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Fois GR, Tran HN, Fiegel V, Blain G, Chiavassa S, Craff E, Delpon G, Evin M, Haddad F, Incerti S, Koumeir C, Métivier V, Mouchard Q, Poirier F, Potiron V, Servagent N, Vandenborre J, Maigne L. Monte Carlo simulations of microdosimetry and radiolytic species production at long time post proton irradiation using GATE and Geant4-DNA. Med Phys 2024. [PMID: 38976841 DOI: 10.1002/mp.17281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/29/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Radiobiological effectiveness of radiation in cancer treatment can be studied at different scales (molecular till organ scale) and different time post irradiation. The production of free radicals and reactive oxygen species during water radiolysis is particularly relevant to understand the fundamental mechanisms playing a role in observed biological outcomes. The development and validation of Monte Carlo tools integrating the simulation of physical, physico-chemical and chemical stages after radiation is very important to maintain with experiments. PURPOSE Therefore, in this study, we propose to validate a new Geant4-DNA chemistry module through the simulation of water radiolysis and Fricke dosimetry experiments on a proton preclinical beam line. MATERIAL AND METHODS In this study, we used the GATE Monte Carlo simulation platform (version 9.3) to simulate a 67.5 MeV proton beam produced with the ARRONAX isochronous cyclotron (IBA Cyclone 70XP) at conventional dose rate (0.2 Gy/s) to simulate the irradiation of ultra-pure liquid water samples and Fricke dosimeter. We compared the depth dose profile with measurements performed with a plane parallel Advanced PTW 34045 Markus ionization chamber. Then, a new Geant4-DNA chemistry application proposed from Geant4 version 11.2 has been used to assess the evolution ofHO • ${\mathrm{HO}}^ \bullet $ ,e aq - ${\mathrm{e}}_{{\mathrm{aq}}}^ - $ ,H 3 O + ${{\mathrm{H}}}_3{{\mathrm{O}}}^ + $ ,H 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ ,H 2 ${{\mathrm{H}}}_2$ ,HO 2 • ${\mathrm{HO}}_2^ \bullet $ ,HO 2 - , O 2 • - ${\mathrm{HO}}_2^ - ,{\mathrm{\ O}}_2^{ \bullet - }$ andHO - ${\mathrm{HO}}^ - $ reactive species along time until 1-h post-irradiation. In particular, the effect of oxygen and pH has been investigated through comparisons with experimental measurements of radiolytic yields forH 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ and Fe3+. RESULTS GATE simulations reproduced, within 4%, the depth dose profile in liquid water. With Geant4-DNA, we were able to reproduce experimentalH 2 O 2 ${{\mathrm{H}}}_2{{\mathrm{O}}}_2$ radiolytic yields 1-h post-irradiation in aerated and deaerated conditions, showing the impact of small changes in oxygen concentrations on species evolution along time. For the Fricke dosimeter, simulated G(Fe3+) is 15.97 ± 0.2 molecules/100 eV which is 11% higher than the measured value (14.4 ± 04 molecules/100 eV). CONCLUSIONS These results aim to be consolidated by new comparisons involving other radiolytic species, such ase aq - ${\mathrm{e}}_{{\mathrm{aq}}}^ - $ or, O 2 • - $,{\mathrm{\ O}}_2^{ \bullet - }$ to further study the mechanisms underlying the FLASH effect observed at ultra-high dose rates (UHDR).
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Affiliation(s)
| | | | | | - Guillaume Blain
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | | | | | - Grégory Delpon
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
| | - Manon Evin
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Ferid Haddad
- GIP ARRONAX, Saint-Herblain, France
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | | | | | - Vincent Métivier
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Quentin Mouchard
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | | | - Vincent Potiron
- Institut de Cancérologie de l'Ouest, Saint-Herblain, France
- Université de Nantes, CNRS, US2B, Saint-Herblain, France
| | - Noël Servagent
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Johan Vandenborre
- Université de Nantes, IMT Atlantique, CNRS, Laboratoire SUBATECH, Nantes, France
| | - Lydia Maigne
- Université Clermont-Auvergne, CNRS, LPCA, Clermont-Ferrand, France
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Tran HN, Archer J, Baldacchino G, Brown JMC, Chappuis F, Cirrone GAP, Desorgher L, Dominguez N, Fattori S, Guatelli S, Ivantchenko V, Méndez JR, Nieminen P, Perrot Y, Sakata D, Santin G, Shin WG, Villagrasa C, Zein S, Incerti S. Review of chemical models and applications in Geant4-DNA: Report from the ESA BioRad III Project. Med Phys 2024. [PMID: 38889367 DOI: 10.1002/mp.17256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/20/2024] Open
Abstract
A chemistry module has been implemented in Geant4-DNA since Geant4 version 10.1 to simulate the radiolysis of water after irradiation. It has been used in a number of applications, including the calculation of G-values and early DNA damage, allowing the comparison with experimental data. Since the first version, numerous modifications have been made to the module to improve the computational efficiency and extend the simulation to homogeneous kinetics in bulk solution. With these new developments, new applications have been proposed and released as Geant4 examples, showing how to use chemical processes and models. This work reviews the models implemented and application developments for modeling water radiolysis in Geant4-DNA as reported in the ESA BioRad III Project.
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Affiliation(s)
| | - Jay Archer
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, LIDYL, Gif-sur-Yvette, France
- CY Cergy Paris Université, CEA, LIDYL, Gif-sur-Yvette, France
| | - Jeremy M C Brown
- Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, Australia
| | - Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Antonio Pablo Cirrone
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud (LNS), Catania, Italy
- Centro Siciliano di Fisica Nucleare e Struttura della Materia, Catania, Italy
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Naoki Dominguez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Serena Fattori
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud (LNS), Catania, Italy
| | - Susanna Guatelli
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - José-Ramos Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | | | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Dousatsu Sakata
- Centre For Medical and Radiation Physics, University of Wollongong, Wollongong, New South Wales, Australia
- Division of Health Sciences, Osaka University, Osaka, Japan
- School of Physics, University of Bristol, Bristol, UK
| | | | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts, USA
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Fontenay-aux-Roses, France
| | - Sara Zein
- Univ. Bordeaux, CNRS, LP2I, UMR 5797, Gradignan, France
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Toigawa T, Kai T, Kumagai Y, Yokoya A. Consideration of the dielectric response for radiation chemistry simulations. J Chem Phys 2024; 160:214119. [PMID: 38836449 DOI: 10.1063/5.0211089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
The spur reaction, a spatially nonhomogeneous chemical reaction following ionization, is crucial in radiolysis or photolysis in liquids, but the spur expansion process has yet to be elucidated. One reason is the need to understand the role of the dielectric response of the solvating molecules surrounding the charged species generated by ionization. The dielectric response corresponds to the time evolution of the permittivity and might affect the chemical reaction-diffusion of the species in a spur expansion process. This study examined the competitive relationship between reaction-diffusion kinetics and the dielectric response by solving the Debye-Smoluchowski equation while considering the dielectric response. The Coulomb force between the charged species gradually decreases with the dielectric response. Our calculation results found a condition where fast recombination occurs before the dielectric response is complete. Although it has been reported that the primary G-values of free electrons depend on the static dielectric constant under low-linear-energy transfer radiation-induced ionization, we propose that considering the dielectric response can provide a deeper insight into fast recombination reactions under high-linear-energy transfer radiation- or photo-induced ionization. Our simulation method enables the understanding of fast radiation-induced phenomena in liquids.
