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Thibaut Y, Gonon G, Martinez JS, Petit M, Babut R, Vaurijoux A, Gruel G, Villagrasa C, Incerti S, Perrot Y. Experimental validation in a neutron exposure frame of the MINAS TIRITH for cell damage simulation. Phys Med Biol 2023; 68:225008. [PMID: 37848039 DOI: 10.1088/1361-6560/ad043d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
In the domains of medicine and space exploration, refining risk assessment models for protecting healthy tissue from ionizing radiation is crucial. Understanding radiation-induced effects requires biological experimentations at the cellular population level and the cellular scale modeling using Monte Carlo track structure codes. We present MINAS TIRITH, a tool using Geant4-DNA Monte Carlo-generated databases to study DNA damage distribution at the cell population scale. It introduces a DNA damage location module and proposes a method to convert double-strand breaks (DSB) into DNA Damage Response foci. We evaluate damage location precision and DSB-foci conversion parameters. MINAS TIRITH's accuracy is validated againstγ-H2AX foci distribution from cell population exposed to monoenergetic neutron beams (2.5 or 15.1 MeV) under different configurations, yielding mixed radiation fields. Strong agreement between simulation and experimental results was found demonstrating MINAS TIRITH's predictive precision in radiation-induced DNA damage topology. Additionally, modeling intercellular damage variability within a population subjected to a specific macroscopic dose identifies subpopulations, enhancing realistic fate models. This approach advances our understanding of radiation-induced effects on cellular systems for risk assessment improvement.
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Affiliation(s)
- Y Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gonon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - J S Martinez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - M Petit
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - R Babut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - A Vaurijoux
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gruel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, LP2i, UMR 5797, F-33170 Gradignan, France
| | - Y Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
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Nicolanti F, Caccia B, Cartoni A, Emfietzoglou D, Faccini R, Incerti S, Kyriakou I, Satta M, Tran HN, Mancini-Terracciano C. Calculation of electron interaction models in N 2 and O 2. Phys Med 2023; 114:102661. [PMID: 37703804 DOI: 10.1016/j.ejmp.2023.102661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/19/2023] [Accepted: 08/05/2023] [Indexed: 09/15/2023] Open
Abstract
Cosmic rays have the potential to significantly affect the atmospheric composition by increasing the rate and changing the types of chemical reactions through ion production. The amount and states of ionization, and the spatial distribution of ions produced are still open questions for atmospheric models. To precisely estimate these quantities, it is necessary to simulate particle-molecule interactions, down to very low energies. Models enabling such simulations require interaction probabilities over a broad energy range and for all energetically allowed scattering processes. In this paper, we focus on electron interaction with the two most abundant molecules in the atmosphere, i.e., N2 and O2, as an initial step. A set of elastic and inelastic cross section models for electron transportation in oxygen and nitrogen molecules valid in the energy range 10 eV - 1 MeV, is presented. Comparison is made with available theoretical and experimental data and a reasonable good agreement is observed. Stopping power is calculated and compared with published data to assess the general consistency and reliability of our results. Good overall agreement is observed, with relative differences lower than 6% with the ESTAR database.
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Affiliation(s)
- F Nicolanti
- Physics Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; INFN, Sec. of Rome, p.le Aldo Moro, 2, 00185, Rome, Italy.
| | - B Caccia
- ISS(Italian National Institute of Health), V. Regina Elena, 299, 00161, Rome, Italy
| | - A Cartoni
- Chemistry Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy
| | - D Emfietzoglou
- Med. Phys. Lab., Dept of Medicine, University of Ioannina, 45110, Ioannina, Greece
| | - R Faccini
- Physics Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; INFN, Sec. of Rome, p.le Aldo Moro, 2, 00185, Rome, Italy
| | - S Incerti
- Université de Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, Chemin du Solarium, 19, 33170, Gradignan, France
| | - I Kyriakou
- Med. Phys. Lab., Dept of Medicine, University of Ioannina, 45110, Ioannina, Greece
| | - M Satta
- Chemistry Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; ISMN-CNR, p. Aldo Moro, 7, 00185, Rome, Italy
| | - H N Tran
- Université de Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, Chemin du Solarium, 19, 33170, Gradignan, France
| | - C Mancini-Terracciano
- Physics Dep., Sapienza U. of Rome, p.le Aldo Moro, 5, 00185, Rome, Italy; INFN, Sec. of Rome, p.le Aldo Moro, 2, 00185, Rome, Italy
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Ballisat L, Beck L, De Sio C, Guatelli S, Sakata D, Incerti S, Tran HN, Duan J, Maclean K, Shi Y, Velthuis J, Rosenfeld A. In-silico calculations of DNA damage induced by α-particles in the 224Ra DaRT decay chain for a better understanding of the radiobiological effectiveness of this treatment. Phys Med 2023; 112:102626. [PMID: 37393861 DOI: 10.1016/j.ejmp.2023.102626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 07/04/2023] Open
Abstract
Diffusing alpha-emitters radiation Therapy (DaRT) is an interstitial brachytherapy technique using 224Ra seeds. For accurate treatment planning a good understanding of the early DNA damage due to α-particles is required. Geant4-DNA was used to calculate the initial DNA damage and radiobiological effectiveness due to α-particles with linear energy transfer (LET) values in the range 57.5-225.9 keV/μm from the 224Ra decay chain. The impact of DNA base pair density on DNA damage has been modelled, as this parameter varies between human cell lines. Results show that the quantity and complexity of DNA damage changes with LET as expected. Indirect damage, due to water radical reactions with the DNA, decreases and becomes less significant at higher LET values as shown in previous studies. As expected, the yield of complex double strand breaks (DSBs), which are harder for a cell to repair, increases approximately linearly with LET. The level of complexity of DSBs and radiobiological effectiveness have been found to increase with LET as expected. The quantity of DNA damage has been shown to increase for increased DNA density in the expected base pair density range of human cells. The change in damage yield as a function of base pair density is largest for higher LET α-particles, an increase of over 50% for individual strand breaks between 62.7 and 127.4 keV/μm. This change in yield shows that the DNA base pair density is an important parameter for modelling DNA damage particularly at higher LET where the DNA damage is greatest and most complex.
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Affiliation(s)
| | - Lana Beck
- School of Physics, University of Bristol, Bristol, UK
| | - Chiara De Sio
- School of Physics, University of Bristol, Bristol, UK
| | - Susanna Guatelli
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
| | - Dousatsu Sakata
- Division of Health Sciences, Osaka University, Osaka 565-0871, Japan
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - Hoang Ngoc Tran
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170 Gradignan, France
| | - Jinyan Duan
- School of Physics, University of Bristol, Bristol, UK
| | - Katie Maclean
- School of Physics, University of Bristol, Bristol, UK
| | - Yuyao Shi
- School of Physics, University of Bristol, Bristol, UK
| | - Jaap Velthuis
- School of Physics, University of Bristol, Bristol, UK
| | - Anatoly Rosenfeld
- Centre for Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia
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Chappuis F, Tran HN, Zein SA, Bailat C, Incerti S, Bochud F, Desorgher L. The general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension to investigate mechanisms underlying the FLASH effect in radiotherapy: Current status and challenges. Phys Med 2023; 110:102601. [PMID: 37201453 DOI: 10.1016/j.ejmp.2023.102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023] Open
Abstract
FLASH radiotherapy is a promising approach to cancer treatment that offers several advantages over conventional radiotherapy. With this novel technique, high doses of radiation are delivered in a short period of time, inducing the so-called FLASH effect - a phenomenon characterized by healthy tissue sparing without alteration of tumor control. The mechanisms behind the FLASH effect remain unknown. One way to approach this problem is to gain insight into the initial parameters that can distinguish FLASH from conventional irradiation by simulating particle transport in aqueous media using the general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension. This review article discusses the current status of Geant4 and Geant4-DNA simulations to investigate mechanisms underlying the FLASH effect, as well as the challenges faced in this research field. One of the primary challenges is to accurately simulate the experimental irradiation parameters. Another challenge is the temporal extension of the simulations. This review also focuses on two hypotheses to explain the FLASH effect - namely the oxygen depletion hypothesis and the inter-track interactions hypothesis - and discusses how the Geant4 toolkit can be used to investigate them. The aim of this review is to provide an overview of Geant4 and Geant4-DNA simulations for FLASH radiotherapy and to highlight the challenges that need to be overcome in order to better study the FLASH effect.
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Affiliation(s)
- Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Hoang Ngoc Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Sara A Zein
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Claude Bailat
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Sébastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - François Bochud
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland.
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Papadopoulos A, Kyriakou I, Incerti S, Santin G, Nieminen P, Daglis IA, Li W, Emfietzoglou D. Space radiation quality factor for Galactic Cosmic Rays and typical space mission scenarios using a microdosimetric approach. Radiat Environ Biophys 2023; 62:221-234. [PMID: 37062024 DOI: 10.1007/s00411-023-01023-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/25/2023] [Indexed: 05/18/2023]
Abstract
Space radiation exposure from omnipresent Galactic Cosmic Rays (GCRs) in interplanetary space poses a serious carcinogenic risk to astronauts due to the-limited or absent-protective effect of the Earth's magnetosphere and, in particular, the terrestrial atmosphere. The radiation risk is directly influenced by the quality of the radiation, i.e., its pattern of energy deposition at the micron/DNA scale. For stochastic biological effects, radiation quality is described by the quality factor, [Formula: see text], which can be defined as a function of Linear Energy Transfer (LET) or the microdosimetric lineal energy ([Formula: see text]). In the present work, the average [Formula: see text] of GCR for different mission scenarios was calculated using a modified version of the microdosimetric Theory of Dual Radiation Action (TDRA). NASA's OLTARIS platform was utilized to generate the radiation environment behind different aluminum shielding (0-30 g/cm2) for a typical mission scenario in low-earth orbit (LEO) and in deep space. The microdosimetric lineal energy spectra of ions ([Formula: see text]) in 1 μm liquid water spheres were calculated by a generalized analytical model which considers energy-loss fluctuations and δ-ray transport inside the irradiated medium. The present TDRA-based [Formula: see text]-values for the LEO and deep space missions were found to differ by up to 10% and 14% from the corresponding ICRP-based [Formula: see text]-values and up to 3% and 6% from NASA's [Formula: see text]-model. In addition, they were found to be in good agreement with the [Formula: see text]-values measured in the International Space Station (ISS) and by the Mars Science Laboratory (MSL) Radiation Assessment Detector (RAD) which represent, respectively, a LEO and deep space orbit.
