Multiple DNA damages induced by water radiolysis demonstrated using a dynamic Monte Carlo code

Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke*; Hirata, Yuho; Tsuchida, Hidetsugu*; Ito, Yuma*; Yokoya, Akinari*

Communications Chemistry (Internet), 8, p.60_1 - 60_9, 2025/03

https://doi.org/10.1038/s42004-025-01453-x

Radiation DNA damage is formed from direct and indirect effects. The direct effect is the interaction between DNA and a radiation, while the indirect effect is the chemical reaction between DNA and radiolytic chemical species. We believed that when the direct effect is induced, multiple lesions are formed within 10 base pairs (about 3.4 nm) of DNA. The damage reduces repair efficiency and induces biological effects. In this study, DNA damage induced by only indirect effects was quantitatively evaluated. Our results indicated that the multiple damage is formed when only 10s of eV energy is deposited to water in the vicinity of DNA, although its formation probability is less than 1%. In other words, the possibility of late biological effects cannot be excluded simply by imparting energy to water in the extreme vicinity of DNA without direct interaction between radiation and DNA. Our results are one of the most important findings for understanding low-dose radiation risk.

Overview of PHITS Ver.3.34 with particular focus on track-structure calculation

Ogawa, Tatsuhiko; Hirata, Yuho; Matsuya, Yusuke; Kai, Takeshi; Sato, Tatsuhiko; Iwamoto, Yosuke; Hashimoto, Shintaro; Furuta, Takuya; Abe, Shinichiro; Matsuda, Norihiro; et al.

EPJ Nuclear Sciences & Technologies (Internet), 10, p.13_1 - 13_8, 2024/11

https://doi.org/10.1051/epjn/2024012

The latest updates on PHITS, a versatile radiation transport code, focusing specifically on track-structure models are presented. Track structure calculations are methods used to simulate the movement of charged particles while explicitly considering each atomic reaction. Initially developed for radiation biology, these calculation methods aimed to analyze the radiation-induced damage to DNA and chromosomes. Several track-structure calculation models, including PHITS-ETS, PHITS-ETS for Si, PHITS-KURBUC, ETSART, and ITSART, have been developed and implemented to PHITS. These models allow users to study the behavior of various particles at the nano-scale across a wide range of materials. Furthermore, potential applications of track-structure calculations have also been proposed so far. This collection of track-structure calculation models, which encompasses diverse conditions, opens up new avenues for research in the field of radiation effects.

Progress of the spoke cavity prototyping for the JAEA-ADS linac

Tamura, Jun; Kondo, Yasuhiro; Yee-Rendon, B.; Meigo, Shinichiro; Maekawa, Fujio; Kako, Eiji*; Umemori, Kensei*; Sakai, Hiroshi*; Domae, Takeshi*

Proceedings of 32nd Linear Accelerator Conference (LINAC 2024) (Internet), p.496 - 498, 2024/10

https://doi.org/10.18429/JACoW-LINAC2024-TUPB078

Liquid water radiolysis induced by secondary electrons generated from MeV-energy carbon ions

Tsuchida, Hidetsugu*; Tezuka, Tomoya*; Kai, Takeshi; Matsuya, Yusuke*; Majima, Takuya*; Saito, Manabu*

Journal of Chemical Physics, 161(10), p.104503_1 - 104503_8, 2024/09

https://doi.org/10.1063/5.0227465

Although fast ion beams can damage DNA by chemical products such as secondary electrons produced by their interaction with water in living cells, the process of formation of these chemical products in the Bragg peak region used in particle therapy is not fully understood. To investigate this process, we performed experiments to evaluate the yields of radiolytic products produced when a liquid water jet in vacuum is irradiated with a MeV-energy carbon beam. In addition, ionization processes in water due to incident ions and secondary electrons were simulated using a radiation transport Monte Carlo code. The results indicated that the primary source of ionization in water is secondary electrons. Finally, we show that these elementary processes contribute to the development of radiation biophysics and biochemistry to study the formation mechanism of DNA damage.