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Affiliation(s)
- Tomohiro Toigawa
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Takeshi Kai
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Yuta Kumagai
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi 263-8555, Japan
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Rafiepour P, Sina S, Amoli ZA, Shekarforoush SS, Farajzadeh E, Mortazavi SMJ. A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study. Phys Eng Sci Med 2024:10.1007/s13246-024-01424-x. [PMID: 38652348 DOI: 10.1007/s13246-024-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Sedigheh Sina
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
- Radiation research center, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
| | - Zahra Alizadeh Amoli
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ebrahim Farajzadeh
- Secondary Standard Dosimetry Laboratory (SSDL), Pars Isotope Co, Karaj, Iran
| | - Seyed Mohammad Javad Mortazavi
- Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
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Matsuya Y, Yoshii Y, Kusumoto T, Akamatsu K, Hirata Y, Sato T, Kai T. A step-by-step simulation code for estimating yields of water radiolysis species based on electron track-structure mode in the PHITS code. Phys Med Biol 2024; 69:035005. [PMID: 38157551 DOI: 10.1088/1361-6560/ad199b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Objective. Time-dependent yields of chemical products resulting from water radiolysis play a great role in evaluating DNA damage response after exposure to ionizing radiation. Particle and Heavy Ion Transport code System (PHITS) is a general-purpose Monte Carlo simulation code for radiation transport, which simulates atomic interactions originating from discrete energy levels of ionizations and electronic excitations as well as molecular excitations as physical stages. However, no chemical code for simulating water radiolysis products exists in the PHITS package.Approach.Here, we developed a chemical simulation code dedicated to the PHITS code, hereafter calledPHITS-Chemcode, which enables the calculation of theGvalues of water radiolysis species (•OH, eaq-, H2, H2O2etc) by electron beams.Main results.The estimatedGvalues during 1 μs are in agreement with the experimental ones and other simulations. ThisPHITS-Chemcode also simulates the radiolysis in the presence of OH radical scavengers, such as tris(hydroxymethyl)aminomethane and dimethyl sulfoxide. Thank to this feature, the contributions of direct and indirect effects on DNA damage induction under various scavenging capacities can be analyzed.Significance.This chemical code coupled with PHITS could contribute to elucidating the mechanism of radiation effects by connecting physical, physicochemical, and chemical processes.
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Affiliation(s)
- Yusuke Matsuya
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
- Faculty of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yuji Yoshii
- Department of Radiological Technology, Faculty of Health Sciences, Hokkaido University of Science, Maeda 7-15, Teine-ku, Sapporo 006-8585, Japan
| | - Tamon Kusumoto
- National Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, 263-8555 Chiba, Japan
| | - Ken Akamatsu
- Institute for Quantum life Science, Quantum Life and Medical Science Directorate, National Institutes of Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa-shi, Kyoto, 619-0215, Japan
| | - Yuho Hirata
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
| | - Tatsuhiko Sato
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
| | - Takeshi Kai
- Nuclear Science and Engineering Center, Research Group for Radiation Transport Analysis, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
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Bradshaw G, O'Leary M, Purser ASF, Villagomez-Bernabe B, Wyett C, Currell F, Webb M. A new approach for simulating inhomogeneous chemical kinetics. Sci Rep 2023; 13:14010. [PMID: 37640793 PMCID: PMC10462703 DOI: 10.1038/s41598-023-39741-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/30/2023] [Indexed: 08/31/2023] Open
Abstract
In this paper, inhomogeneous chemical kinetics are simulated by describing the concentrations of interacting chemical species by a linear expansion of basis functions in such a manner that the coupled reaction and diffusion processes are propagated through time efficiently by tailor-made numerical methods. The approach is illustrated through modelling [Formula: see text]- and [Formula: see text]-radiolysis in thin layers of water and at their solid interfaces from the start of the chemical phase until equilibrium was established. The method's efficiency is such that hundreds of such systems can be modelled in a few hours using a single core of a typical laptop, allowing the investigation of the effects of the underlying parameter space. Illustrative calculations showing the effects of changing dose-rate and water-layer thickness are presented. Other simulations are presented which show the approach's capability to solve problems with spherical symmetry (an approximation to an isolated radiolytic spur), where the hollowing out of an initial Gaussian distribution is observed, in line with previous calculations. These illustrative simulations show the generality and the computational efficiency of this approach to solving reaction-diffusion problems. Furthermore, these example simulations illustrate the method's suitability for simulating solid-fluid interfaces, which have received a lot of experimental attention in contrast to the lack of computational studies.
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Affiliation(s)
- Georgia Bradshaw
- Department of Mathematics, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK.
| | - Mel O'Leary
- Department of Chemistry, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- Dalton Cumbrian Facility, West Lakes Science and Technology Park, Moor Row, CA24 3HA, UK
| | - Arthur S F Purser
- Department of Chemistry, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
| | - Balder Villagomez-Bernabe
- Department of Chemistry, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- Dalton Cumbrian Facility, West Lakes Science and Technology Park, Moor Row, CA24 3HA, UK
- St Luke's Cancer Centre, The Royal Hospital, Egerton Rd, Guildford, GU2 7XX, UK
| | - Cyrus Wyett
- Department of Chemistry, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- Dalton Cumbrian Facility, West Lakes Science and Technology Park, Moor Row, CA24 3HA, UK
| | - Frederick Currell
- Department of Chemistry, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
- Dalton Cumbrian Facility, West Lakes Science and Technology Park, Moor Row, CA24 3HA, UK
| | - Marcus Webb
- Department of Mathematics, University of Manchester, Oxford Rd, Manchester, M13 9PL, UK
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Bian J, Duran J, Shin WG, Ramos-Méndez J, Sankey JC, Childress L, Seuntjens J, Enger SA. GEANT4-DNA simulation of temperature-dependent and pH-dependent yields of chemical radiolytic species. Phys Med Biol 2023; 68:124002. [PMID: 37230081 DOI: 10.1088/1361-6560/acd90d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/25/2023] [Indexed: 05/27/2023]
Abstract
Objective.GEANT4-DNA can simulate radiation chemical yield (G-value) for radiolytic species such as the hydrated electron (eaq-) with the independent reaction times (IRT) method, however, only at room temperature and neutral pH. This work aims to modify the GEANT4-DNA source code to enable the calculation ofG-values for radiolytic species at different temperatures and pH values.Approach.In the GEANT4-DNA source code, values of chemical parameters such as reaction rate constant, diffusion coefficient, Onsager radius, and water density were replaced by corresponding temperature-dependent polynomials. The initial concentration of hydrogen ion (H+)/hydronium ion (H3O+) was scaled for a desired pH using the relationship pH = -log10[H+]. To validate our modifications, two sets of simulations were performed. (A) A water cube with 1.0 km sides and a pH of 7 was irradiated with an isotropic electron source of 1 MeV. The end time was 1μs. The temperatures varied from 25 °C to 150 °C. (B) The same setup as (A) was used, however, the temperature was set to 25 °C while the pH varied from 5 to 9. The results were compared with published experimental and simulated work.Main results.The IRT method in GEANT4-DNA was successfully modified to simulateG-values for radiolytic species at different temperatures and pH values. Our temperature-dependent results agreed with experimental data within 0.64%-9.79%, and with simulated data within 3.52%-12.47%. The pH-dependent results agreed well with experimental data within 0.52% to 3.19% except at a pH of 5 (15.99%) and with simulated data within 4.40%-5.53%. The uncertainties were below ±0.20%. Overall our results agreed better with experimental than simulation data.Significance.Modifications in the GEANT4-DNA code enabled the calculation ofG-values for radiolytic species at different temperatures and pH values.