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Affiliation(s)
- Alexis Papadopoulos
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110, Ioannina, Greece
| | - Ioanna Kyriakou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110, Ioannina, Greece
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I, UMR 5797, F-33170, Gradignan, France
| | - Giovanni Santin
- ESA/ESTEC Space Environments and Effects Section, ESTEC, Keplerlaan 1, 2200 AG, Noordwijk, ZH, The Netherlands
| | - Petteri Nieminen
- ESA/ESTEC Space Environments and Effects Section, ESTEC, Keplerlaan 1, 2200 AG, Noordwijk, ZH, The Netherlands
| | - Ioannis A Daglis
- Department of Physics, National and Kapodistrian University of Athens, 15784, Athens, Greece
- Hellenic Space Center, 15231, Athens, Greece
| | - Weibo Li
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
- Federal Office for Radiation Protection (BfS), Ingolstädter Landstraße 1, 85764, Oberschleißheim, Germany
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Department of Medicine, University of Ioannina, 45110, Ioannina, Greece.
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Chappuis F, Grilj V, Tran HN, Zein SA, Bochud F, Bailat C, Incerti S, Desorgher L. Modeling of scavenging systems in water radiolysis with Geant4-DNA. Phys Med 2023; 108:102549. [PMID: 36921424 DOI: 10.1016/j.ejmp.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE This paper presents the capabilities of the Geant4-DNA Monte Carlo toolkit to simulate water radiolysis with scavengers using the step-by-step (SBS) or the independent reaction times (IRT) methods. It features two examples of application areas: (1) computing the escape yield of H2O2 following a 60Co γ-irradiation and (2) computing the oxygen depletion in water irradiated with 1 MeV electrons. METHODS To ease the implementation of the chemical stage in Geant4-DNA, we developed a user interface that helps define the chemical reactions and set the concentration of scavengers. The first application area example required two computational steps to perform water radiolysis using NO2- and NO3- as scavengers and a 60Co irradiation. The oxygen depletion computation technique for the second application area example consisted of simulating track segments of 1 MeV electrons and determining the radio-induced loss and gain of oxygen molecules. RESULTS The production of H2O2 under variable scavenging levels is consistent with the literature; the mean relative difference between the SBS and IRT methods is 7.2 % ± 0.5 %. For the oxygen depletion 1 µs post-irradiation, the mean relative difference between both methods is equal to 9.8 % ± 0.3 %. The results in the microsecond scale depend on the initial partial pressure of oxygen in water. In addition, the computed oxygen depletions agree well with the literature. CONCLUSIONS The Geant4-DNA toolkit makes it possible to simulate water radiolysis in the presence of scavengers. This feature offers perspectives in radiobiology, with the possibility of simulating cell-relevant scavenging mechanisms.
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Affiliation(s)
- Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Veljko Grilj
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Hoang Ngoc Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Sara A Zein
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - François Bochud
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Claude Bailat
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Sébastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Thibaut Y, Gonon G, Martinez JS, Petit M, Vaurijoux A, Gruel G, Villagrasa C, Incerti S, Perrot Y. MINAS TIRITH: a new tool for simulating radiation-induced DNA damage at the cell population level. Phys Med Biol 2023; 68. [PMID: 36623319 DOI: 10.1088/1361-6560/acb196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Objective. The mechanisms of radiation-induced DNA damage can be understood via the fundamental acquisition of knowledge through a combination of experiments and modeling. Currently, most biological experiments are performed by irradiating an entire cell population, whereas modeling of radiation-induced effects is usually performed via Monte Carlo simulations with track structure codes coupled to realistic DNA geometries of a single-cell nucleus. However, the difference in scale between the two methods hinders a direct comparison because the dose distribution in the cell population is not necessarily uniform owing to the stochastic nature of the energy deposition. Thus, this study proposed the MINAS TIRITH tool to model the distribution of radiation-induced DNA damage in a cell population.Approach. The proposed method is based on precomputed databases of microdosimetric parameters and DNA damage distributions generated using the Geant4-DNA Monte Carlo Toolkit. First, a specific energyzwas assigned to each cell of an irradiated population for a particular absorbed doseDabs,following microdosimetric formalism. Then, each cell was assigned a realistic number of DNA damage events according to the specific energyz,respecting the stochastic character of its occurrence.Main results. This study validated the MINAS TIRITH tool by comparing its results with those obtained using the Geant4-DNA track structure code and a Geant4-DNA based simulation chain for DNA damage calculation. The different elements of comparison indicated consistency between MINAS TIRITH and the Monte Carlo simulation in case of the dose distribution in the population and the calculation of the amount of DNA damage.Significance. MINAS TIRITH is a new approach for the calculation of radiation-induced DNA damage at the cell population level that facilitates reasonable simulation times compared to those obtained with track structure codes. Moreover, this tool enables a more direct comparison between modeling and biological experimentation.
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Affiliation(s)
- Y Thibaut
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gonon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - J S Martinez
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - M Petit
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - A Vaurijoux
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - G Gruel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - C Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, LP2i, UMR 5797, F-33170 Gradignan, France
| | - Y Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LDRI, PSE-SANTE/SERAMED/LRAcc, PSE-SANTE/SDOS/LMDN, BP 17, F-92262 Fontenay-aux-Roses, France
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Li Z, Michelet C, Incerti S, Ivanchenko V, Novak M, Guatelli S, Seznec H. Implementation of the EPICS2017 database for photons in Geant4. Phys Med 2022; 95:94-115. [PMID: 35149324 DOI: 10.1016/j.ejmp.2022.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/06/2022] [Accepted: 01/23/2022] [Indexed: 10/19/2022] Open
Abstract
This paper describes in detail the implementation of Geant4 Livermore electromagnetic physics models based on the EPICS2017 database for the low energy transport of photons. These models describe four photon processes: gamma conversion, Compton scattering, photoelectric effect and Rayleigh scattering. New parameterizations based on EPICS2017 were performed for scattering functions of Compton effect, subshell cross-sections of the photoelectric effect and form factors of Rayleigh scattering, in order to improve the precision of fitted values compared to tabulated values. Comparisons between new and old parameterizations were also carried out to evaluate the precision of the new parameterizations. The models were tested through a comparative study, in which the mass attenuation coefficient was calculated for both total photon interaction and each process using Geant4 simulations based on EPICS2017 and EPDL97 respectively. The results obtained from the simulations were found in good agreement with the XCOM reference data.
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Affiliation(s)
- Zhuxin Li
- CNRS, Université Bordeaux, CENBG, UMR5797, Gradignan F-33170, France.
| | - Claire Michelet
- CNRS, Université Bordeaux, CENBG, UMR5797, Gradignan F-33170, France.
| | - Sébastien Incerti
- CNRS, Université Bordeaux, CENBG, UMR5797, Gradignan F-33170, France.
| | - Vladimir Ivanchenko
- Tomsk State University, Tomsk 634050, Russia; CERN, Geneve 23, CH1211, Switzerland.
| | | | - Susanna Guatelli
- Center for Medical and Radiation Physics, University of Wollongong, New South Wales 2522, Australia.
| | - Hervé Seznec
- CNRS, Université Bordeaux, CENBG, UMR5797, Gradignan F-33170, France.
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10
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Chappuis F, Tran HN, Incerti S, Kacem H, Grilj V, Froidevaux P, Goncalves PJ, Bochud F, Bailat C, Vozenin MC, Desorgher L. FLASH Mechanisms Track (Oral Presentations) MODELLING OF WATER RADIOLYSIS FOR ULTRA-HIGH DOSE RATE (FLASH) ELECTRON BEAMS IN GEANT4-DNA. Phys Med 2022. [DOI: 10.1016/s1120-1797(22)01520-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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11
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Michelet C, Li Z, Jalenques H, Incerti S, Barberet P, Devès G, Delville MH, Seznec H. A Geant4 simulation of X-ray emission for three-dimensional proton imaging of microscopic samples. Phys Med 2022; 94:85-93. [PMID: 35007939 DOI: 10.1016/j.ejmp.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/16/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
PURPOSE Proton computed microtomography is a technique that reveals the inner content of microscopic samples. The density distribution of the material (in g·cm-3) is obtained from proton transmission tomography (STIM: Scanning Transmission Ion Microscopy) and the element content from X-ray emission tomography (PIXE: Particle Induced X-ray Emission). A precise quantification of chemical elements is difficult for thick samples, because of the variations of X-ray production cross-sections and of X-ray absorption. Both phenomena are at the origin of an attenuation of the measured X-ray spectra, which leads to an underestimation of the element content. Our aim is to quantify the accuracy of a specific correction method that we designed for thick samples. METHODS In this study, we describe how the 3D variations in the mass density were taken into account in the reconstruction code, in order to quantify the correction according to the position of the proton beam and the position and aperture angle of the X-ray detector. Moreover, we assess the accuracy of the reconstructed densities using Geant4 simulations on numerical phantoms, used as references. RESULTS The correction process was successfully applied and led, for the largest regions of interest (little affected by partial volume effects), to an accuracy ≤ 4% for phosphorus (compared to about 40% discrepancy without correction). CONCLUSION This study demonstrates the accuracy of the correction method implemented in the tomographic reconstruction code for thick samples. It also points out some advantages offered by Geant4 simulations: i) they produce projection data that are totally independent of the inversion method used for the image reconstruction; ii) one or more physical processes (X-ray absorption, proton energy loss) can be artificially turned off, in order to precisely quantify the effect of the different phenomena involved in the attenuation of X-ray spectra.
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Affiliation(s)
- Claire Michelet
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France.
| | - Zhuxin Li
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France.
| | - H Jalenques
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France
| | - Sébastien Incerti
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France.
| | - Philippe Barberet
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France.
| | - Guillaume Devès
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France.
| | - Marie-Hélène Delville
- CNRS, Univ. Bordeaux, ICMCB, UMR5026, 87 avenue du Dr. A. Schweitzer, Pessac F-33608, France.
| | - Hervé Seznec
- CNRS, Université Bordeaux, CENBG, UMR5797, F-33170 Gradignan, France.
