperature and neutral pH. This work aims to modify the GEANT4-DNA source code to enable the calculation ofG-values for radiolytic species at different temperatures and pH values.Approach.In the GEANT4-DNA source code, values of chemical parameters such as reaction rate constant, diffusion coefficient, Onsager radius, and water density were replaced by corresponding temperature-dependent polynomials. The initial concentration of hydrogen ion (H+)/hydronium ion (H3O+) was scaled for a desired pH using the relationship pH = -log10[H+]. To validate our modifications, two sets of simulations were performed. (A) A water cube with 1.0 km sides and a pH of 7 was irradiated with an isotropic electron source of 1 MeV. The end time was 1μs. The temperatures varied from 25 °C to 150 °C. (B) The same setup as (A) was used, however, the temperature was set to 25 °C while the pH varied from 5 to 9. The results were compared with published experimental and simulated work.Main results.The IRT method in GEANT4-DNA was successfully modified to simulateG-values for radiolytic species at different temperatures and pH values. Our temperature-dependent results agreed with experimental data within 0.64%-9.79%, and with simulated data within 3.52%-12.47%. The pH-dependent results agreed well with experimental data within 0.52% to 3.19% except at a pH of 5 (15.99%) and with simulated data within 4.40%-5.53%. The uncertainties were below ±0.20%. Overall our results agreed better with experimental than simulation data.Significance.Modifications in the GEANT4-DNA code enabled the calculation ofG-values for radiolytic species at different temperatures and pH values.
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Affiliation(s)
- Jingyi Bian
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Juan Duran
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA-02114, United States of America
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, CA, United States of America
| | - Jack C Sankey
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Lilian Childress
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Jan Seuntjens
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Shirin A Enger
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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13
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D-Kondo JN, Garcia-Garcia OR, LaVerne JA, Faddegon B, Schuemann J, Shin WG, Ramos-Méndez J. An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry. Phys Med Biol 2023; 68:10.1088/1361-6560/acd6d0. [PMID: 37201533 PMCID: PMC10355172 DOI: 10.1088/1361-6560/acd6d0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/18/2023] [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 10μM to 1 mM with [H2O2] yields calculated for 100 MeV protons at conventional and FLASH dose rates of 0.286 Gy s-1and 500 Gy s-1, 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, San Francisco, CA 94115, United States of America
| | - Omar R. Garcia-Garcia
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - Jay A. LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Wook-Geun Shin
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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14
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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] [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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15
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Adjei D, Trinh ND, Mostafavi M. Application of Geant4-DNA for simulating water radiolysis induced by Auger electron-emitting radionuclides. JOURNAL OF RADIATION RESEARCH 2023; 64:369-378. [PMID: 36702611 PMCID: PMC10036101 DOI: 10.1093/jrr/rrac105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/06/2022] [Indexed: 06/18/2023]
Abstract
Auger-emitting radionuclides have potential application in targeted radiotherapy, particularly for metastatic cancers. This possibility, especially, is stemmed from their characteristic short-range (a few μm) in biological systems allowing localization of high dose within small tumours. To explore this potential application, a Geant4 Monte Carlo toolkit has been employed to simulate the energy deposition of different radionuclides in a water model. The Geant4 Monte Carlo toolkit has model packages to simulate the interaction of radiation with matter and with diverse applications such as studies in science and medicine. In this study, the Geant4-DNA package was used to simulate the radiolytic yields induced by some Auger electron-emitting (AE) radionuclides including; I-131, I-125 and Pd-103, In-111, Ru-97 and Rh-103 m in water model. The results showed that the transient yield of the radiolytic species is characterized by the kinetic energies of the emitted electrons. It was observed that almost all the radionuclides, except I-131, deposited more energy in their proximity thereby inducing a high density of spurs to interact in a short time. It is, therefore, important to consider the kinetic energies of the emitted particles in choosing a radionuclide for specified targeted radiotherapy. This means that apart from their toxicity, compatibility with chelator and carrier molecules, and method of production, we can predict radionuclides such as In-111, Ru-97, Pb-103 m and I-125 could be relevant for targeted radiotherapy for the treatment of metastasis lesions, or tiny tumours at the cellular level, and tumours after surgical resection.