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Affiliation(s)
- Jingyi Bian
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Juan Duran
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Wook-Geun Shin
- Physics Division, Department of Radiation Oncology, Massachusetts General Hospital & Harvard Medical School, Boston, MA-02114, United States of America
| | - Jose Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, CA, United States of America
| | - Jack C Sankey
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Lilian Childress
- Department of Physics, McGill University, Montreal, Quebec, Canada
| | - Jan Seuntjens
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Shirin A Enger
- Medical Physics Unit, Department of Oncology, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Chappuis F, Tran HN, Zein SA, Bailat C, Incerti S, Bochud F, Desorgher L. The general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension to investigate mechanisms underlying the FLASH effect in radiotherapy: Current status and challenges. Phys Med 2023; 110:102601. [PMID: 37201453 DOI: 10.1016/j.ejmp.2023.102601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023] Open
Abstract
FLASH radiotherapy is a promising approach to cancer treatment that offers several advantages over conventional radiotherapy. With this novel technique, high doses of radiation are delivered in a short period of time, inducing the so-called FLASH effect - a phenomenon characterized by healthy tissue sparing without alteration of tumor control. The mechanisms behind the FLASH effect remain unknown. One way to approach this problem is to gain insight into the initial parameters that can distinguish FLASH from conventional irradiation by simulating particle transport in aqueous media using the general-purpose Geant4 Monte Carlo toolkit and its Geant4-DNA extension. This review article discusses the current status of Geant4 and Geant4-DNA simulations to investigate mechanisms underlying the FLASH effect, as well as the challenges faced in this research field. One of the primary challenges is to accurately simulate the experimental irradiation parameters. Another challenge is the temporal extension of the simulations. This review also focuses on two hypotheses to explain the FLASH effect - namely the oxygen depletion hypothesis and the inter-track interactions hypothesis - and discusses how the Geant4 toolkit can be used to investigate them. The aim of this review is to provide an overview of Geant4 and Geant4-DNA simulations for FLASH radiotherapy and to highlight the challenges that need to be overcome in order to better study the FLASH effect.
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Affiliation(s)
- Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Hoang Ngoc Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Sara A Zein
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Claude Bailat
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Sébastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - François Bochud
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland.
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9
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Chappuis F, Grilj V, Tran HN, Zein SA, Bochud F, Bailat C, Incerti S, Desorgher L. Modeling of scavenging systems in water radiolysis with Geant4-DNA. Phys Med 2023; 108:102549. [PMID: 36921424 DOI: 10.1016/j.ejmp.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE This paper presents the capabilities of the Geant4-DNA Monte Carlo toolkit to simulate water radiolysis with scavengers using the step-by-step (SBS) or the independent reaction times (IRT) methods. It features two examples of application areas: (1) computing the escape yield of H2O2 following a 60Co γ-irradiation and (2) computing the oxygen depletion in water irradiated with 1 MeV electrons. METHODS To ease the implementation of the chemical stage in Geant4-DNA, we developed a user interface that helps define the chemical reactions and set the concentration of scavengers. The first application area example required two computational steps to perform water radiolysis using NO2- and NO3- as scavengers and a 60Co irradiation. The oxygen depletion computation technique for the second application area example consisted of simulating track segments of 1 MeV electrons and determining the radio-induced loss and gain of oxygen molecules. RESULTS The production of H2O2 under variable scavenging levels is consistent with the literature; the mean relative difference between the SBS and IRT methods is 7.2 % ± 0.5 %. For the oxygen depletion 1 µs post-irradiation, the mean relative difference between both methods is equal to 9.8 % ± 0.3 %. The results in the microsecond scale depend on the initial partial pressure of oxygen in water. In addition, the computed oxygen depletions agree well with the literature. CONCLUSIONS The Geant4-DNA toolkit makes it possible to simulate water radiolysis in the presence of scavengers. This feature offers perspectives in radiobiology, with the possibility of simulating cell-relevant scavenging mechanisms.
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Affiliation(s)
- Flore Chappuis
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Veljko Grilj
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Hoang Ngoc Tran
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Sara A Zein
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - François Bochud
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Claude Bailat
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland
| | - Sébastien Incerti
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, F-33170 Gradignan, France
| | - Laurent Desorgher
- Institute of Radiation Physics (IRA), Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland.
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10
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Kai T, Toigawa T, Matsuya Y, Hirata Y, Tezuka T, Tsuchida H, Yokoya A. Initial yield of hydrated electron production from water radiolysis based on first-principles calculation. RSC Adv 2023; 13:7076-7086. [PMID: 36875880 PMCID: PMC9977407 DOI: 10.1039/d2ra07274b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/16/2023] [Indexed: 03/05/2023] Open
Abstract
Many scientific insights into water radiolysis have been applied for developing life science, including radiation-induced phenomena, such as DNA damage and mutation induction or carcinogenesis. However, the generation mechanism of free radicals due to radiolysis remains to be fully understood. Consequently, we have encountered a crucial problem in that the initial yields connecting radiation physics to chemistry must be parameterized. We have been challenged in the development of a simulation tool that can unravel the initial free radical yields, from physical interaction by radiation. The presented code enables the first-principles calculation of low energy secondary electrons resulting from the ionization, in which the secondary electron dynamics are simulated while considering dominant collision and polarization effects in water. In this study, using this code, we predicted the yield ratio between ionization and electronic excitation from a delocalization distribution of secondary electrons. The simulation result presented a theoretical initial yield of hydrated electrons. In radiation physics, the initial yield predicted from parameter analysis of radiolysis experiments in radiation chemistry was successfully reproduced. Our simulation code helps realize a reasonable spatiotemporal connection from radiation physics to chemistry, which would contribute to providing new scientific insights for precise understanding of underlying mechanisms of DNA damage induction.