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štěpán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol 2021; 66. [PMID: 34412044 DOI: 10.1088/1361-6560/ac1f39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022]
Abstract
The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for·OH, e-aq, and H2with published experimental data. For H2O2and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by137Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - J A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - N Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - J Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, United States of America
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - W-G Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - S Incerti
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - A McNamara
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - H Paganetti
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - J Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, United States of America
| | - J Schuemann
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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14
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Bhar M, Mora S, Kadri O, Zein S, Manai K, Incerti S. Monte Carlo study of patient and medical staff radiation exposures during interventional cardiology. Phys Med 2021; 82:200-210. [PMID: 33652203 DOI: 10.1016/j.ejmp.2021.01.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/15/2020] [Accepted: 01/12/2021] [Indexed: 10/22/2022] Open
Abstract
The aim of this study is to assess the radiation exposure of the patient and the medical staff during interventional cardiology procedures. Realistic exposure scenarios were developed using the adult reference anthropomorphic phantoms adopted by the International Commission on Radiological Protection (ICRP110Male and ICRP110Female), and the radiation transport code Geant4 (version 10.3). The calculated equivalent and effective doses were normalised by the simulated Kerma-Area Product (KAP), resulting in two conversion coefficients HT/KAP and E/KAP. To properly evaluate the risk of exposure, several dose-dependent parameters have been investigated, namely: radiological parameters (tube kilovoltage peak (kVp), type of projection, field size (FOV)), and operator positions. Four projections (AP,PA,LAO25° and RAO25°) were simulated for three X-ray energy spectra (80,100 and 120 kVp) with four different values of FOV (15×15 cm2,20×20 cm2,25×25 cm2 and 30×30 cm2). The results showed that the conversion coefficients values increase with increasing tube voltage as well as the FOV size. Recommended projection during the interventional cardiology procedures, whenever possible, should be the PA projection rather than AP projection. The most critical projection for the patient and the main operator is the RAO25° projection and the LAO25° projection respectively. The comparison of our results with the literature data showed good agreement allowing their use in the dosimetric characterization of interventional cardiology procedures.
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Affiliation(s)
- M Bhar
- Higher Institute of Medical Technologies of Tunis, Tunis El Manar University, Tunisia; Nuclear Physics and High Energy Unit, Faculty of Sciences of Tunis, Tunis El Manar University, Tunisia.
| | - S Mora
- University Hospital Center of Bordeaux. Bordeaux, France
| | - O Kadri
- Nuclear Physics and High Energy Unit, Faculty of Sciences of Tunis, Tunis El Manar University, Tunisia
| | - S Zein
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, 33175 Gradignan, France
| | - K Manai
- Nuclear Physics and High Energy Unit, Faculty of Sciences of Tunis, Tunis El Manar University, Tunisia
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, 33175 Gradignan, France
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15
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Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S, Villagrasa C. Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber. Med Phys 2020; 48:890-901. [PMID: 33232522 PMCID: PMC7986154 DOI: 10.1002/mp.14612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Purpose Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA. Methods This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT. Results Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA. Conclusion Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.
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Affiliation(s)
- Hoang Ngoc Tran
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
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16
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Arce P, Bolst D, Bordage MC, Brown JMC, Cirrone P, Cortés-Giraldo MA, Cutajar D, Cuttone G, Desorgher L, Dondero P, Dotti A, Faddegon B, Fedon C, Guatelli S, Incerti S, Ivanchenko V, Konstantinov D, Kyriakou I, Latyshev G, Le A, Mancini-Terracciano C, Maire M, Mantero A, Novak M, Omachi C, Pandola L, Perales A, Perrot Y, Petringa G, Quesada JM, Ramos-Méndez J, Romano F, Rosenfeld AB, Sarmiento LG, Sakata D, Sasaki T, Sechopoulos I, Simpson EC, Toshito T, Wright DH. Report on G4-Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group. Med Phys 2020; 48:19-56. [PMID: 32392626 DOI: 10.1002/mp.14226] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 04/26/2020] [Accepted: 04/30/2020] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Geant4 is a Monte Carlo code extensively used in medical physics for a wide range of applications, such as dosimetry, micro- and nanodosimetry, imaging, radiation protection, and nuclear medicine. Geant4 is continuously evolving, so it is crucial to have a system that benchmarks this Monte Carlo code for medical physics against reference data and to perform regression testing. AIMS To respond to these needs, we developed G4-Med, a benchmarking and regression testing system of Geant4 for medical physics. MATERIALS AND METHODS G4-Med currently includes 18 tests. They range from the benchmarking of fundamental physics quantities to the testing of Monte Carlo simulation setups typical of medical physics applications. Both electromagnetic and hadronic physics processes and models within the prebuilt Geant4 physics lists are tested. The tests included in G4-Med are executed on the CERN computing infrastructure via the use of the geant-val web application, developed at CERN for Geant4 testing. The physical observables can be compared to reference data for benchmarking and to results of previous Geant4 versions for regression testing purposes. RESULTS This paper describes the tests included in G4-Med and shows the results derived from the benchmarking of Geant4 10.5 against reference data. DISCUSSION Our results indicate that the Geant4 electromagnetic physics constructor G4EmStandardPhysics_option4 gives a good agreement with the reference data for all the tests. The QGSP_BIC_HP physics list provided an overall adequate description of the physics involved in hadron therapy, including proton and carbon ion therapy. New tests should be included in the next stage of the project to extend the benchmarking to other physical quantities and application scenarios of interest for medical physics. CONCLUSION The results presented and discussed in this paper will aid users in tailoring physics lists to their particular application.
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Affiliation(s)
| | - D Bolst
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - M-C Bordage
- CRCT (INSERM and Paul Sabatier University), Toulouse, France
| | - J M C Brown
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | | | | | - D Cutajar
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | - L Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital, Lausanne, Switzerland
| | | | - A Dotti
- SLAC National Accelerator Laboratory, Stanford, CA, USA
| | - B Faddegon
- University of California, San Francisco, CA, USA
| | - C Fedon
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - S Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, France
| | - V Ivanchenko
- Tomsk State University, Tomsk, Russian Federation.,CERN, Geneva, Switzerland
| | - D Konstantinov
- NRC "Kurchatov Institute" - IHEP, Protvino, Russian Federation
| | - I Kyriakou
- Medical Physics Laboratory, University of Ioannina, Ioannina, Greece
| | - G Latyshev
- NRC "Kurchatov Institute" - IHEP, Protvino, Russian Federation
| | - A Le
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | | | | | | | - C Omachi
- Nagoya Proton Therapy Center, Nagoya, Japan
| | | | - A Perales
- Medical Physics Department of Clínica Universidad de Navarra, Pamplona, Spain
| | - Y Perrot
- IRSN, Fontenay-aux-Roses, France
| | | | | | | | - F Romano
- INFN Catania Section, Catania, Italy.,Medical Physics Department, National Physical Laboratory, Teddington, UK
| | - A B Rosenfeld
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | - D Sakata
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | | | - I Sechopoulos
- Radboud University Medical Center, Nijmegen, The Netherlands.,Dutch Expert Center for Screening (LRCB), Nijmegen, The Netherlands
| | - E C Simpson
- Department of Nuclear Physics, Research School of Physics, Australian National University, Canberra, Australia
| | - T Toshito
- Nagoya Proton Therapy Center, Nagoya, Japan
| | - D H Wright
- SLAC National Accelerator Laboratory, Stanford, CA, USA
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17
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Engels E, Bakr S, Bolst D, Sakata D, Li N, Lazarakis P, McMahon SJ, Ivanchenko V, Rosenfeld AB, Incerti S, Kyriakou I, Emfietzoglou D, Lerch MLF, Tehei M, Corde S, Guatelli S. Advances in modelling gold nanoparticle radiosensitization using new Geant4-DNA physics models. Phys Med Biol 2020; 65:225017. [PMID: 32916674 DOI: 10.1088/1361-6560/abb7c2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Gold nanoparticles have demonstrated significant radiosensitization of cancer treatment with x-ray radiotherapy. To understand the mechanisms at the basis of nanoparticle radiosensitization, Monte Carlo simulations are used to investigate the dose enhancement, given a certain nanoparticle concentration and distribution in the biological medium. Earlier studies have ordinarily used condensed history physics models to predict nanoscale dose enhancement with nanoparticles. This study uses Geant4-DNA complemented with novel track structure physics models to accurately describe electron interactions in gold and to calculate the dose surrounding gold nanoparticle structures at nanoscale level. The computed dose in silico due to a clinical kilovoltage beam and the presence of gold nanoparticles was related to in vitro brain cancer cell survival using the local effect model. The comparison of the simulation results with radiobiological experimental measurements shows that Geant4-DNA and local effect model can be used to predict cell survival in silico in the case of x-ray kilovoltage beams.
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Affiliation(s)
- Elette Engels
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia. Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
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Bordes J, Incerti S, Mora-Ramirez E, Tranel J, Rossi C, Bezombes C, Bordenave J, Bardiès M, Brown R, Bordage MC. Monte Carlo dosimetry of a realistic multicellular model of follicular lymphoma in a context of radioimmunotherapy. Med Phys 2020; 47:5222-5234. [PMID: 32623743 DOI: 10.1002/mp.14370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/20/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Small-scale dosimetry studies generally consider an artificial environment where the tumors are spherical and the radionuclides are homogeneously biodistributed. However, tumor shapes are irregular and radiopharmaceutical biodistributions are heterogeneous, impacting the energy deposition in targeted radionuclide therapy. To bring realism, we developed a dosimetric methodology based on a three-dimensional in vitro model of follicular lymphoma incubated with rituximab, an anti-CD20 monoclonal antibody used in the treatment of non-Hodgkin lymphomas, which might be combined with a radionuclide. The effects of the realistic geometry and biodistribution on the absorbed dose were highlighted by comparison with literature data. Additionally, to illustrate the possibilities of this methodology, the effect of different radionuclides on the absorbed dose distribution delivered to the in vitro tumor were compared. METHODS The starting point was a model named multicellular aggregates of lymphoma cells (MALC). Three MALCs of different dimensions and their rituximab biodistribution were considered. Geometry, antibody location and concentration were extracted from selective plane illumination microscopy. Assuming antibody radiolabeling with Auger electron (125 I and 111 In) and β- particle emitters (177 Lu, 131 I and 90 Y), we simulated energy deposition in MALCs using two Monte Carlo codes: Geant4-DNA with "CPA100" physics models for Auger electron emitters and Geant4 with "Livermore" physics models for β- particle emitters. RESULTS MALCs had ellipsoid-like shapes with major radii, r, of ~0.25, ~0.5 and ~1.3 mm. Rituximab was concentrated in the periphery of the MALCs. The absorbed doses delivered by 177 Lu, 131 I and 90 Y in MALCs were compared with literature data for spheres with two types of homogeneous biodistributions (on the surface or throughout the volume). Compared to the MALCs, the mean absorbed doses delivered in spheres with surface biodistributions were between 18% and 38% lower, while with volume biodistribution they were between 15% and 29% higher. Regarding the radionuclides comparison, the relationship between MALC dimensions, rituximab biodistribution and energy released per decay impacted the absorbed doses. Despite releasing less energy, 125 I delivered a greater absorbed dose per decay than 111 In in the r ~ 0.25 mm MALC (6.78·10-2 vs 6.26·10-2 µGy·Bq-1 ·s-1 ). Similarly, the absorbed doses per decay in the r ~ 0.5 mm MALC for 177 Lu (2.41·10-2 µGy·Bq-1 ·s-1 ) and 131 I (2.46·10-2 µGy·Bq-1 ·s-1 ) are higher than for 90 Y (1.98·10-2 µGy·Bq-1 ·s-1 ). Furthermore, radionuclides releasing more energy per decay delivered absorbed dose more uniformly through the MALCs. Finally, when considering the radiopharmaceutical effective half-life, due to the biological half-life of rituximab being best matched by the physical half-life of 177 Lu and 131 I compared to 90 Y, the first two radionuclides delivered higher absorbed doses. CONCLUSION In the simulated configurations, β- emitters delivered higher and more uniform absorbed dose than Auger electron emitters. When considering radiopharmaceutical half-lives, 177 Lu and 131 I delivered absorbed doses higher than 90 Y. In view of real irradiation of MALCs, such a work may be useful to select suited radionuclides and to help explain the biological effects.