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Affiliation(s)
- Daniel Adjei
- Corresponding author. Institut de Chimie Physique UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France. E-mail: /
| | | | - Mehran Mostafavi
- Institut de Chimie Physique UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
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16
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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] [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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17
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Bui A, Bekerat H, Childress L, Sankey J, Seuntjens J, Enger SA. Effects of incoming particle energy and cluster size on the G-value of hydrated electrons. Phys Med 2023; 107:102540. [PMID: 36804695 DOI: 10.1016/j.ejmp.2023.102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
In hydrated electron (e-aq) dosimetry, absorbed radiation dose to water is measured by monitoring the concentration of radiation-induced e-aq. However, to obtain accurate dose, the radiation chemical yield of e-aq, G(e-aq), is needed for the radiation quality/setup under investigation. The aim of this study was to investigate the time-evolution of the G-values for the main generated reactive species during water radiolysis using GEANT4-DNA. The effects of cluster size and linear energy transfer (LET) on G(e-aq) were examined. Validity of GEANT4-DNA for calculation of G(e-aq) for clinically relevant energies was studied. Three scenarios were investigated with different phantom sizes and incoming electron energies (1 keV to 1 MeV). The time evolution of G(e-aq) was in good agreement with published data and did not change with decreasing phantom size. The time-evolution of the G-values increases with increasing LET for all radiolytic species. The particle tracks formed with high-energy electrons are separated and the resulting reactive species develop independently in time. With decreasing energy, the mean separation distance between reactive species decreases. The particle tracks might not initially overlap but will overlap shortly thereafter due to diffusion of reactive species, increasing the probability of e-aq recombination with other species. This also explains the decrease of G(e-aq) with cluster size and LET. Finally, if all factors are kept constant, as the incoming electron energy increases to clinically relevant energies, G(e-aq) remains similar to its value at 1 MeV, hence GEANT4-DNA can be used for clinically relevant energies.
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Affiliation(s)
- Alaina Bui
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada.
| | - Hamed Bekerat
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada; Radiation Oncology Department, Jewish General Hospital, Montréal, Quebec, Canada
| | - Lilian Childress
- Department of Physics, McGill University, Montréal, Quebec, Canada
| | - Jack Sankey
- Department of Physics, McGill University, Montréal, Quebec, Canada
| | - Jan Seuntjens
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada; Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Shirin A Enger
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montréal, Quebec, Canada; Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Quebec, Canada
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18
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Chatzipapas KP, Tran NH, Dordevic M, Zivkovic S, Zein S, Shin W, Sakata D, Lampe N, Brown JMC, Ristic‐Fira A, Petrovic I, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application. PRECISION RADIATION ONCOLOGY 2023. [DOI: 10.1002/pro6.1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Affiliation(s)
| | - Ngoc Hoang Tran
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zivkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zein
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Wook‐Geun Shin
- Physics Division, Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School Boston Massachusetts USA
| | | | | | - Jeremy M. C. Brown
- Department of Physics and Astronomy Swinburne University of Technology Melbourne Australia
| | - Aleksandra Ristic‐Fira
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ioanna Kyriakou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Susanna Guatelli
- Centre for Medical Radiation Physics University of Wollongong Wollongong New South Wales Australia
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
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19
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Modeling of DNA Damage Repair and Cell Response in Relation to p53 System Exposed to Ionizing Radiation. Int J Mol Sci 2022; 23:ijms231911323. [PMID: 36232625 PMCID: PMC9569799 DOI: 10.3390/ijms231911323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Repair of DNA damage induced by ionizing radiation plays an important role in the cell response to ionizing radiation. Radiation-induced DNA damage also activates the p53 system, which determines the fate of cells. The kinetics of repair, which is affected by the cell itself and the complexity of DNA damage, influences the cell response and fate via affecting the p53 system. To mechanistically study the influences of the cell response to different LET radiations, we introduce a new repair module and a p53 system model with NASIC, a Monte Carlo track structure code. The factors determining the kinetics of the double-strand break (DSB) repair are modeled, including the chromosome environment and complexity of DSB. The kinetics of DSB repair is modeled considering the resection-dependent and resection-independent compartments. The p53 system is modeled by simulating the interactions among genes and proteins. With this model, the cell responses to low- and high-LET irradiation are simulated, respectively. It is found that the kinetics of DSB repair greatly affects the cell fate and later biological effects. A large number of DSBs and a slow repair process lead to severe biological consequences. High-LET radiation induces more complex DSBs, which can be repaired by slow processes, subsequently resulting in a longer cycle arrest and, furthermore, apoptosis and more secreting of TGFβ. The Monte Carlo track structure simulation with a more realistic repair module and the p53 system model developed in this study can expand the functions of the NASIC code in simulating mechanical radiobiological effects.