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Affiliation(s)
- Takeshi Kai
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency 2-4 Shirane Shirakata, Tokai-mura, Naka-gun Ibaraki 319-1195 Japan
| | - Tomohiro Toigawa
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency 2-4 Shirane Shirakata, Tokai-mura, Naka-gun Ibaraki 319-1195 Japan
| | - Yusuke Matsuya
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency 2-4 Shirane Shirakata, Tokai-mura, Naka-gun Ibaraki 319-1195 Japan.,Faculty of Health Sciences, Hokkaido University Kita-12 Nishi-5, Kita-ku Sapporo Hokkaido 060-0812 Japan
| | - Yuho Hirata
- Nuclear Science and Engineering Center, Japan Atomic Energy Agency 2-4 Shirane Shirakata, Tokai-mura, Naka-gun Ibaraki 319-1195 Japan
| | - Tomoya Tezuka
- Department of Nuclear Engineering, Kyoto University Nishikyo-ku Kyoto 615-8530 Japan
| | - Hidetsugu Tsuchida
- Department of Nuclear Engineering, Kyoto University Nishikyo-ku Kyoto 615-8530 Japan.,Quantum Science and Engineering Center, Kyoto University Gokasho, Uji Kyoto 611-0011 Japan
| | - Akinari Yokoya
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 2-4 Shirane Shirakata, Tokai-mura, Naka-gun Ibaraki 319-1195 Japan
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11
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Chatzipapas KP, Tran NH, Dordevic M, Zivkovic S, Zein S, Shin W, Sakata D, Lampe N, Brown JMC, Ristic‐Fira A, Petrovic I, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S. Simulation of DNA damage using Geant4‐DNA: an overview of the “molecularDNA” example application. PRECISION RADIATION ONCOLOGY 2023. [DOI: 10.1002/pro6.1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Affiliation(s)
| | - Ngoc Hoang Tran
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Milos Dordevic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zivkovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Sara Zein
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
| | - Wook‐Geun Shin
- Physics Division, Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School Boston Massachusetts USA
| | | | | | - Jeremy M. C. Brown
- Department of Physics and Astronomy Swinburne University of Technology Melbourne Australia
| | - Aleksandra Ristic‐Fira
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ivan Petrovic
- Vinca Institute of Nuclear Sciences, National Institute of the Republic of Serbia University of Belgrade, Vinca Belgrade Serbia
| | - Ioanna Kyriakou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory Department of Medicine University of Ioannina Ioannina Greece
| | - Susanna Guatelli
- Centre for Medical Radiation Physics University of Wollongong Wollongong New South Wales Australia
| | - Sébastien Incerti
- University of Bordeaux, CNRS, LP2I Bordeaux, UMR 5797 Gradignan France
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12
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Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B. TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac79f9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/17/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Current Monte Carlo simulations of DNA damage have been reported only at ambient temperature. The aim of this work is to use TOPAS-nBio to simulate the yields of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) produced in plasmids under low-LET irradiation incorporating the effect of the temperature changes in the environment. A new feature was implemented in TOPAS-nBio to incorporate reaction rates used in the simulation of the chemical stage of water radiolysis as a function of temperature. The implemented feature was verified by simulating temperature-dependent G-values of chemical species in liquid water from 20 °C to 90 °C. For radiobiology applications, temperature dependent SSB and DSB yields were calculated from 0 °C to 42 °C, the range of available published measured data. For that, supercoiled DNA plasmids dissolved in aerated solutions containing EDTA irradiated by Cobalt-60 gamma-rays were simulated. TOPAS-nBio well reproduced published temperature-dependent G-values in liquid water and the yields of SSB and DSB for the temperature range considered. For strand break simulations, the model shows that the yield of SSB and DSB increased linearly with the temperature at a rate of (2.94 ± 0.17) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99) and (0.13 ± 0.01) × 10−10 Gy–1 Da–1 °C–1 (R
2 = 0.99), respectively. The extended capability of TOPAS-nBio is a complementary tool to simulate realistic conditions for a large range of environmental temperatures, allowing refined investigations of the biological effects of radiation.
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13
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Zhu K, Wu C, Peng X, Ji X, Luo S, Liu Y, Wang X. Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA. Int J Mol Sci 2022; 23:ijms23116343. [PMID: 35683021 PMCID: PMC9181653 DOI: 10.3390/ijms23116343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fiber model and new physics constructors with the ELastic Scattering of Electrons and Positrons by neutral Atoms (ELSEPA) model were used to describe the DNA geometry and the physical stage of water radiolysis with the Geant4-DNA toolkit, respectively. Three key parameters (the energy threshold model for strand breaks, the physics model and the maximum distance to distinguish DSB clusters) of scoring DNA damage were studied to investigate the impact on the uncertainties of DNA damage. On the basis of comparison of our results with experimental data and published findings, we were able to accurately predict the yield of various types of DNA damage. Our results indicated that the difference in physics constructor can cause up to 56.4% in the DNA double-strand break (DSB) yields. The DSB yields were quite sensitive to the energy threshold for strand breaks (SB) and the maximum distance to classify the DSB clusters, which were even more than 100 times and four times than the default configurations, respectively.
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Affiliation(s)
- Kun Zhu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Chun Wu
- School of Nursing, University of South China, Hengyang 421001, China;
| | - Xiaoyu Peng
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Xuantao Ji
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Siyuan Luo
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Yuchen Liu
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
| | - Xiaodong Wang
- School of Nuclear Science and Technology, University of South China, Hengyang 421001, China; (K.Z.); (X.P.); (X.J.); (S.L.); (Y.L.)
- Correspondence:
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14
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Hu A, Qiu R, Wu Z, Zhang H, Li J. CPU-GPU coupling independent reaction times method in NASIC and application in water radiolysis by FLASH irradiation. Biomed Phys Eng Express 2022; 8. [DOI: 10.1088/2057-1976/ac52d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 11/11/2022]
Abstract
Abstract
The mechanism of the FLASH effect remains unclear and could be revealed by studying chemical reactions during irradiation. Monte Carlo simulation of the radiolytic species is an effective tool to analyze chemical reactions, but the simulation is limited by computing costs of the step-by-step simulation of radiolytic species, especially when considering beam with complex time structure. The complexity of the time structure of beams from accelerators in FLASH radiotherapy requires a high-performance Monte Carlo code. In this work, we develop a CPU-GPU coupling accelerating code with the independent reaction times (IRT) method to extend the chemical module of our nanodosimetry Monte Carlo code NASIC. Every chemical molecule in the microenvironment contains time information to consider the reactions from different tracks and simulate beams with complex time structures. Performance test shows that our code significantly improved the computing efficiency of the chemical module by four orders of magnitude. Then the code is used to study the oxygen depletion hypothesis in FLASH radiotherapy for different conditions by setting different parameters. The transient oxygen consumption rate values in the water are calculated when the pulses width ranges from 2 ps to 2 μs, the total dose ranges from 0.5 Gy to 100 Gy and the initial oxygen concentration ranges from 0.1% to 21%. The time evolution curves are simulated to study the effect of the time structure of an electron linear accelerator. Results show that the total dose in several microseconds is a better indicator reflecting the radiolytic oxygen consumption rate than the dose rate. The initial oxygen greatly affects the oxygen consumption rate because of the reaction competition. The diffusion of oxygen determined by the physiological parameters is the key factor affecting oxygen depletion during the radiation using electron linear accelerators. Our code provides an efficient tool for simulating water radiolysis in different conditions
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15
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Review of the Geant4-DNA Simulation Toolkit for Radiobiological Applications at the Cellular and DNA Level. Cancers (Basel) 2021; 14:cancers14010035. [PMID: 35008196 PMCID: PMC8749997 DOI: 10.3390/cancers14010035] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary A brief description of the methodologies to simulate ionizing radiation transport in biologically relevant matter is presented. Emphasis is given to the physical, chemical, and biological models of Geant4-DNA that enable mechanistic radiobiological modeling at the cellular and DNA level, important to improve the efficacy of existing and novel radiotherapeutic modalities for the treatment of cancer. Abstract The Geant4-DNA low energy extension of the Geant4 Monte Carlo (MC) toolkit is a continuously evolving MC simulation code permitting mechanistic studies of cellular radiobiological effects. Geant4-DNA considers the physical, chemical, and biological stages of the action of ionizing radiation (in the form of x- and γ-ray photons, electrons and β±-rays, hadrons, α-particles, and a set of heavier ions) in living cells towards a variety of applications ranging from predicting radiotherapy outcomes to radiation protection both on earth and in space. In this work, we provide a brief, yet concise, overview of the progress that has been achieved so far concerning the different physical, physicochemical, chemical, and biological models implemented into Geant4-DNA, highlighting the latest developments. Specifically, the “dnadamage1” and “molecularDNA” applications which enable, for the first time within an open-source platform, quantitative predictions of early DNA damage in terms of single-strand-breaks (SSBs), double-strand-breaks (DSBs), and more complex clustered lesions for different DNA structures ranging from the nucleotide level to the entire genome. These developments are critically presented and discussed along with key benchmarking results. The Geant4-DNA toolkit, through its different set of models and functionalities, offers unique capabilities for elucidating the problem of radiation quality or the relative biological effectiveness (RBE) of different ionizing radiations which underlines nearly the whole spectrum of radiotherapeutic modalities, from external high-energy hadron beams to internal low-energy gamma and beta emitters that are used in brachytherapy sources and radiopharmaceuticals, respectively.
