Hoang Ngoc Tran1, José Ramos-Méndez2, Wook-Geun Shin3,4, Yann Perrot1, Bruce Faddegon2, Shogo Okada5, Mathieu Karamitros6, Marie Davídková7, Václav Štěpán7, Sébastien Incerti3, Carmen Villagrasa1. 1. IRSN, Institut de Radioprotection et de Sûreté Nucléaire, BP17, Fontenay aux Roses, 92262, France. 2. Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94115, USA. 3. Université de Bordeaux, CNRS/IN2P3, UMR5797, Centre d'Études Nucléaires de Bordeaux Gradignan, Gradignan, 33175, France. 4. Department of Radiation Convergence Engineering, Yonsei University, Wonju, 26493, Korea. 5. KEK, 1-1, Oho, Tsukuba, Ibaraki, 305-0801, Japan. 6. Radiation Laboratory, University of Notre Dame, Notre Dame, In, 46556, USA. 7. Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Prague, Czech Republic.
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.
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.
Authors: Dousatsu Sakata; Nathanael Lampe; Mathieu Karamitros; Ioanna Kyriakou; Oleg Belov; Mario A Bernal; David Bolst; Marie-Claude Bordage; Vincent Breton; Jeremy M C Brown; Ziad Francis; Vladimir Ivanchenko; Sylvain Meylan; Koichi Murakami; Shogo Okada; Ivan Petrovic; Aleksandra Ristic-Fira; Giovanni Santin; David Sarramia; Takashi Sasaki; Wook-Geun Shin; Nicolas Tang; Hoang N Tran; Carmen Villagrasa; Dimitris Emfietzoglou; Petteri Nieminen; Susanna Guatelli; Sebastien Incerti Journal: Phys Med Date: 2019-05-17 Impact factor: 2.685
Authors: S Incerti; I Kyriakou; M A Bernal; M C Bordage; Z Francis; S Guatelli; V Ivanchenko; M Karamitros; N Lampe; S B Lee; S Meylan; C H Min; W G Shin; P Nieminen; D Sakata; N Tang; C Villagrasa; H N Tran; J M C Brown Journal: Med Phys Date: 2018-06-14 Impact factor: 4.071
Authors: Nathanael Lampe; Mathieu Karamitros; Vincent Breton; Jeremy M C Brown; Ioanna Kyriakou; Dousatsu Sakata; David Sarramia; Sébastien Incerti Journal: Phys Med Date: 2018-04-05 Impact factor: 2.685
Authors: J Schuemann; A L McNamara; J Ramos-Méndez; J Perl; K D Held; H Paganetti; S Incerti; B Faddegon Journal: Radiat Res Date: 2019-01-04 Impact factor: 2.841
Authors: J Ramos-Méndez; J A LaVerne; N Domínguez-Kondo; J Milligan; V Štěpán; K Stefanová; Y Perrot; C Villagrasa; W-G Shin; S Incerti; A McNamara; H Paganetti; J Perl; J Schuemann; B Faddegon Journal: Phys Med Biol Date: 2021-09-03 Impact factor: 4.174