Independent reaction times method in Geant4‐DNA: Implementation and performance

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 th...

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Veröffentlicht in:Medical physics (Lancaster) 2020-11, Vol.47 (11), p.5919-5930
Hauptverfasser: Ramos‐Méndez, José, Shin, Wook‐Geun, Karamitros, Mathieu, Domínguez‐Kondo, Jorge, Tran, Ngoc Hoang, Incerti, Sebastien, Villagrasa, Carmen, Perrot, Yann, Štěpán, Václav, Okada, Shogo, Moreno‐Barbosa, Eduardo, Faddegon, Bruce
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container_end_page 5930
container_issue 11
container_start_page 5919
container_title Medical physics (Lancaster)
container_volume 47
creator Ramos‐Méndez, José
Shin, Wook‐Geun
Karamitros, Mathieu
Domínguez‐Kondo, Jorge
Tran, Ngoc Hoang
Incerti, Sebastien
Villagrasa, Carmen
Perrot, Yann
Štěpán, Václav
Okada, Shogo
Moreno‐Barbosa, Eduardo
Faddegon, Bruce
description 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 eaq‐ 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 eaq‐ 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 eaq‐, 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.
doi_str_mv 10.1002/mp.14490
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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 eaq‐ 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 eaq‐ 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 eaq‐, 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.</description><identifier>ISSN: 0094-2405</identifier><identifier>EISSN: 2473-4209</identifier><identifier>DOI: 10.1002/mp.14490</identifier><identifier>PMID: 32970844</identifier><language>eng</language><publisher>United States: American Association of Physicists in Medicine</publisher><subject>Computer Simulation ; DNA ; Geant4‐DNA ; independent reaction times ; LET ; Linear Energy Transfer ; Medical Physics ; Models, Chemical ; Monte Carlo ; Monte Carlo Method ; Physics ; radiolysis ; Reaction Time ; track‐structure ; Water</subject><ispartof>Medical physics (Lancaster), 2020-11, Vol.47 (11), p.5919-5930</ispartof><rights>2020 American Association of Physicists in Medicine</rights><rights>2020 American Association of Physicists in Medicine.</rights><rights>Attribution - NonCommercial - NoDerivatives</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5100-dac7d37846a73b936eda448dc689fa8e14ce6c8006a6a05e2b79057b443c50543</citedby><cites>FETCH-LOGICAL-c5100-dac7d37846a73b936eda448dc689fa8e14ce6c8006a6a05e2b79057b443c50543</cites><orcidid>0000-0002-1738-8019 ; 0000-0002-8106-5142 ; 0000-0002-0619-2053 ; 0000-0001-9043-5857</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fmp.14490$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fmp.14490$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>230,314,776,780,881,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32970844$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-02988428$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Ramos‐Méndez, José</creatorcontrib><creatorcontrib>Shin, Wook‐Geun</creatorcontrib><creatorcontrib>Karamitros, Mathieu</creatorcontrib><creatorcontrib>Domínguez‐Kondo, Jorge</creatorcontrib><creatorcontrib>Tran, Ngoc Hoang</creatorcontrib><creatorcontrib>Incerti, Sebastien</creatorcontrib><creatorcontrib>Villagrasa, Carmen</creatorcontrib><creatorcontrib>Perrot, Yann</creatorcontrib><creatorcontrib>Štěpán, Václav</creatorcontrib><creatorcontrib>Okada, Shogo</creatorcontrib><creatorcontrib>Moreno‐Barbosa, Eduardo</creatorcontrib><creatorcontrib>Faddegon, Bruce</creatorcontrib><title>Independent reaction times method in Geant4‐DNA: Implementation and performance</title><title>Medical physics (Lancaster)</title><addtitle>Med Phys</addtitle><description>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 eaq‐ 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 eaq‐ 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 eaq‐, 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. 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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 eaq‐ 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 eaq‐ 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 eaq‐, 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.</abstract><cop>United States</cop><pub>American Association of Physicists in Medicine</pub><pmid>32970844</pmid><doi>10.1002/mp.14490</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-1738-8019</orcidid><orcidid>https://orcid.org/0000-0002-8106-5142</orcidid><orcidid>https://orcid.org/0000-0002-0619-2053</orcidid><orcidid>https://orcid.org/0000-0001-9043-5857</orcidid><oa>free_for_read</oa></addata></record>
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subjects Computer Simulation
DNA
Geant4‐DNA
independent reaction times
LET
Linear Energy Transfer
Medical Physics
Models, Chemical
Monte Carlo
Monte Carlo Method
Physics
radiolysis
Reaction Time
track‐structure
Water
title Independent reaction times method in Geant4‐DNA: Implementation and performance
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