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16
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Sakata D, Suzuki M, Hirayama R, Abe Y, Muramatsu M, Sato S, Belov O, Kyriakou I, Emfietzoglou D, Guatelli S, Incerti S, Inaniwa T. Performance Evaluation for Repair of HSGc-C5 Carcinoma Cell Using Geant4-DNA. Cancers (Basel) 2021; 13:6046. [PMID: 34885155 PMCID: PMC8656964 DOI: 10.3390/cancers13236046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 12/27/2022] Open
Abstract
Track-structure Monte Carlo simulations are useful tools to evaluate initial DNA damage induced by irradiation. In the previous study, we have developed a Gean4-DNA-based application to estimate the cell surviving fraction of V79 cells after irradiation, bridging the gap between the initial DNA damage and the DNA rejoining kinetics by means of the two-lesion kinetics (TLK) model. However, since the DNA repair performance depends on cell line, the same model parameters cannot be used for different cell lines. Thus, we extended the Geant4-DNA application with a TLK model for the evaluation of DNA damage repair performance in HSGc-C5 carcinoma cells which are typically used for evaluating proton/carbon radiation treatment effects. For this evaluation, we also performed experimental measurements for cell surviving fractions and DNA rejoining kinetics of the HSGc-C5 cells irradiated by 70 MeV protons at the cyclotron facility at the National Institutes for Quantum and Radiological Science and Technology (QST). Concerning fast- and slow-DNA rejoining, the TLK model parameters were adequately optimized with the simulated initial DNA damage. The optimized DNA rejoining speeds were reasonably agreed with the experimental DNA rejoining speeds. Using the optimized TLK model, the Geant4-DNA simulation is now able to predict cell survival and DNA-rejoining kinetics for HSGc-C5 cells.
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Affiliation(s)
- Dousatsu Sakata
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Masao Suzuki
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (M.S.); (R.H.)
| | - Ryoichi Hirayama
- Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (M.S.); (R.H.)
| | - Yasushi Abe
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Masayuki Muramatsu
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Shinji Sato
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
| | - Oleg Belov
- Veksler and Baldin Laboratory of High Energy Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia;
- Institute of System Analysis and Management, Dubna State University, 141980 Dubna, Russia
| | - Ioanna Kyriakou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110 Ioannina, Greece; (I.K.); (D.E.)
| | - Dimitris Emfietzoglou
- Medical Physics Laboratory, Medical School, University of Ioannina, 45110 Ioannina, Greece; (I.K.); (D.E.)
| | - Susanna Guatelli
- Centre For Medical Radiation Physics, University of Wollongong, Wollongong 2522, Australia;
| | - Sebastien Incerti
- Centre d’Études Nucléaires de Bordeaux Gradignan, CNRS/IN2P3, UMR5797, Université de Bordeaux, F-33170 Gradignan, France;
| | - Taku Inaniwa
- Department of Accelerator and Medical Physics, Institute for Quantum Medical Science, QST, Chiba 263-8555, Japan; (Y.A.); (M.M.); (S.S.); (T.I.)
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17
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Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štěpán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol 2021; 66. [PMID: 34412044 DOI: 10.1088/1361-6560/ac1f39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022]
Abstract
The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for·OH, e-aq, and H2with published experimental data. For H2O2and H·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by137Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for·OH and H·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
| | - J A LaVerne
- Radiation Laboratory and Department of Physics, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - N Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico
| | - J Milligan
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, United States of America
| | - V Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - K Stefanová
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, Prague, Czech Republic
| | - Y Perrot
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - C Villagrasa
- Laboratoire de Dosimétrie des Rayonnements Ionisants, Institut de Radioprotection et Sûreté Nucléaire, Fontenay aux Roses, BP. 17, F-92262, France
| | - W-G Shin
- Department of Radiation Oncology, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - S Incerti
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - A McNamara
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - H Paganetti
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - J Perl
- SLAC National Accelerator Laboratory, Menlo Park, CA, United States of America
| | - J Schuemann
- Department of Radiation Oncology, Physics Division, Massachusetts General Hospital & Harvard Medical School, Boston, MA, United States of America
| | - B Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, United States of America
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18
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Shin WG, Ramos-Mendez J, Tran NH, Okada S, Perrot Y, Villagrasa C, Incerti S. Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields. Phys Med 2021; 88:86-90. [PMID: 34198026 PMCID: PMC11152247 DOI: 10.1016/j.ejmp.2021.05.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/12/2021] [Accepted: 05/21/2021] [Indexed: 12/31/2022] Open
Abstract
This paper demonstrates the impact of the pre-chemical stage, especially the dissociation scheme and the associated probabilities, on water radiolysis simulation using the Geant4-DNA Monte Carlo track structure simulation toolkit. The models and parameters provided by TRACs have been collected and implemented into Geant4-DNA. In order to evaluate their influence on water radiolysis simulation, the radiochemical yields (G-values) are evaluated as a function of time and LET using the "chem6" Geant4-DNA example, and they are compared with published experimental and calculated data. The new pre-chemical models lead to a better agreement with literature data than the default pre-chemical models of Geant4-DNA, especially for OH radicals and H2O2. The revised chemistry constructor "G4EmDNAChemistry_option3" is available in Geant4-DNA version 10.7.