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20
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Lai Y, Chi Y, Jia X. Mechanistic modelling of oxygen enhancement ratio of radiation via Monte Carlo simulation-based DNA damage calculation. Phys Med Biol 2022; 67:10.1088/1361-6560/ac8853. [PMID: 35944522 PMCID: PMC10152552 DOI: 10.1088/1361-6560/ac8853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
Objective.Oxygen plays an important role in affecting the cellular radio-sensitivity to ionizing radiation. The objective of this study is to build a mechanistic model to compute oxygen enhancement ratio (OER) using a GPU-based Monte Carlo (MC) simulation package gMicroMC for microscopic radiation transport simulation and DNA damage calculation.Approach.We first simulated the water radiolysis process in the presence of DNA and oxygen for 1 ns and recorded the produced DNA damages. In this process, chemical reactions among oxygen, water radiolysis free radicals and DNA molecules were considered. We then applied a probabilistic approach to model the reactions between oxygen and indirect DNA damages for a maximal reaction time oft0. Finally, we defined two parametersP0andP1, representing probabilities for DNA damages without and with oxygen fixation effect not being restored in the repair process, to compute the final DNA double strand breaks (DSBs). As cell survival fraction is mainly determined by the number of DSBs, we assumed that the same numbers of DSBs resulted in the same cell survival rates, which enabled us to compute the OER as the ratio of doses producing the same number of DSBs without and with oxygen. We determined the three parameters (t0,P0andP1) by fitting the OERs obtained in our computation to a set of published experimental data under x-ray irradiation. We then validated the model by performing OER studies under proton irradiation and studied model sensitivity to parameter values.Main results.We obtained the model parameters ast0= 3.8 ms,P0= 0.08, andP1= 0.28 with a mean difference of 3.8% between the OERs computed by our model and that obtained from experimental measurements under x-ray irradiation. Applying the established model to proton irradiation, we obtained OERs as functions of oxygen concentration, LET, and dose values, which generally agreed with published experimental data. The parameter sensitivity analysis revealed that the absolute magnitude of the OER curve relied on the values ofP0andP1, while the curve was subject to a horizontal shift when adjustingt0.Significance.This study developed a mechanistic model that fully relies on microscopic MC simulations to compute OER.