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Affiliation(s)
- Julien Bordes
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France
| | - Sébastien Incerti
- Université de Bordeaux, CENBG, UMR 5797, Gradignan, F-33170, France.,CNRS, IN2P3, CENBG, UMR 5797, Gradignan, F-33170, France
| | - Erick Mora-Ramirez
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France.,Escuela de Física, CICANUM, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Jonathan Tranel
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France.,Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Cédric Rossi
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France.,CHU Dijon, Hématologie Clinique, Hôpital François Mitterand, Dijon, 21000, France
| | - Christine Bezombes
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France
| | - Julie Bordenave
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France
| | - Manuel Bardiès
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France
| | - Richard Brown
- Institute of Nuclear Medicine, University College London, 235 Euston Road, London, NW1 2BU, UK
| | - Marie-Claude Bordage
- CRCT, UMR 1037 INSERM, Université Paul Sabatier, Toulouse, F-31037, France.,UMR 1037, CRCT, Université Toulouse III-Paul Sabatier, Toulouse, F-31037, France
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19
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Lampe N, Marin P, Coulon M, Micheau P, Maigne L, Sarramia D, Piquemal F, Incerti S, Biron DG, Ghio C, Sime-Ngando T, Hindre T, Breton V. Reducing the ionizing radiation background does not significantly affect the evolution of Escherichia coli populations over 500 generations. Sci Rep 2019; 9:14891. [PMID: 31624294 PMCID: PMC6797783 DOI: 10.1038/s41598-019-51519-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/30/2019] [Indexed: 12/31/2022] Open
Abstract
Over millennia, life has been exposed to ionizing radiation from cosmic rays and natural radioisotopes. Biological experiments in underground laboratories have recently demonstrated that the contemporary terrestrial radiation background impacts the physiology of living organisms, yet the evolutionary consequences of this biological stress have not been investigated. Explaining the mechanisms that give rise to the results of underground biological experiments remains difficult, and it has been speculated that hereditary mechanisms may be involved. Here, we have used evolution experiments in standard and very low-radiation backgrounds to demonstrate that environmental ionizing radiation does not significantly impact the evolutionary trajectories of E. coli bacterial populations in a 500 generations evolution experiment.
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Affiliation(s)
- Nathanael Lampe
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
| | - Pierre Marin
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
| | - Marianne Coulon
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
| | - Pierre Micheau
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
| | - Lydia Maigne
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
| | - David Sarramia
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
| | - Fabrice Piquemal
- Laboratoire Souterrain de Modane, 1125 Route de Bardonèche, F-73500, Modane, France.,Université de Bordeaux, CNRS/IN2P3, CENBG, F-33170, Gradignan, France
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, CENBG, F-33170, Gradignan, France
| | - David G Biron
- CNRS UMR 6023, Université Clermont-Auvergne, Laboratoire "Microorganismes: Génome et Environnement" (LMGE), F-63000, Clermont-Ferrand, France
| | - Camille Ghio
- CNRS UMR 6023, Université Clermont-Auvergne, Laboratoire "Microorganismes: Génome et Environnement" (LMGE), F-63000, Clermont-Ferrand, France
| | - Télesphore Sime-Ngando
- CNRS UMR 6023, Université Clermont-Auvergne, Laboratoire "Microorganismes: Génome et Environnement" (LMGE), F-63000, Clermont-Ferrand, France
| | - Thomas Hindre
- Univ. Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, F-38000, Grenoble, France.
| | - Vincent Breton
- Université Clermont Auvergne, CNRS/IN2P3, LPC, F-63000, Clermont-Ferrand, France
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20
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Michelet C, Li Z, Yang W, Incerti S, Desbarats P, Giovannelli JF, Barberet P, Delville MH, Gordillo N, Devès G, Seznec H. A Geant4 simulation for three-dimensional proton imaging of microscopic samples. Phys Med 2019; 65:172-180. [PMID: 31494371 DOI: 10.1016/j.ejmp.2019.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 11/18/2022] Open
Abstract
Proton imaging can be carried out on microscopic samples by focusing the beam to a diameter ranging from a few micrometers down to a few tens of nanometers, depending on the required beam intensity and spatial resolution. Three-dimensional (3D) imaging by tomography is obtained from proton transmission (STIM: Scanning Transmission Ion Microscopy) and/or X-ray emission (PIXE: Particle Induced X-ray Emission). In these experiments, the samples are dehydrated for under vacuum analysis. In situ quantification of nanoparticles has been carried out at CENBG in the frame of nanotoxicology studies, on cells and small organisms used as biological models, especially on Caenorhabditis elegans (C. elegans) nematodes. Tomography experiments reveal the distribution of mass density and chemical content (in g.cm-3) within the analyzed volume. These density values are obtained using an inversion algorithm. To investigate the effect of this data reduction process, we defined different numerical phantoms, including a (dehydrated) C. elegans phantom whose geometry and density were derived from experimental data. A Monte Carlo simulation based on the Geant4 toolkit was developed. Using different simulation and reconstruction conditions, we compared the resulting tomographic images to the initial numerical reference phantom. A study of the relative error between the reconstructed and the reference images lead to the result that 20 protons per shot can be considered as an optimal number for 3D STIM imaging. Preliminary results for PIXE tomography are also presented, showing the interest of such numerical phantoms to produce reference data for future studies on X-ray signal attenuation in thick samples.
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Affiliation(s)
- Claire Michelet
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Zhuxin Li
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France
| | - Wen Yang
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France
| | - Sébastien Incerti
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Pascal Desbarats
- Laboratoire Bordelais de Recherche en Informatique (LaBRI, UMR5800) Univ. Bordeaux, 351 Cours de la Libération, F-33405 Talence cedex, France.
| | | | - Philippe Barberet
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Marie-Hélène Delville
- CNRS, Univ. Bordeaux, ICMCB, UMR5026, 87 avenue du Dr. A. Schweitzer, Pessac F-33608, France.
| | - Nuria Gordillo
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France
| | - Guillaume Devès
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
| | - Hervé Seznec
- CENBG, UMR5797, Université de Bordeaux, CNRS, F-33170 Gradignan, France.
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21
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Coussot G, Le Postollec A, Faye C, Baqué M, Vandenabeele-Trambouze O, Incerti S, Vigier F, Chaput D, Cottin H, Przybyla B, Berger T, Dobrijevic M. Photochemistry on the Space Station-Antibody Resistance to Space Conditions after Exposure Outside the International Space Station. Astrobiology 2019; 19:1053-1062. [PMID: 30817173 DOI: 10.1089/ast.2018.1907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Antibody-based analytical instruments are under development to detect signatures of life on planetary bodies. Antibodies are molecular recognition reagents able to detect their target at sub-nanomolar concentrations, with high affinity and specificity. Studying antibody binding performances under space conditions is mandatory to convince space agencies of the adequacy of this promising tool for planetary exploration. To complement previous ground-based experiments on antibody resistance to simulated irradiation, we evaluate in this paper the effects of antibody exposure to real space conditions during the EXPOSE-R2 mission outside the International Space Station. The absorbed dose of ionizing radiation recorded during the 588 days of this mission (220 mGy) corresponded to the absorbed dose expected during a mission to Mars. Moreover, samples faced, at the same time as irradiation, thermal cycles, launch constraints, and long-term storage. A model biochip was used in this study with antibodies in freeze-dried form and under two formats: free or covalently grafted to a solid surface. We found that antibody-binding performances were not significantly affected by cosmic radiation, and more than 40% of the exposed antibody, independent of its format, was still functional during all this experiment. We conclude that antibody-based instruments are well suited for in situ analysis on planetary bodies.
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Affiliation(s)
- Gaëlle Coussot
- 1Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélie Le Postollec
- 2Laboratoire d'Astrophysique de Bordeaux (LAB), Université de Bordeaux, CNRS, Pessac, France
| | | | - Mickaël Baqué
- 4German Aerospace Center (DLR), Institute of Planetary Research, Management and Infrastructure, Research Group Astrobiological Laboratories, Berlin, Germany
| | - Odile Vandenabeele-Trambouze
- 5Université de Bretagne Occidentale (UBO), IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Plouzané, France
| | - Sébastien Incerti
- 6Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), UMR 5797, Université de Bordeaux, Gradignan, France
| | | | - Didier Chaput
- 7Centre National d'Etudes Spatiales, DCT/ME/EM, Toulouse, France
| | - Hervé Cottin
- 8Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR 7583, Université Paris Est Créteil et Université Paris Diderot, Institut Pierre Simon Laplace, Créteil, France
| | - Bartos Przybyla
- 9German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Thomas Berger
- 9German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Michel Dobrijevic
- 2Laboratoire d'Astrophysique de Bordeaux (LAB), Université de Bordeaux, CNRS, Pessac, France
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22
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Coussot G, Le Postollec A, Incerti S, Baqué M, Faye C, Vandenabeele-Trambouze O, Cottin H, Ravelet C, Peyrin E, Fiore E, Vigier F, Caron J, Chaput D, Przybyla B, Berger T, Dobrijevic M. Photochemistry on the Space Station-Aptamer Resistance to Space Conditions: Particles Exposure from Irradiation Facilities and Real Exposure Outside the International Space Station. Astrobiology 2019; 19:1063-1074. [PMID: 30817199 DOI: 10.1089/ast.2018.1896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Some microarray-based instruments that use bioaffinity receptors such as antibodies or aptamers are under development to detect signatures of past or present life on planetary bodies. Studying the resistance of such instruments against space constraints and cosmic rays in particular is a prerequisite. We used several ground-based facilities to study the resistance of aptamers to various types of particles (protons, electrons, neutrons, and carbon ions) at different energies and fluences. We also tested the resistance of aptamers during the EXPOSE-R2 mission outside the International Space Station (ISS). The accumulated dose measured after the 588 days of this mission (220 mGy) corresponds to the accumulated dose that can be expected during a mission to Mars. We found that the recognition ability of fluorescently labeled aptamers was not significantly affected during short-term exposure experiments taking into account only one type of radiation at a time. However, we demonstrated that the same fluorescent dye was significantly affected by temperature variations (-21°C to +58°C) and storage throughout the entirety of the ISS experiment (60% of signal loss). This induced a large variability of aptamer signal in our analysis. However, we found that >50% of aptamers were still functional after the whole EXPOSE-R2 mission. We conclude that aptamer-based instruments are well suited for in situ analysis on planetary bodies, but the detection step requires additional investigations.