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Affiliation(s)
- Wook-Geun Shin
- UMR 5797, Bordeaux University, CNRS, CENBG, 33170 Gradignan, France; Department of Radiation Oncology, Seoul National University Hospital, 03080 Seoul, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, 03080 Seoul, Republic of Korea.
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, San Francisco 94143, CA, United States
| | - Ngoc Hoang Tran
- UMR 5797, Bordeaux University, CNRS, CENBG, 33170 Gradignan, France
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92262 Fontenay-aux-Roses, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, 92262 Fontenay-aux-Roses, France
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19
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Geant4-DNA Modeling of Water Radiolysis beyond the Microsecond: An On-Lattice Stochastic Approach. Int J Mol Sci 2021; 22:ijms22116023. [PMID: 34199598 PMCID: PMC8199710 DOI: 10.3390/ijms22116023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/18/2023] Open
Abstract
In this work, we use the next sub-volume method (NSM) to investigate the possibility of using the compartment-based (“on-lattice”) model to simulate water radiolysis. We, first, start with a brief description of the reaction-diffusion master equation (RDME) in a spatially discretized simulation volume (“mesh”), which is divided into sub-volumes (or “voxels”). We then discuss the choice of voxel size and merging technique of a given mesh, along with the evolution of the system using the hierarchical algorithm for the RDME (“hRDME”). Since the compartment-based model cannot describe high concentration species of early radiation-induced spurs, we propose a combination of the particle-based step-by-step (“SBS”) Brownian dynamics model and the compartment-based model (“SBS-RDME model”) for the simulation. We, finally, use the particle-based SBS Brownian dynamics model of Geant4-DNA as a reference to test the model implementation through several benchmarks. We find that the compartment-based model can efficiently simulate the system with a large number of species and for longer timescales, beyond the microsecond, with a reasonable computing time. Our aim in developing this model is to study the production and evolution of reactive oxygen species generated under irradiation with different dose rate conditions, such as in FLASH and conventional radiotherapy.
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20
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Abstract
Historically, the field of radiation chemistry began shortly after the discovery of radioactivity, and its development has been closely related to discoveries in other related fields such as radiation and nuclear physics. Radiolysis of water and radiation chemistry have been very important in elucidating how radiation affects living matter and how it induces DNA damage. Nowadays, we recognize the importance of chemistry to understanding the effects of radiation on cells; however, it took several decades to obtain this insight, and much is still unknown. The radiolysis of water and aqueous solutions have been the subject of much experimental and theoretical research for many decades. One important concept closely related to radiation chemistry is radiation track structure. Track structure results from early physical and physicochemical events that lead to a highly non-homogenous distribution of radiolytic species. Because ionizing radiation creates unstable species that are distributed non-homogenously, the use of conventional reaction kinetics methods does not describe this chemistry well. In recent years, several methods have been developed for simulating radiation chemistry. In this review, we give a brief history of the field and the development of the simulation codes. We review the current methods used to simulate radiolysis of water and radiation chemistry, and we describe several radiation chemistry codes and their applications.
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Affiliation(s)
- Ianik Plante
- KBR, 2400 NASA Parkway, Houston, TX 77058, United States of America
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21
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Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štěpán V, Incerti S, Villagrasa C. Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber. Med Phys 2020; 48:890-901. [PMID: 33232522 PMCID: PMC7986154 DOI: 10.1002/mp.14612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/11/2023] Open
Abstract
Purpose Simulation of indirect damage originating from the attack of free radical species produced by ionizing radiation on biological molecules based on the independent pair approximation is investigated in this work. In addition, a new approach, relying on the independent pair approximation that is at the origin of the independent reaction time (IRT) method, is proposed in the chemical stage of Geant4‐DNA. Methods This new approach has been designed to respect the current Geant4‐DNA chemistry framework while proposing a variant IRT method. Based on the synchronous algorithm, this implementation allows us to access the information concerning the position of radicals and may make it more convenient for biological damage simulations. Estimates of the evolution of free species as well as biological hits in a segment of DNA chromatin fiber in Geant4‐DNA were compared for the dynamic time step approach of the step‐by‐step (SBS) method, currently used in Geant4‐DNA, and this newly implemented IRT. Results Results show a gain in computation time of a factor of 30 for high LET particle tracks with a better than 10% agreement on the number of DNA hits between the value obtained with the IRT method as implemented in this work and the SBS method currently available in Geant4‐DNA. Conclusion Offering in Geant4‐DNA more efficient methods for the chemical step based on the IRT method is a task in progress. For the calculation of biological damage, information on the position of chemical species is a crucial point. This can be achieved using the method presented in this paper.
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Affiliation(s)
- Hoang Ngoc Tran
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Yann Perrot
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Sébastien Incerti
- Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France
| | - Carmen Villagrasa
- IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France
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22
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Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res 2020; 194:9-21. [PMID: 32401689 DOI: 10.1667/rr15531.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/11/2020] [Indexed: 12/21/2022]
Abstract
The cellular response to ionizing radiation continues to be of significant research interest in cancer radiotherapy, and DNA is recognized as the critical target for most of the biologic effects of radiation. Incident particles can cause initial DNA damages through physical and chemical interactions within a short time scale. Initial DNA damages can undergo repair via different pathways available at different stages of the cell cycle. The misrepair of DNA damage results in genomic rearrangement and causes mutations and chromosome aberrations, which are drivers of cell death. This work presents an integrated study of simulating cell response after proton irradiation with energies of 0.5-500 MeV (LET of 60-0.2 keV/µm). A model of a whole nucleus with fractal DNA geometry was implemented in TOPAS-nBio for initial DNA damage simulations. The default physics and chemistry models in TOPAS-nBio were used to describe interactions of primary particles, secondary particles, and radiolysis products within the nucleus. The initial DNA double-strand break (DSB) yield was found to increase from 6.5 DSB/Gy/Gbp at low-linear energy transfer (LET) of 0.2 keV/µm to 21.2 DSB/Gy/Gbp at high LET of 60 keV/µm. A mechanistic repair model was applied to predict the characteristics of DNA damage repair and dose response of chromosome aberrations. It was found that more than 95% of the DSBs are repaired within the first 24 h and the misrepaired DSB fraction increases rapidly with LET and reaches 15.8% at 60 keV/µm with an estimated chromosome aberration detection threshold of 3 Mbp. The dicentric and acentric fragment yields and the dose response of micronuclei formation after proton irradiation were calculated and compared with experimental results.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Stephen J McMahon
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, United Kingdom
| | - Jose Ramos-Mendez
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Nicholas T Henthorn
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, California 94143
| | - Kathryn D Held
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Joseph Perl
- SLAC National Accelerator Laboratory, Menlo Park, California
| | - Junli Li
- Department of Engineering Physics, Tsinghua University, Beijing 100084, P.R. China.,Key Laboratory of Particle & Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, P.R. China
| | - Harald Paganetti
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02114
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23
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DNA Damage Baseline Predicts Resilience to Space Radiation and Radiotherapy. Cell Rep 2020; 33:108434. [PMID: 33242409 PMCID: PMC7784531 DOI: 10.1016/j.celrep.2020.108434] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/22/2020] [Accepted: 11/04/2020] [Indexed: 12/11/2022] Open
Abstract
Deep space exploration will require real-time, minimally invasive monitoring of astronaut health to mitigate the potential health impairments caused by space radiation and microgravity. Genotoxic stress in humans can be monitored by quantifying the amount of DNA double-strand breaks (DSBs) in immune cells from a simple finger prick. In a cohort of 674 healthy donors, we show that the endogenous level of DSBs increases with age and with latent cytomegalovirus infection. To map the range of human responses to space radiation, we then study DSB induction and repair in immune cells from 319 healthy donors after the cells are exposed to galactic cosmic ray components and lymphocytes from 30 cancer patients after radiotherapy. Individuals with low baseline DSB have fewer clinical complications, enhanced DNA damage repair responses, and a functional dose-dependent cytokine response in healthy donor cells. This supports the use of DSB monitoring for health resilience in space.