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Affiliation(s)
- Youfang Lai
- Innovative Technology of Radiotherapy Computations and Hardware (iTORCH) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, United States of America
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, United States of America
| | - Yujie Chi
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, United States of America
| | - Xun Jia
- Innovative Technology of Radiotherapy Computations and Hardware (iTORCH) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, United States of America
- Now at Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, MD, United States of America
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21
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Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B. TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac79f9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Current Monte Carlo simulations of DNA damage have been reported only at ambient temperature. The aim of this work is to use TOPAS-nBio to simulate the yields of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) produced in plasmids under low-LET irradiation incorporating the effect of the temperature changes in the environment. A new feature was implemented in TOPAS-nBio to incorporate reaction rates used in the simulation of the chemical stage of water radiolysis as a function of temperature. The implemented feature was verified by simulating temperature-dependent G-values of chemical species in liquid water from 20 °C to 90 °C. For radiobiology applications, temperature dependent SSB and DSB yields were calculated from 0 °C to 42 °C, the range of available published measured data. For that, supercoiled DNA plasmids dissolved in aerated solutions containing EDTA irradiated by Cobalt-60 gamma-rays were simulated. TOPAS-nBio well reproduced published temperature-dependent G-values in liquid water and the yields of SSB and DSB for the temperature range considered. For strand break simulations, the model shows that the yield of SSB and DSB increased linearly with the temperature at a rate of (2.94 ± 0.17) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99) and (0.13 ± 0.01) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99), respectively. The extended capability of TOPAS-nBio is a complementary tool to simulate realistic conditions for a large range of environmental temperatures, allowing refined investigations of the biological effects of radiation.
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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] [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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Hu A, Qiu R, Wu Z, Zhang H, Li J. CPU-GPU coupling independent reaction times method in NASIC and application in water radiolysis by FLASH irradiation. Biomed Phys Eng Express 2022; 8. [DOI: 10.1088/2057-1976/ac52d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 11/11/2022]
Abstract
Abstract
The mechanism of the FLASH effect remains unclear and could be revealed by studying chemical reactions during irradiation. Monte Carlo simulation of the radiolytic species is an effective tool to analyze chemical reactions, but the simulation is limited by computing costs of the step-by-step simulation of radiolytic species, especially when considering beam with complex time structure. The complexity of the time structure of beams from accelerators in FLASH radiotherapy requires a high-performance Monte Carlo code. In this work, we develop a CPU-GPU coupling accelerating code with the independent reaction times (IRT) method to extend the chemical module of our nanodosimetry Monte Carlo code NASIC. Every chemical molecule in the microenvironment contains time information to consider the reactions from different tracks and simulate beams with complex time structures. Performance test shows that our code significantly improved the computing efficiency of the chemical module by four orders of magnitude. Then the code is used to study the oxygen depletion hypothesis in FLASH radiotherapy for different conditions by setting different parameters. The transient oxygen consumption rate values in the water are calculated when the pulses width ranges from 2 ps to 2 μs, the total dose ranges from 0.5 Gy to 100 Gy and the initial oxygen concentration ranges from 0.1% to 21%. The time evolution curves are simulated to study the effect of the time structure of an electron linear accelerator. Results show that the total dose in several microseconds is a better indicator reflecting the radiolytic oxygen consumption rate than the dose rate. The initial oxygen greatly affects the oxygen consumption rate because of the reaction competition. The diffusion of oxygen determined by the physiological parameters is the key factor affecting oxygen depletion during the radiation using electron linear accelerators. Our code provides an efficient tool for simulating water radiolysis in different conditions
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Review of the Geant4-DNA Simulation Toolkit for Radiobiological Applications at the Cellular and DNA Level. Cancers (Basel) 2021; 14:cancers14010035. [PMID: 35008196 PMCID: PMC8749997 DOI: 10.3390/cancers14010035] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [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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D-Kondo N, Moreno-Barbosa E, Štěphán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J. DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions. Phys Med Biol 2021; 66. [PMID: 34787099 DOI: 10.1088/1361-6560/ac3a22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022]
Abstract
The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by60Co or137Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.