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Affiliation(s)
- Gaëlle Coussot
- 1Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Aurélie Le Postollec
- 2Laboratoire d'Astrophysique de Bordeaux (LAB), Université de Bordeaux, CNRS, B18N, Pessac, France
| | - Sébastien Incerti
- 3Centre d'Etudes Nucléaires de Bordeaux Gradignan (CENBG), UMR 5797, Université de Bordeaux, Gradignan, France
| | - Mickaël Baqué
- 4German Aerospace Center (DLR), Institute of Planetary Research, Management and Infrastructure, Research Group Astrobiological Laboratories, Berlin, Germany
| | | | - Odile Vandenabeele-Trambouze
- 6IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO), Plouzané, France
| | - Hervé Cottin
- 7Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR 7583, Université Paris Est Créteil et Université Paris Diderot, Institut Pierre Simon Laplace, Créteil, France
| | - Corinne Ravelet
- 8Département de Pharmacochimie Moléculaire, UMR 5063, Université Grenoble Alpes, CNRS, St. Martin d'Hères, France
| | - Eric Peyrin
- 8Département de Pharmacochimie Moléculaire, UMR 5063, Université Grenoble Alpes, CNRS, St. Martin d'Hères, France
| | - Emmanuelle Fiore
- 8Département de Pharmacochimie Moléculaire, UMR 5063, Université Grenoble Alpes, CNRS, St. Martin d'Hères, France
| | | | - Jérôme Caron
- 9Département de Radiothérapie, Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France
| | - Didier Chaput
- 10DCT/ME/EM, Centre National d'Etudes Spatiales, Toulouse, France
| | - Bartos Przybyla
- 11German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Thomas Berger
- 11German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Michel Dobrijevic
- 2Laboratoire d'Astrophysique de Bordeaux (LAB), Université de Bordeaux, CNRS, B18N, Pessac, France
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23
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Torfeh E, Simon M, Muggiolu G, Devès G, Vianna F, Bourret S, Incerti S, Barberet P, Seznec H. Monte-Carlo dosimetry and real-time imaging of targeted irradiation consequences in 2-cell stage Caenorhabditis elegans embryo. Sci Rep 2019; 9:10568. [PMID: 31332255 PMCID: PMC6646656 DOI: 10.1038/s41598-019-47122-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/11/2019] [Indexed: 12/26/2022] Open
Abstract
Charged-particle microbeams (CPMs) provide a unique opportunity to investigate the effects of ionizing radiation on living biological specimens with a precise control of the delivered dose, i.e. the number of particles per cell. We describe a methodology to manipulate and micro-irradiate early stage C. elegans embryos at a specific phase of the cell division and with a controlled dose using a CPM. To validate this approach, we observe the radiation-induced damage, such as reduced cell mobility, incomplete cell division and the appearance of chromatin bridges during embryo development, in different strains expressing GFP-tagged proteins in situ after irradiation. In addition, as the dosimetry of such experiments cannot be extrapolated from random irradiations of cell populations, realistic three-dimensional models of 2 cell-stage embryo were imported into the Geant4 Monte-Carlo simulation toolkit. Using this method, we investigate the energy deposit in various chromatin condensation states during the cell division phases. The experimental approach coupled to Monte-Carlo simulations provides a way to selectively irradiate a single cell in a rapidly dividing multicellular model with a reproducible dose. This method opens the way to dose-effect investigations following targeted irradiation.
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Affiliation(s)
- Eva Torfeh
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France
| | - Marina Simon
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France
| | - Giovanna Muggiolu
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France
| | - Guillaume Devès
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France
| | - François Vianna
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,François Vianna: Institut de Radioprotection et de Sûreté Nucléaire, Bat.159, BP3, 13115, St-Paul-Lez-Durance, Cedex, France
| | - Stéphane Bourret
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France
| | - Sébastien Incerti
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France
| | - Philippe Barberet
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France. .,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.
| | - Hervé Seznec
- Université de Bordeaux, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France. .,CNRS, UMR5797, Centre d'Etudes Nucléaires Bordeaux Gradignan (CENBG), Chemin du Solarium, 33175, Gradignan, France.
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24
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Tang N, Bueno M, Meylan S, Incerti S, Clairand I, Villagrasa C. SIMULATION OF EARLY RADIATION-INDUCED DNA DAMAGE ON DIFFERENT TYPES OF CELL NUCLEI. Radiat Prot Dosimetry 2019; 183:26-31. [PMID: 30535369 DOI: 10.1093/rpd/ncy237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This work presents a comparison of simulated early radiation-induced DNA damage represented by yields of double-strand breaks (DSB) in three different human cell nuclei geometries representing fibroblasts, lymphocytes and endothelial cells for protons and alpha particles of different energies and for different irradiation configurations. Each cell nucleus model includes a multi-scale description of the DNA target from the molecular level to the whole human genome representation (6 Gbp) in the G0/G1 phase of the cell cycle and was generated with the DnaFabric software. The three nuclei differ in shape, volume, and therefore DNA density. A calculation chain based on Geant4-DNA that takes into account the physical, physico-chemical and chemical stages was used to simulate the irradiation of the different cell nuclei. Results show an increase of DSB/primary/μm with an increase of DNA density and an increase of DSB/Gy/Gbp with an increase of the cell nucleus volume which indicates that the cell nucleus shape and size have an impact on early DNA damage, which may play a role in latter effects.
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Affiliation(s)
- Nicolas Tang
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | - Marta Bueno
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | | | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux Gradignan, CENBG, chemin du solarium, Gradignan, France
| | - Isabelle Clairand
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, Fontenay aux Roses, France
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Tang N, Bueno M, Meylan S, Incerti S, Tran HN, Vaurijoux A, Gruel G, Villagrasa C. Influence of chromatin compaction on simulated early radiation-induced DNA damage using Geant4-DNA. Med Phys 2019; 46:1501-1511. [DOI: 10.1002/mp.13405] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/07/2019] [Accepted: 01/21/2019] [Indexed: 11/11/2022] Open
Affiliation(s)
- N. Tang
- IRSN; Institut de Radioprotection et de Sûreté Nucléaire; BP17 92262 Fontenay aux Roses France
| | - M. Bueno
- IRSN; Institut de Radioprotection et de Sûreté Nucléaire; BP17 92262 Fontenay aux Roses France
| | - S. Meylan
- SymAlgo Technologies; 75 rue Léon Frot 75011 Paris France
| | - S. Incerti
- Université de Bordeaux CNRS/IN2P3 Centre d'Etudes Nucléaires de Bordeaux; Gradignan CENBG; chemin du solarium, BP120 33175 Gradignan France
| | - H. N. Tran
- IRSN; Institut de Radioprotection et de Sûreté Nucléaire; BP17 92262 Fontenay aux Roses France
| | - A. Vaurijoux
- IRSN; Institut de Radioprotection et de Sûreté Nucléaire; BP17 92262 Fontenay aux Roses France
| | - G. Gruel
- IRSN; Institut de Radioprotection et de Sûreté Nucléaire; BP17 92262 Fontenay aux Roses France
| | - C. Villagrasa
- IRSN; Institut de Radioprotection et de Sûreté Nucléaire; BP17 92262 Fontenay aux Roses France
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Kyriakou I, Ivanchenko V, Sakata D, Bordage M, Guatelli S, Incerti S, Emfietzoglou D. Influence of track structure and condensed history physics models of Geant4 to nanoscale electron transport in liquid water. Phys Med 2019; 58:149-154. [DOI: 10.1016/j.ejmp.2019.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/31/2018] [Accepted: 01/01/2019] [Indexed: 12/20/2022] Open
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Schuemann J, McNamara AL, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B. TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology. Radiat Res 2019; 191:125-138. [PMID: 30609382 DOI: 10.1667/rr15226.1] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The TOPAS Monte Carlo (MC) system is used in radiation therapy and medical imaging research, having played a significant role in making Monte Carlo simulations widely available for proton therapy related research. While TOPAS provides detailed simulations of patient scale properties, the fundamental unit of the biological response to radiation is a cell. Thus, our goal was to develop TOPAS-nBio, an extension of TOPAS dedicated to advance understanding of radiobiological effects at the (sub-)cellular, (i.e., the cellular and sub-cellular) scale. TOPAS-nBio was designed as a set of open source classes that extends TOPAS to model radiobiological experiments. TOPAS-nBio is based on and extends Geant4-DNA, which extends the Geant4 toolkit, the basis of TOPAS, to include very low-energy interactions of particles down to vibrational energies, explicitly simulates every particle interaction (i.e., without using condensed histories) and propagates radiolysis products. To further facilitate the use of TOPAS-nBio, a graphical user interface was developed. TOPAS-nBio offers full track-structure Monte Carlo simulations, integration of chemical reactions within the first millisecond, an extensive catalogue of specialized cell geometries as well as sub-cellular structures such as DNA and mitochondria, and interfaces to mechanistic models of DNA repair kinetics. We compared TOPAS-nBio simulations to measured and published data of energy deposition patterns and chemical reaction rates (G values). Our simulations agreed well within the experimental uncertainties. Additionally, we expanded the chemical reactions and species provided in Geant4-DNA and developed a new method based on independent reaction times (IRT), including a total of 72 reactions classified into 6 types between neutral and charged species. Chemical stage simulations using IRT were a factor of 145 faster than with step-by-step tracking. Finally, we applied the geometric/chemical modeling to obtain initial yields of double-strand breaks (DSBs) in DNA fibers for proton irradiations of 3 and 50 MeV and compared the effect of including chemical reactions on the number and complexity of DSB induction. Over half of the DSBs were found to include chemical reactions with approximately 5% of DSBs caused only by chemical reactions. In conclusion, the TOPAS-nBio extension to the TOPAS MC application offers access to accurate and detailed multiscale simulations, from a macroscopic description of the radiation field to microscopic description of biological outcome for selected cells. TOPAS-nBio offers detailed physics and chemistry simulations of radiobiological experiments on cells simulating the initially induced damage and links to models of DNA repair kinetics.