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24
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Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štěpán V, Okada S, Moreno-Barbosa E, Faddegon B. Independent reaction times method in Geant4-DNA: Implementation and performance. Med Phys 2020; 47:5919-5930. [PMID: 32970844 DOI: 10.1002/mp.14490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/13/2020] [Indexed: 11/10/2022] Open
Abstract
PURPOSE The simulation of individual particle tracks and the chemical stage following water radiolysis in biological tissue is an effective means of improving our knowledge of the physico-chemical contribution to the biological effect of ionizing radiation. However, the step-by-step simulation of the reaction kinetics of radiolytic species is the most time-consuming task in Monte Carlo track-structure simulations, with long simulation times that are an impediment to research. In this work, we present the implementation of the independent reaction times (IRT) method in Geant4-DNA Monte Carlo toolkit to improve the computational efficiency of calculating G-values, defined as the number of chemical species created or lost per 100 eV of deposited energy. METHODS The computational efficiency of IRT, as implemented, is compared to that from available Geant4-DNA step-by-step simulations for electrons, protons and alpha particles covering a wide range of linear energy transfer (LET). The accuracy of both methods is verified using published measured data from fast electron irradiations for • OH and e aq - for time-dependent G-values. For IRT, simulations in the presence of scavengers irradiated by cobalt-60 γ-ray and 2 MeV protons are compared with measured data for different scavenging capacities. In addition, a qualitative assessment comparing measured LET-dependent G-values with Geant4-DNA calculations in pure liquid water is presented. RESULTS The IRT improved the computational efficiency by three orders of magnitude relative to the step-by-step method while differences in G-values by 3.9% at 1 μs were found. At 7 ps, • OH and e aq - yields calculated with IRT differed from recent published measured data by 5% ± 4% and 2% ± 4%, respectively. At 1 μs, differences were 9% ± 5% and 6% ± 7% for • OH and e aq - , respectively. Uncertainties are one standard deviation. Finally, G-values at different scavenging capacities and LET-dependent G-values reproduced the behavior of measurements for all radiation qualities. CONCLUSION The comprehensive validation of the Geant4-DNA capabilities to accurately simulate the chemistry following water radiolysis is an ongoing work. The implementation presented in this work is a necessary step to facilitate performing such a task.
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Affiliation(s)
- José Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Wook-Geun Shin
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France.,Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea
| | - Mathieu Karamitros
- Radiation Laboratory, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jorge Domínguez-Kondo
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Ngoc Hoang Tran
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Sebastien Incerti
- Centre d'Études Nucléaires de Bordeaux Gradignan, Université de Bordeaux, CNRS/IN2P3, UMR5797, Gradignan, 33175, France
| | - Carmen Villagrasa
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Yann Perrot
- Institut de Radioprotection et de Sûreté Nucléaire, IRSN, BP17, Fontenay-aux-Roses, 92262, France
| | - Václav Štěpán
- Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic
| | - Shogo Okada
- KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Eduardo Moreno-Barbosa
- Facultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla PUE, 72000, Mexico
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA
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25
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Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B. LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy. Radiat Res 2020; 194:351-362. [PMID: 32857855 PMCID: PMC7644138 DOI: 10.1667/rade-20-00084.1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023]
Abstract
FLASH radiotherapy delivers a high dose (≥10 Gy) at a high rate (≥40 Gy/s). In this way, particles are delivered in pulses as short as a few nanoseconds. At that rate, intertrack reactions between chemical species produced within the same pulse may affect the heterogeneous chemistry stage of water radiolysis. This stochastic process suits the capabilities of the Monte Carlo method, which can model intertrack effects to aid in radiobiology research, including the design and interpretation of experiments. In this work, the TOPAS-nBio Monte Carlo track-structure code was expanded to allow simulations of intertrack effects in the chemical stage of water radiolysis. Simulation of the behavior of radiolytic yields over a long period of time (up to 50 s) was verified by simulating radiolysis in a Fricke dosimeter irradiated by 60Co γ rays. In addition, LET-dependent G values of protons delivered in single squared pulses of widths, 1 ns, 1 µs and 10 µs, were obtained and compared to simulations using no intertrack considerations. The Fricke simulation for the calculated G value of Fe3+ ion at 50 s was within 0.4% of the accepted value from ICRU Report 34. For LET-dependent G values at the end of the chemical stage, intertrack effects were significant at LET values below 2 keV/µm. Above 2 keV/µm the reaction kinetics remained limited locally within each track and thus, effects of intertrack reactions remained low. Therefore, when track structure simulations are used to investigate the biological damage of FLASH irradiation, these intertrack reactions should be considered. The TOPAS-nBio framework with the expansion to intertrack chemistry simulation provides a useful tool to assist in this task.
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Affiliation(s)
- J. Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - N. Domínguez-Kondo
- Facultad de Ciencias Físico-Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - J. Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - A. McNamara
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - E. Moreno-Barbosa
- Facultad de Ciencias Físico-Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Bruce Faddegon
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
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26
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Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Phys Med Biol 2020; 65:085015. [PMID: 32101803 DOI: 10.1088/1361-6560/ab7a6b] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monte Carlo (MC) track structure simulation tools are commonly used for predicting radiation induced DNA damage by modeling the physical and chemical reactions at the nanometer scale. However, the outcome of these MC simulations is particularly sensitive to the adopted parameters which vary significantly across studies. In this study, a previously developed full model of nuclear DNA was used to describe the DNA geometry. The TOPAS-nBio MC toolkit was used to investigate the impact of physics and chemistry models as well as three key parameters (the energy threshold for direct damage, the chemical stage time length, and the probability of damage between hydroxyl radical reactions with DNA) on the induction of DNA damage. Our results show that the difference in physics and chemistry models alone can cause differences up to 34% and 16% in the DNA double strand break (DSB) yield, respectively. Additionally, changing the direct damage threshold, chemical stage length, and hydroxyl damage probability can cause differences of up to 28%, 51%, and 71% in predicted DSB yields, respectively, for the configurations in this study.
