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.
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.
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DOI：
10.1002/mp.14612
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发表时间：
2021-03
期刊：
影响因子：
3.8
通讯作者：
Villagrasa C
中科院分区：
文献类型：
--
作者：
Tran HN;Ramos-Méndez J;Shin WG;Perrot Y;Faddegon B;Okada S;Karamitros M;Davídková M;Štěpán V;Incerti S;Villagrasa C
本文研究了基于独立对近似的电离辐射自由基对生物分子的间接损伤模拟。此外，在Geant4‐DNA的化学阶段提出了一种新的方法，该方法依赖于独立反应时间（IRT）方法的起源处的独立对近似。这种新方法旨在尊重当前的Geant4 - DNA化学框架，同时提出一种变体IRT方法。基于同步算法，该实现使我们能够访问有关自由基位置的信息，并可能使其更便于生物损伤模拟。用目前在Geant4 - DNA中使用的动态时间步法（SBS）和新实现的IRT对Geant4 - DNA中自由物种的进化和DNA染色质纤维片段的生物撞击进行了比较。结果表明，高LET粒子轨迹的计算时间增加了30倍，本工作中实现的IRT方法与目前在Geant4‐DNA中可用的SBS方法获得的DNA命中数之间的一致性优于10%。在Geant4‐DNA中提供基于IRT方法的更有效的化学步骤方法是一项正在进行的任务。在生物损伤的计算中，化学物质的位置信息是至关重要的。这可以用本文提出的方法来实现。
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. 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 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. 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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影响因子：
--
作者：
CLIFFORD, P;GREEN, NJB;PILLING, MJ
通讯作者：
PILLING, MJ
影响因子：
3.8
作者：
Incerti, S.;Ivanchenko, A.;Zacharatou, C.
通讯作者：
Zacharatou, C.
影响因子：
2.9
作者：
Bluett, VM;Green, NJB
通讯作者：
Green, NJB
DOI：
10.1016/j.nima.2016.06.125
发表时间：
2016-11-01
影响因子：
1.4
作者：
Allison, J.;Amako, K.;Yoshida, H.
通讯作者：
Yoshida, H.
影响因子：
3.8
作者：
Incerti, S.;Kyriakou, I.;Brown, J. M. C.
通讯作者：
Brown, J. M. C.