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Affiliation(s)
- J Schuemann
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A L McNamara
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ramos-Méndez
- b Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - J Perl
- c SLAC National Accelerator Laboratory, Menlo Park, California
| | - K D Held
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - H Paganetti
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - S Incerti
- d CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.,e University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - B Faddegon
- b Department of Radiation Oncology, University of California San Francisco, San Francisco, California
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Schuemann J, McNamara AL, Warmenhoven JW, Henthorn NT, Kirkby KJ, Merchant MJ, Ingram S, Paganetti H, Held KD, Ramos-Mendez J, Faddegon B, Perl J, Goodhead DT, Plante I, Rabus H, Nettelbeck H, Friedland W, Kundrát P, Ottolenghi A, Baiocco G, Barbieri S, Dingfelder M, Incerti S, Villagrasa C, Bueno M, Bernal MA, Guatelli S, Sakata D, Brown JMC, Francis Z, Kyriakou I, Lampe N, Ballarini F, Carante MP, Davídková M, Štěpán V, Jia X, Cucinotta FA, Schulte R, Stewart RD, Carlson DJ, Galer S, Kuncic Z, Lacombe S, Milligan J, Cho SH, Sawakuchi G, Inaniwa T, Sato T, Li W, Solov'yov AV, Surdutovich E, Durante M, Prise KM, McMahon SJ. A New Standard DNA Damage (SDD) Data Format. Radiat Res 2018; 191:76-92. [PMID: 30407901 DOI: 10.1667/rr15209.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called "indirect" damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.
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Affiliation(s)
- J Schuemann
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A L McNamara
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J W Warmenhoven
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - N T Henthorn
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - K J Kirkby
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - M J Merchant
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - S Ingram
- b Division of Cancer Sciences, The University of Manchester, Manchester, United Kingdom
| | - H Paganetti
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - K D Held
- a Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - J Ramos-Mendez
- c Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - B Faddegon
- c Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - J Perl
- d SLAC National Accelerator Laboratory, Menlo Park, California
| | - D T Goodhead
- e Medical Research Council, Harwell, United Kingdom
| | | | - H Rabus
- g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.,h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - H Nettelbeck
- g Physikalisch-Technische Bundesanstalt (PTB), Braunschweig, Germany.,h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - W Friedland
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - P Kundrát
- i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - A Ottolenghi
- j Physics Department, University of Pavia, Pavia, Italy
| | - G Baiocco
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,j Physics Department, University of Pavia, Pavia, Italy
| | - S Barbieri
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,j Physics Department, University of Pavia, Pavia, Italy
| | - M Dingfelder
- k Department of Physics, East Carolina University, Greenville, North Carolina
| | - S Incerti
- l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France.,m University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - C Villagrasa
- h Task Group 6.2 "Computational Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany.,n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France
| | - M Bueno
- n Institut de Radioprotection et Sûreté Nucléaire, F-92262 Fontenay aux Roses Cedex, France
| | - M A Bernal
- o Applied Physics Department, Gleb Wataghin Institute of Physics, State University of Campinas, Campinas, SP, Brazil
| | - S Guatelli
- p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia
| | - D Sakata
- p Centre for Medical Radiation Physics, University of Wollongong, Wollongong, NSW, Australia
| | - J M C Brown
- q Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
| | - Z Francis
- r Department of Physics, Faculty of Science, Saint Joseph University, Beirut, Lebanon
| | - I Kyriakou
- s Medical Physics Laboratory, University of Ioannina Medical School, Ioannina, Greece
| | - N Lampe
- l CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - F Ballarini
- j Physics Department, University of Pavia, Pavia, Italy.,t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy
| | - M P Carante
- j Physics Department, University of Pavia, Pavia, Italy.,t Italian National Institute of Nuclear Physics, Section of Pavia, I-27100 Pavia, Italy
| | - M Davídková
- u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic
| | - V Štěpán
- u Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Řež, Czech Republic
| | - X Jia
- v Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F A Cucinotta
- w Health Physics and Diagnostic Sciences, University of Nevada Las Vegas, Las Vegas, Nevada
| | - R Schulte
- x Division of Biomedical Engineering Sciences, School of Medicine, Loma Linda University, Loma Linda, California
| | - R D Stewart
- y Department of Radiation Oncology, University of Washington, Seattle, Washington
| | - D J Carlson
- z Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut
| | - S Galer
- aa Medical Radiation Science Group, National Physical Laboratory, Teddington, United Kingdom
| | - Z Kuncic
- bb School of Physics, University of Sydney, Sydney, NSW, Australia
| | - S Lacombe
- cc Institut des Sciences Moléculaires d'Orsay (UMR 8214) University Paris-Sud, CNRS, University Paris-Saclay, 91405 Orsay Cedex, France
| | | | - S H Cho
- ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - G Sawakuchi
- ee Department of Radiation Physics and Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - T Inaniwa
- ff Department of Accelerator and Medical Physics, National Institute of Radiological Sciences, Chiba, Japan
| | - T Sato
- gg Japan Atomic Energy Agency, Nuclear Science and Engineering Center, Tokai 319-1196, Japan
| | - W Li
- i Institute of Radiation Protection, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,hh Task Group 7.7 "Internal Micro- and Nanodosimetry", European Radiation Dosimetry Group e.V., Neuherberg, Germany
| | - A V Solov'yov
- ii MBN Research Center, 60438 Frankfurt am Main, Germany
| | - E Surdutovich
- jj Department of Physics, Oakland University, Rochester, Michigan
| | - M Durante
- kk GSI Helmholtzzentrum für Schwerionenforschung, Biophysics Department, Darmstadt, Germany
| | - K M Prise
- ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - S J McMahon
- ll Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
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29
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Incerti S, Kyriakou I, Bernal MA, Bordage MC, Francis Z, Guatelli S, Ivanchenko V, Karamitros M, Lampe N, Lee SB, Meylan S, Min CH, Shin WG, Nieminen P, Sakata D, Tang N, Villagrasa C, Tran HN, Brown JMC. Geant4-DNA example applications for track structure simulations in liquid water: A report from the Geant4-DNA Project. Med Phys 2018; 45. [PMID: 29901835 DOI: 10.1002/mp.13048] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/03/2018] [Accepted: 06/04/2018] [Indexed: 01/11/2023] Open
Abstract
This Special Report presents a description of Geant4-DNA user applications dedicated to the simulation of track structures (TS) in liquid water and associated physical quantities (e.g., range, stopping power, mean free path…). These example applications are included in the Geant4 Monte Carlo toolkit and are available in open access. Each application is described and comparisons to recent international recommendations are shown (e.g., ICRU, MIRD), when available. The influence of physics models available in Geant4-DNA for the simulation of electron interactions in liquid water is discussed. Thanks to these applications, the authors show that the most recent sets of physics models available in Geant4-DNA (the so-called "option4" and "option 6" sets) enable more accurate simulation of stopping powers, dose point kernels, and W-values in liquid water, than the default set of models ("option 2") initially provided in Geant4-DNA. They also serve as reference applications for Geant4-DNA users interested in TS simulations.
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Affiliation(s)
- S Incerti
- University of Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
| | - I Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, 45110, Ioannina, Greece
| | - M A Bernal
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - M C Bordage
- Université Toulouse III-Paul Sabatier, UMR1037 CRCT, Toulouse, France
- Inserm, UMR1037 CRCT, Toulouse, France
| | - Z Francis
- Department of Physics, Faculty of Sciences, Université Saint Joseph, Beirut, Lebanon
| | - S Guatelli
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
- Illawarra Health & Medical Research Institute, University of Wollongong, Wollongong, Australia
| | - V Ivanchenko
- Geant4 Associates International Ltd., Hebden Bridge, UK
- Tomsk State University, Tomsk, Russia
| | - M Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - N Lampe
- Vicinity Centres, Data Science & Insights, Office Tower One, 1341 Dandenong Rd, Chadstone, Victoria, 3148, Australia
| | - S B Lee
- Proton Therapy Center, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, Korea
| | - S Meylan
- SymAlgo Technologies, 75 rue Léon Frot, 75011, Paris, France
| | - C H Min
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Korea
| | - W G Shin
- Department of Radiation Convergence Engineering, Yonsei University, Wonju, Korea
| | | | - D Sakata
- University of Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
- Centre for Medical Radiation Physics, University of Wollongong, Wollongong, Australia
| | - N Tang
- IRSN, Institut de Radioprotection et de Sureté Nucléaire, 92262, Fontenay-aux-Roses, France
| | - C Villagrasa
- IRSN, Institut de Radioprotection et de Sureté Nucléaire, 92262, Fontenay-aux-Roses, France
| | - H N Tran
- Division of Nuclear Physics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - J M C Brown
- Department of Radiation Science and Technology, Delft University of Technology, Delft, The Netherlands
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30
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Lampe N, Karamitros M, Breton V, Brown JMC, Kyriakou I, Sakata D, Sarramia D, Incerti S. Mechanistic DNA damage simulations in Geant4-DNA part 1: A parameter study in a simplified geometry. Phys Med 2018; 48:135-145. [PMID: 29628360 DOI: 10.1016/j.ejmp.2018.02.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/24/2017] [Accepted: 02/14/2018] [Indexed: 01/06/2023] Open
Abstract
Mechanistic modelling of DNA damage in Monte Carlo simulations is highly sensitive to the parameters that define DNA damage. In this work, we use a simple testing geometry to investigate how different choices of physics models and damage model parameters can change the estimation of DNA damage in a mechanistic DNA damage simulation built in Geant4-DNA. The choice of physics model can lead to variations by up to a factor of two in the yield of physically induced strand breaks, and the parameters that determine scavenging, and physical and chemical single strand break induction can have even larger consequences. Using low energy electrons as primary particles, a variety of parameters are tested in this geometry in order to arrive at a parameter set consistent with past simulation studies. We find that the modelling of scavenging can play an important role in determining results, and speculate that high-scavenging regimes, where only chemical radicals within 1 nm of DNA are simulated, could provide a good means of testing mechanistic DNA simulations.
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Affiliation(s)
- Nathanael Lampe
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, F-63000 Clermont-Ferrand, France; Université de Bordeaux, CNRS/IN2P3, CENBG, F-33175 Gradignan, France
| | | | - Vincent Breton
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, F-63000 Clermont-Ferrand, France
| | - Jeremy M C Brown
- Radiation Science and Technology, Delft University of Technology, Mekelweg 15, Delft 26295B, The Netherlands
| | - Ioanna Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Dousatsu Sakata
- Université de Bordeaux, CNRS/IN2P3, CENBG, F-33175 Gradignan, France
| | - David Sarramia
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, F-63000 Clermont-Ferrand, France
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, CENBG, F-33175 Gradignan, France.