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Affiliation(s)
- Hongyu Zhu
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, United States of America. Department of Engineering Physics, Tsinghua University, Beijing 100084, People's Republic of China. Key Laboratory of Particle and Radiation Imaging (Tsinghua University), Ministry of Education, Beijing 100084, People's Republic of China
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27
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Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z, Schuemann J. Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams. Phys Med Biol 2019; 64:175005. [PMID: 31295730 PMCID: PMC11222020 DOI: 10.1088/1361-6560/ab314c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gold nanoparticle (GNP) radio-enhancement is a promising technique to increase the dose deposition in a tumor while sparing neighboring healthy tissue. Previous experimental studies showed effects on cell survival and tumor control for keV x-rays but surprisingly also for MV-photons, proton and carbon-ion beams. In a systematic study, we use the Monte Carlo simulation tool TOPAS-nBio to model the GNP radio-enhancement within a cell as a function of GNP concentration, size and clustering for a wide range of energies for photons, protons and, for the first time, carbon-ions. Moreover, we include water radiolysis, which has been recognized as a major pathway of GNP mediated radio-enhancement. At a GNP concentration of 0.5% and a GNP diameter of 10 nm, the dose enhancement ratio was highest for 50 keV x-rays (1.36) and decreased in the orthovoltage (1.04 at 250 keV) and megavoltage range (1.01 at 1 MeV). The dose enhancement linearly increased with GNP concentration and decreased with GNP size and degree of clustering for all radiation modalities. While the highest physical dose enhancement at 5% concentrations was only 1.003 for 10 MeV protons and 1.004 for 100 MeV carbon-ions, we find the number of hydroxyl ([Formula: see text]) altered by 23% and 3% after 1 [Formula: see text]s at low, clinically-relevant concentrations. For the same concentration and proton-impact, the G-value is most sensitive to the nanoparticle size with 46 times more radical interactions at GNPs for 2 nm than for 50 nm GNP diameter within 1 [Formula: see text]s. Nanoparticle clustering was found to decrease the number of interactions at GNPs, e.g. for a cluster of 25 GNPs by a factor of 3.4. The changes in G-value correlate to the average distance between the chemical species and the GNPs. While the radiochemistry of GNP-loaded water has yet to be fully understood, this work offers a first relative quantification of radiolysis products for a broad parameter-set.
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Affiliation(s)
- Benedikt Rudek
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts, MA, United States of America. Department of Physics, Boston University, Boston, Massachusetts, MA, United States of America. Department of Ionizing Radiation, Physikalisch-Technische Bundesanstalt, Braunschweig, Germany. Author to whom any correspondence should be addressed
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28
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Forster JC, Marcu LG, Bezak E. Approaches to combat hypoxia in cancer therapy and the potential for in silico models in their evaluation. Phys Med 2019; 64:145-156. [PMID: 31515013 DOI: 10.1016/j.ejmp.2019.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/17/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
AIM The negative impact of tumour hypoxia on cancer treatment outcome has been long-known, yet there has been little success combating it. This paper investigates the potential role of in silico modelling to help test emerging hypoxia-targeting treatments in cancer therapy. METHODS A Medline search was undertaken on the current landscape of in silico models that simulate cancer therapy and evaluate their ability to test hypoxia-targeting treatments. Techniques and treatments to combat tumour hypoxia and their current challenges are also presented. RESULTS Hypoxia-targeting treatments include tumour reoxygenation, hypoxic cell radiosensitization with nitroimidazoles, hypoxia-activated prodrugs and molecular targeting. Their main challenges are toxicity and not achieving adequate delivery to hypoxic regions of the tumour. There is promising research toward combining two or more of these techniques. Different types of in silico therapy models have been developed ranging from temporal to spatial and from stochastic to deterministic models. Numerous models have compared the effectiveness of different radiotherapy fractionation schedules for controlling hypoxic tumours. Similarly, models could help identify and optimize new treatments for overcoming hypoxia that utilize novel hypoxia-targeting technology. CONCLUSION Current therapy models should attempt to incorporate more sophisticated modelling of tumour angiogenesis/vasculature and vessel perfusion in order to become more useful for testing hypoxia-targeting treatments, which typically rely upon the tumour vasculature for delivery of additional oxygen, (pro)drugs and nanoparticles.
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Affiliation(s)
- Jake C Forster
- SA Medical Imaging, Department of Nuclear Medicine, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia; Department of Physics, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Loredana G Marcu
- Faculty of Science, University of Oradea, Oradea 410087, Romania; Cancer Research Institute and School of Health Sciences, University of South Australia, Adelaide SA 5001, Australia.
| | - Eva Bezak
- Department of Physics, University of Adelaide, North Terrace, Adelaide SA 5005, Australia; Cancer Research Institute and School of Health Sciences, University of South Australia, Adelaide SA 5001, Australia
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29
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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: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [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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30
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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] [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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Ramos-Méndez J, Perl J, Schuemann J, McNamara A, Paganetti H, Faddegon B. Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio. Phys Med Biol 2018; 63:105014. [PMID: 29697057 PMCID: PMC6027650 DOI: 10.1088/1361-6560/aac04c] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Simulation of water radiolysis and the subsequent chemistry provides important information on the effect of ionizing radiation on biological material. The Geant4 Monte Carlo toolkit has added chemical processes via the Geant4-DNA project. The TOPAS tool simplifies the modeling of complex radiotherapy applications with Geant4 without requiring advanced computational skills, extending the pool of users. Thus, a new extension to TOPAS, TOPAS-nBio, is under development to facilitate the configuration of track-structure simulations as well as water radiolysis simulations with Geant4-DNA for radiobiological studies. In this work, radiolysis simulations were implemented in TOPAS-nBio. Users may now easily add chemical species and their reactions, and set parameters including branching ratios, dissociation schemes, diffusion coefficients, and reaction rates. In addition, parameters for the chemical stage were re-evaluated and updated from those used by default in Geant4-DNA to improve the accuracy of chemical yields. Simulation results of time-dependent and LET-dependent primary yields Gx (chemical species per 100 eV deposited) produced at neutral pH and 25 °C by short track-segments of charged particles were compared to published measurements. The LET range was 0.05-230 keV µm-1. The calculated Gx values for electrons satisfied the material balance equation within 0.3%, similar for protons albeit with long calculation time. A smaller geometry was used to speed up proton and alpha simulations, with an acceptable difference in the balance equation of 1.3%. Available experimental data of time-dependent G-values for [Formula: see text] agreed with simulated results within 7% ± 8% over the entire time range; for [Formula: see text] over the full time range within 3% ± 4%; for H2O2 from 49% ± 7% at earliest stages and 3% ± 12% at saturation. For the LET-dependent Gx, the mean ratios to the experimental data were 1.11 ± 0.98, 1.21 ± 1.11, 1.05 ± 0.52, 1.23 ± 0.59 and 1.49 ± 0.63 (1 standard deviation) for [Formula: see text], [Formula: see text], H2, H2O2 and [Formula: see text], respectively. In conclusion, radiolysis and subsequent chemistry with Geant4-DNA has been successfully incorporated in TOPAS-nBio. Results are in reasonable agreement with published measured and simulated data.
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Affiliation(s)
- J Ramos-Méndez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, United States of America. Author to whom any correspondence should be addressed
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