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Affiliation(s)
- N D-Kondo
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - E Moreno-Barbosa
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - V Štěphán
- 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
| | - S Incerti
- Univ. Bordeaux, CNRS/IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B De Celis Alonso
- Faculty of Mathematics and Physics Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J Schuemann
- Department of Radiation Oncology, Massachusets General Hospital and Hardvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
| | - J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America
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A Geant4-DNA Evaluation of Radiation-Induced DNA Damage on a Human Fibroblast. Cancers (Basel) 2021; 13:cancers13194940. [PMID: 34638425 PMCID: PMC8508455 DOI: 10.3390/cancers13194940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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27
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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] [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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Shin WG, Ramos-Mendez J, Tran NH, Okada S, Perrot Y, Villagrasa C, Incerti S. Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields. Phys Med 2021; 88:86-90. [PMID: 34198026 PMCID: PMC11152247 DOI: 10.1016/j.ejmp.2021.05.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/12/2021] [Accepted: 05/21/2021] [Indexed: 12/31/2022] Open
Abstract
This paper demonstrates the impact of the pre-chemical stage, especially the dissociation scheme and the associated probabilities, on water radiolysis simulation using the Geant4-DNA Monte Carlo track structure simulation toolkit. The models and parameters provided by TRACs have been collected and implemented into Geant4-DNA. In order to evaluate their influence on water radiolysis simulation, the radiochemical yields (G-values) are evaluated as a function of time and LET using the "chem6" Geant4-DNA example, and they are compared with published experimental and calculated data. The new pre-chemical models lead to a better agreement with literature data than the default pre-chemical models of Geant4-DNA, especially for OH radicals and H2O2. The revised chemistry constructor "G4EmDNAChemistry_option3" is available in Geant4-DNA version 10.7.
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Affiliation(s)
- Wook-Geun Shin
- UMR 5797, Bordeaux University, CNRS, CENBG, 33170 Gradignan, France; Department of Radiation Oncology, Seoul National University Hospital, 03080 Seoul, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, 03080 Seoul, Republic of Korea.
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, San Francisco 94143, CA, United States
| | - Ngoc Hoang Tran
- UMR 5797, Bordeaux University, CNRS, CENBG, 33170 Gradignan, France
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92262 Fontenay-aux-Roses, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92262 Fontenay-aux-Roses, France
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Lai Y, Jia X, Chi Y. Recent Developments on gMicroMC: Transport Simulations of Proton and Heavy Ions and Concurrent Transport of Radicals and DNA. Int J Mol Sci 2021; 22:ijms22126615. [PMID: 34205577 PMCID: PMC8233829 DOI: 10.3390/ijms22126615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mechanistic Monte Carlo (MC) simulation of radiation interaction with water and DNA is important for the understanding of biological responses induced by ionizing radiation. In our previous work, we employed the Graphical Processing Unit (GPU)-based parallel computing technique to develop a novel, highly efficient, and open-source MC simulation tool, gMicroMC, for simulating electron-induced DNA damages. In this work, we reported two new developments in gMicroMC: the transport simulation of protons and heavy ions and the concurrent transport of radicals in the presence of DNA. We modeled these transports based on electromagnetic interactions between charged particles and water molecules and the chemical reactions between radicals and DNA molecules. Various physical properties, such as Linear Energy Transfer (LET) and particle range, from our simulation agreed with data published by NIST or simulation results from other CPU-based MC packages. The simulation results of DNA damage under the concurrent transport of radicals and DNA agreed with those from nBio-Topas simulation in a comprehensive testing case. GPU parallel computing enabled high computational efficiency. It took 41 s to simultaneously transport 100 protons with an initial kinetic energy of 10 MeV in water and 470 s to transport 105 radicals up to 1 µs in the presence of DNA.
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Affiliation(s)
- Youfang Lai
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, USA;
- Innovative Technology of Radiotherapy Computation and Hardware (iTORCH) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, USA
| | - Xun Jia
- Innovative Technology of Radiotherapy Computation and Hardware (iTORCH) Laboratory, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75287, USA
- Correspondence: (X.J.); (Y.C.)
| | - Yujie Chi
- Department of Physics, University of Texas at Arlington, Arlington, TX 76019, USA;
- Correspondence: (X.J.); (Y.C.)
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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] [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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