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Lazarakis P, Incerti S, Ivanchenko V, Kyriakou I, Emfietzoglou D, Corde S, Rosenfeld AB, Lerch M, Tehei M, Guatelli S. Investigation of track structure and condensed history physics models for applications in radiation dosimetry on a micro and nano scale in Geant4. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aaa6aa] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Tello JJ, Incerti S, Francis Z, Tran H, Bernal MA. Numerical insight into the Dual Radiation Action Theory. Phys Med 2017; 43:120-126. [PMID: 29195554 DOI: 10.1016/j.ejmp.2017.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022] Open
Abstract
This work studies the first and second order mechanisms for the induction of lethal lesions in DNA after irradiation with protons and α-particles. The purpose is to numerically study the mechanisms behind the Dual Radiation Action Theory (DRAT) for these heavy particles. A genetic material geometrical model with atomic resolution is used. It accounts for the explicit position of 5.47 × 109 base pairs, organized up to the chromatin level. The GEANT4-DNA Monte Carlo code was employed to simulate the interaction of these ions with the genetic material model. The number of lethal lesions induced by one- and two-track mechanisms was determined as a function of dose. Values of the α/β ratio were estimated as well as corresponding relative biological effectiveness (RBE). The number of lethal lesions produced by one-track and two-track mechanisms depends on the dose and squared dose, respectively, as predicted by the DRAT. RBE values consistent with experimental results were found, at least for LET below ∼100 keV/μm. Double strand break spatial distributions are qualitatively analyzed. According to this work, the α parameter determined from cellular surviving curves depends on both the physical α and β parameters introduced here, and on the specific energy deposited by a single track into the region of interest. We found an increment of the β parameter with LET, yet at a slower rate than α so that the α/β ratio increases with LET. In addition, we observed and explained the saturation of the α parameter as the dose increases above ∼6 Gy.
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Affiliation(s)
- John J Tello
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, Brazil; University of Pavia, Physics Department, via Bassi 6, I-27100 Pavia, Italy; INFN-Sezione di Pavia, via Bassi 6, I-27100 Pavia, Italy
| | - Sébastien Incerti
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France; University of Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Ziad Francis
- Saint Joseph University, Faculty of Science, R.U. Mathematics and Modelling, Department of Physics, Beirut, Lebanon
| | - Hoang Tran
- IRFU/DPhN, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M A Bernal
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, Brazil.
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Meylan S, Incerti S, Karamitros M, Tang N, Bueno M, Clairand I, Villagrasa C. Simulation of early DNA damage after the irradiation of a fibroblast cell nucleus using Geant4-DNA. Sci Rep 2017; 7:11923. [PMID: 28931851 PMCID: PMC5607336 DOI: 10.1038/s41598-017-11851-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/30/2017] [Indexed: 01/17/2023] Open
Abstract
In order to improve the understanding of the mechanisms involved in the generation of early DNA damage, a new calculation chain based on the Geant4-DNA toolkit was developed. This work presents for the first time the simulation of the physical, physicochemical and chemical stages of early radiation damage at the scale of an entire human genome (fibroblast, male) and using Geant4-DNA models. The DnaFabric software was extended to generate and export this nucleus model to a text file with a specific format that can be read by Geant4 user applications. This calculation chain was used to simulate the irradiation of the nucleus by primary protons of different energies (0,5; 0,7; 0,8; 1; 1,5; 2; 3; 4; 5; 10; 20 MeV) and the results, in terms of DNA double strand breaks, agree with experimental data found in the literature (pulsed field electrophoresis technique). These results show that the simulation is consistent and that its parameters are well balanced. Among the different parameters that can be adjusted, our results demonstrate that the criterion used to select direct strand break appears to have a very significant role on the final number of simulated double strand breaks.
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Affiliation(s)
- Sylvain Meylan
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92962, Fontenay-aux-Roses, France.
| | - Sébastien Incerti
- Univ, Bordeaux, CENBG, UMR 5797, F-33170, Gradignan, France.,CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France
| | - Mathieu Karamitros
- CNRS, IN2P3, CENBG, UMR 5797, F-33170, Gradignan, France.,Notre Dame Radiation Laboratory, 102 Radiation Research Building Notre Dame, Indiana, 46556, USA
| | - Nicolas Tang
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92962, Fontenay-aux-Roses, France
| | - Marta Bueno
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92962, Fontenay-aux-Roses, France
| | - Isabelle Clairand
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92962, Fontenay-aux-Roses, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92962, Fontenay-aux-Roses, France.
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Guatelli S, Incerti S. Monte Carlo simulations for medical physics: From fundamental physics to cancer treatment. Phys Med 2017; 33:179-181. [PMID: 28111100 DOI: 10.1016/j.ejmp.2017.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/02/2017] [Indexed: 01/11/2023] Open
Affiliation(s)
- S Guatelli
- Centre For Medical Radiation Physics (CMRP), University of Wollongong (UOW), Wollongong, NSW, Australia.
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Lampe N, Biron DG, Brown JMC, Incerti S, Marin P, Maigne L, Sarramia D, Seznec H, Breton V. Simulating the Impact of the Natural Radiation Background on Bacterial Systems: Implications for Very Low Radiation Biological Experiments. PLoS One 2016; 11:e0166364. [PMID: 27851794 PMCID: PMC5112919 DOI: 10.1371/journal.pone.0166364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/27/2016] [Indexed: 11/19/2022] Open
Abstract
At very low radiation dose rates, the effects of energy depositions in cells by ionizing radiation is best understood stochastically, as ionizing particles deposit energy along tracks separated by distances often much larger than the size of cells. We present a thorough analysis of the stochastic impact of the natural radiative background on cells, focusing our attention on E. coli grown as part of a long term evolution experiment in both underground and surface laboratories. The chance per day that a particle track interacts with a cell in the surface laboratory was found to be 6 × 10-5 day-1, 100 times less than the expected daily mutation rate for E. coli under our experimental conditions. In order for the chance cells are hit to approach the mutation rate, a gamma background dose rate of 20 μGy hr-1 is predicted to be required.
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Affiliation(s)
- Nathanael Lampe
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - David G. Biron
- Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes Génome et Environnement, UMR CNRS 6023, BP 10448, F-63000 Clermont-Ferrand, France
| | - Jeremy M. C. Brown
- School of Mathematics and Physics, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Sébastien Incerti
- Université de Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Pierre Marin
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - Lydia Maigne
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - David Sarramia
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
| | - Hervé Seznec
- Université de Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France
- CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Vincent Breton
- Clermont Université, Université Blaise Pascal, CNRS/IN2P3, Laboratoire de Physique Corpusculaire, BP 10448, F-63000 Clermont-Ferrand, France
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Belov OV, Batmunkh M, Incerti S, Lkhagva O. Radiation damage to neuronal cells: Simulating the energy deposition and water radiolysis in a small neural network. Phys Med 2016; 32:1510-1520. [PMID: 27865670 DOI: 10.1016/j.ejmp.2016.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/21/2023] Open
Abstract
Radiation damage to the central nervous system (CNS) has been an on-going challenge for the last decades primarily due to the issues of brain radiotherapy and radiation protection for astronauts during space travel. Although recent findings revealed a number of molecular mechanisms associated with radiation-induced impairments in behaviour and cognition, some uncertainties exist in the initial neuronal cell injury leading to the further development of CNS malfunction. The present study is focused on the investigation of early biological damage induced by ionizing radiations in a sample neural network by means of modelling physico-chemical processes occurring in the medium after exposure. For this purpose, the stochastic simulation of incident particle tracks and water radiation chemistry was performed in realistic neuron phantoms constructed using experimental data on cell morphology. The applied simulation technique is based on using Monte-Carlo processes of the Geant4-DNA toolkit. The calculations were made for proton, 12C, and 56Fe particles of different energy within a relatively wide range of linear energy transfer values from a few to hundreds of keV/μm. The results indicate that the neuron morphology is an important factor determining the accumulation of microscopic radiation dose and water radiolysis products in neurons. The estimation of the radiolytic yields in neuronal cells suggests that the observed enhancement in the levels of reactive oxygen species may potentially lead to oxidative damage to neuronal components disrupting the normal communication between cells of the neural network.
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Affiliation(s)
- Oleg V Belov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia.
| | - Munkhbaatar Batmunkh
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, 6 Joliot-Curie St., 141980 Dubna, Moscow Region, Russia
| | - Sébastien Incerti
- Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan, France; CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Oidov Lkhagva
- Natural Science Division, National University of Mongolia, 1 University St., 210646 Ulaanbaatar, Mongolia
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Lampe N, Marin P, Castor J, Warot G, Incerti S, Maigne L, Sarramia D, Breton V. Background study of absorbed dose in biological experiments at the Modane Underground Laboratory. EPJ Web Conf 2016. [DOI: 10.1051/epjconf/201612400006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kyriakou I, Incerti S, Francis Z. Technical Note: Improvements in geant4 energy-loss model and the effect on low-energy electron transport in liquid water. Med Phys 2016; 42:3870-6. [PMID: 26133588 DOI: 10.1118/1.4921613] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE The geant4-DNA physics models are upgraded by a more accurate set of electron cross sections for ionization and excitation in liquid water. The impact of the new developments on low-energy electron transport simulations by the geant4 Monte Carlo toolkit is examined for improving its performance in dosimetry applications at the subcellular and nanometer level. METHODS The authors provide an algorithm for an improved implementation of the Emfietzoglou model dielectric response function of liquid water used in the geant4-DNA existing model. The algorithm redistributes the imaginary part of the dielectric function to ensure a physically motivated behavior at the binding energies, while retaining all the advantages of the original formulation, e.g., the analytic properties and the fulfillment of the f-sum-rule. In addition, refinements in the exchange and perturbation corrections to the Born approximation used in the geant4-DNA existing model are also made. RESULTS The new ionization and excitation cross sections are significantly different from those of the geant4-DNA existing model. In particular, excitations are strongly enhanced relative to ionizations, resulting in higher W-values and less diffusive dose-point-kernels at sub-keV electron energies. CONCLUSIONS An improved energy-loss model for the excitation and ionization of liquid water by low-energy electrons has been implemented in geant4-DNA. The suspiciously low W-values and the unphysical long tail in the dose-point-kernel have been corrected owing to a different partitioning of the dielectric function.
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Affiliation(s)
- I Kyriakou
- Medical Physics Laboratory, University of Ioannina Medical School, Ioannina 45110, Greece
| | - S Incerti
- Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, Université de Bordeaux, Gradignan 33175, France and Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, CNRS/IN2P3, Gradignan 33175, France
| | - Z Francis
- Department of Physics, Faculty of Sciences, Saint Joseph University, Mkalles, Beirut, Lebanon
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Francis Z, Seif E, Incerti S, Champion C, Karamitros M, Bernal MA, Ivanchenko VN, Mantero A, Tran HN, El Bitar Z. Carbon ion fragmentation effects on the nanometric level behind the Bragg peak depth. Phys Med Biol 2016; 59:7691-702. [PMID: 25415376 DOI: 10.1088/0031-9155/59/24/7691] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In this study, fragmentation yields of carbon therapy beams are estimated using the Geant4 simulation toolkit version 9.5. Simulations are carried out in a step-by-step mode using the Geant4-DNA processes for each of the major contributing fragments. The energy of the initial beam is taken 400 MeV amu(-1) as this is the highest energy, which is used for medical accelerators and this would show the integral role of secondary contributions in radiotherapy irradiations. The obtained results showed that 64% of the global dose deposition is initiated by carbon ions, while up to 36% is initiated by the produced fragments including all their isotopes. The energy deposition clustering yields of each of the simulated fragments are then estimated using the DBSCAN clustering algorithm and they are compared to the yields of the incident primary beam.
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Affiliation(s)
- Z Francis
- Faculty of Sciences, Department of Physics, Université Saint Joseph, Beirut, Lebanon
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Incerti S, Bordage MC, Bardiès M, Bordy JM, Gschwind R. Preface. EPJ Web Conf 2016. [DOI: 10.1051/epjconf/201612400001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Incerti S, Bordage MC, Bardiès M, Bordy JM, Gschwind R. Opening address. EPJ Web Conf 2016. [DOI: 10.1051/epjconf/201612400002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Apostolakis J, Asai M, Bagulya A, Brown JMC, Burkhardt H, Chikuma N, Cortes-Giraldo MA, Elles S, Grichine V, Guatelli S, Incerti S, Ivanchenko VN, Jacquemier J, Kadri O, Maire M, Pandola L, Sawkey D, Toshito T, Urban L, Yamashita T. Progress in Geant4 Electromagnetic Physics Modelling and Validation. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/1742-6596/664/7/072021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ambrožová I, Vondráček V, Šefl M, Štěpán V, Pachnerová Brabcová K, Ploc O, Incerti S, Davídková M. Microdosimetry for a carbon ion beam using track-etched detectors. Radiat Prot Dosimetry 2015; 166:247-252. [PMID: 25862534 DOI: 10.1093/rpd/ncv131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Track-etched detectors (TED) have been used as linear energy transfer (LET) spectrometers in heavy ion beams for many years. LET spectra and depth-dose distribution of a carbon ion beam were measured behind polymethylmethacrylate degraders at Heavy Ion Medical Accelerator in Chiba, Japan. The measurements were performed along monoenergetic beam with energy 290 MeV u(-1) in different positions: (1) at beam extraction area, (2) at beginning, (3) maximum and (4) behind the Bragg peak region (0, 117, 147 and 151 mm of water-equivalent depth, respectively). The LET spectra inside and outside of the primary ion beam have been evaluated. TED record only heavy charged particles with LET above 8-10 keV µm(-1), while electrons and ions with lower LET are not detected. The Geant4 simulation toolkit version 4.9.6.P01 has been used to estimate the contribution of non-detected particles to absorbed dose. Presented results demonstrate the applicability of TED for microdosimetry measurements in therapeutic carbon ion beams.
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Affiliation(s)
- I Ambrožová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - V Vondráček
- Proton Therapy Center, Budínova 2437/1a, Prague 180 00, Czech Republic
| | - M Šefl
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, Prague 115 19, Czech Republic
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, Gradignan 33175, France
| | - K Pachnerová Brabcová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic Department of Applied Physics, Chalmers University of Technology, Fysikgränd 3, Göteborg SE-412 96, Sweden
| | - O Ploc
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, Gradignan 33175, France
| | - M Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
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Pachnerová Brabcová K, Štěpán V, Karamitros M, Karabín M, Dostálek P, Incerti S, Davídková M, Sihver L. Contribution of indirect effects to clustered damage in DNA irradiated with protons. Radiat Prot Dosimetry 2015; 166:44-48. [PMID: 25897140 DOI: 10.1093/rpd/ncv159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protons are the dominant particles both in galactic cosmic rays and in solar particle events and, furthermore, proton irradiation becomes increasingly used in tumour treatment. It is believed that complex DNA damage is the determining factor for the consequent cellular response to radiation. DNA plasmid pBR322 was irradiated at U120-M cyclotron with 30 MeV protons and treated with two Escherichia coli base excision repair enzymes. The yields of SSBs and DSBs were analysed using agarose gel electrophoresis. DNA has been irradiated in the presence of hydroxyl radical scavenger (coumarin-3-carboxylic acid) in order to distinguish between direct and indirect damage of the biological target. Pure scavenger solution was used as a probe for measurement of induced OH· radical yields. Experimental OH· radical yield kinetics was compared with predictions computed by two theoretical models-RADAMOL and Geant4-DNA. Both approaches use Geant4-DNA for description of physical stages of radiation action, and then each of them applies a distinct model for description of the pre-chemical and chemical stage.
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Affiliation(s)
- K Pachnerová Brabcová
- Department of Applied Physics, Chalmers University of Technology, Fysikgränd 3, Göteborg SE-412 96, Sweden Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - V Štěpán
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - M Karamitros
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France
| | - M Karabín
- Department of Biotechnology, Institute of Chemical Technology Prague, Technická 5, Prague 166 28, Czech Republic
| | - P Dostálek
- Department of Biotechnology, Institute of Chemical Technology Prague, Technická 5, Prague 166 28, Czech Republic
| | - S Incerti
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux-Gradignan, CENBG, Chemin du Solarium, BP 120, 33175 Gradignan, France
| | - M Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Na Truhlářce 39/64, Prague 180 00, Czech Republic
| | - L Sihver
- Department of Applied Physics, Chalmers University of Technology, Fysikgränd 3, Göteborg SE-412 96, Sweden Atominstitut, TU Wien, Stadionallee 2, 1020 Vienna, Austria
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Byrne HL, Domanova W, McNamara AL, Incerti S, Kuncic Z. The cytoplasm as a radiation target: an in silico study of microbeam cell irradiation. Phys Med Biol 2015; 60:2325-37. [PMID: 25715947 DOI: 10.1088/0031-9155/60/6/2325] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We performed in silico microbeam cell irradiation modelling to quantitatively investigate ionisations resulting from soft x-ray and alpha particle microbeams targeting the cytoplasm of a realistic cell model. Our results on the spatial distribution of ionisations show that as x-rays are susceptible to scatter within a cell that can lead to ionisations in the nucleus, soft x-ray microbeams may not be suitable for investigating the DNA damage response to radiation targeting the cytoplasm alone. In contrast, ionisations from an ideal alpha microbeam are tightly confined to the cytoplasm, but a realistic alpha microbeam degrades upon interaction with components upstream of the cellular target. Thus it is difficult to completely rule out a contribution from alpha particle hits to the nucleus when investigating DNA damage response to cytoplasmic irradiation. We find that although the cytoplasm targeting efficiency of an alpha microbeam is better than that of a soft x-ray microbeam (the probability of stray alphas hitting the nucleus is 0.2% compared to 3.6% for x-rays), stray alphas produce more ionisations in the nucleus and thus have greater potential for initiating damage responses therein. Our results suggest that observed biological responses to cytoplasmic irradiation include a small component that can be attributed to stray ionisations in the nucleus resulting from the stochastic nature of particle interactions that cause out-of-beam scatter. This contribution is difficult to isolate experimentally, thus demonstrating the value of the in silico approach.
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Affiliation(s)
- H L Byrne
- Institute of Medical Physics, School of Physics, University of Sydney, NSW 2006, Australia
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Incerti S. Special section: selected papers from the Geant4 2013 international user conference at the physics-medicine-biology frontier. Phys Med Biol 2014; 59:7565-71. [DOI: 10.1088/0031-9155/59/24/7565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Dos Santos M, Clairand I, Gruel G, Barquinero JF, Incerti S, Villagrasa C. Influence of chromatin condensation on the number of direct DSB damages induced by ions studied using a Monte Carlo code. Radiat Prot Dosimetry 2014; 161:469-473. [PMID: 24615262 DOI: 10.1093/rpd/ncu029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The purpose of this work is to evaluate the influence of the chromatin condensation on the number of direct double-strand break (DSB) damages induced by ions. Two geometries of chromosome territories containing either condensed or decondensed chromatin were implemented as biological targets in the Geant4 Monte Carlo simulation code and proton and alpha irradiation was simulated using the Geant4-DNA processes. A DBSCAN algorithm was used in order to detect energy deposition clusters that could give rise to single-strand breaks or DSBs on the DNA molecule. The results of this study show an increase in the number and complexity of DNA DSBs in condensed chromatin when compared with decondensed chromatin.
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Affiliation(s)
- M Dos Santos
- Institut de Radioprotection et de Sureté Nucléaire, IRSN, BP17, Fontenay aux roses 92962, France
| | - I Clairand
- Institut de Radioprotection et de Sureté Nucléaire, IRSN, BP17, Fontenay aux roses 92962, France
| | - G Gruel
- Institut de Radioprotection et de Sureté Nucléaire, IRSN, BP17, Fontenay aux roses 92962, France
| | - J F Barquinero
- Institut de Radioprotection et de Sureté Nucléaire, IRSN, BP17, Fontenay aux roses 92962, France
| | - S Incerti
- Centre d'Etudes Nucléaires de Bordeaux Gradignan, CENBG, Université de Bordeaux 1, CNRS/IN2P3, chemin du solarium, BP 120, Gradignan 33175, France
| | - C Villagrasa
- Institut de Radioprotection et de Sureté Nucléaire, IRSN, BP17, Fontenay aux roses 92962, France
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Shin J, Park S, Jeong J, Jeong C, Lim Y, SHIN D, Incerti S, Lee S. SU-E-T-241: Monte Carlo Simulation Study About the Prediction of Proton-Induced DNA Strand Breakage On the Double Helix Structure. Med Phys 2014. [DOI: 10.1118/1.4888572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Perrot Y, Payno H, Delage E, Incerti S, Debiton E, Peyrode C, Chezal J, Miot-Noirault E, Degoul F, Maigne L. SU-E-T-565: RAdiation Resistance of Cancer CElls Using GEANT4 DNA: RACE. Med Phys 2014. [DOI: 10.1118/1.4888900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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