Consideration of the dielectric response for radiation chemistry simulations

Toigawa, Tomohiro; Kai, Takeshi; Kumagai, Yuta; Yokoya, Akinari*

Journal of Chemical Physics, 160(21), p.214119_1 - 214119_9, 2024/06

https://doi.org/10.1063/5.0211089

The spur reaction is crucial for determining radiolysis or photolysis in liquid, 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.

Changes in molecular conformation and electronic structure of DNA under C ions based on first-principles calculations

Sekikawa, Takuya; Matsuya, Yusuke; Hwang, B.*; Ishizaka, Masato*; Kawai, Hiroyuki*; Ono, Yoshiaki*; Sato, Tatsuhiko; Kai, Takeshi

Nuclear Instruments and Methods in Physics Research B, 548, p.165231_1 - 165231_6, 2024/03

https://doi.org/10.1016/j.nimb.2023.165231

One of the main causes of radiation effects on the human body is thought to be damage to DNA, which carries genetic information. However, it is not fully understood what kind of molecular structural changes DNA undergoes upon radiation damage. Since it has been reported that various types of DNA damage are formed when DNA is irradiated, our group has investigated the relationship between DNA damage and various patterns of radiation-induced ionization induced by radiation. Although we have so far analyzed DNA damage in a simple system using a rigid body model of DNA, more detailed calculations are required to analyze the molecular structural changes in DNA, which are considered to be important in considering the effects on the human body. In this study, we attempted to clarify the molecular conformational changes of DNA using OpenMX, a first-principles calculation software that can discuss electronic states based on molecular structures. Specifically, we calculated the most stable structure, band dispersion, and wave function of DNA under the assumption that one and two electrons are ionized by various radiation. In the presentation, we will discuss the relationship between the energy dependence of each incident radiation type and the molecular conformational change of DNA. In addition, the radiation-induced changes in the basic physical properties of DNA (corresponding to the initial stage of DNA damage) will be discussed from the viewpoints of both radiation physics and solid state physics.

A Step-by-step simulation code for estimating yields of water radiolysis species based on electron track-structure mode in the PHITS code

Matsuya, Yusuke; Yoshii, Yuji*; Kusumoto, Tamon*; Akamatsu, Ken*; Hirata, Yuho; Sato, Tatsuhiko; Kai, Takeshi

Physics in Medicine & Biology, 69(3), p.035005_1 - 035005_12, 2024/02

https://doi.org/10.1088/1361-6560/ad199b

Time-dependent yields of chemical products resulted in 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 allows to determine several atomic interactions such as ionizations and electronic excitations as physical stage. However, a chemical code for simulating products of water radiolysis does not exist in the PHITS package. Here, we developed a chemical simulation code dedicated for the PHITS code, hereafter called PHITS-Chem code, which enables calculating G values of water radiolysis species (OH radical, e, H, HO etc) by electron beams. The estimated G values during 1 s are in agreement with the experimental ones and other simulations. This PHITS-Chem code enables simulating the dynamics in the presence of OH radical scavenger, and is useful for evaluating contributions of direct and indirect effects on DNA damage induction. This code will be included and be available in the future version of PHITS.

Fabrication progress of the prototype spoke cavity for the JAEA-ADS linac

Tamura, Jun; Kondo, Yasuhiro; Yee-Rendon, B.; Meigo, Shinichiro; Maekawa, Fujio; Kako, Eiji*; Umemori, Kensei*; Sakai, Hiroshi*; Domae, Takeshi*

Journal of Physics; Conference Series, 2687(5), p.052008_1 - 052008_6, 2024/01

https://doi.org/10.1088/1742-6596/2687/5/052008

Analysis of the radioactivity concentrations in radioactive waste generated from JRR-3, JRR-4 and JRTF facilities, 2

Tobita, Minoru*; Goto, Katsunori*; Omori, Takeshi*; Osone, Osamu*; Haraga, Tomoko; Aono, Ryuji; Konda, Miki; Tsuchida, Daiki; Mitsukai, Akina; Ishimori, Kenichiro

JAEA-Data/Code 2023-011, 32 Pages, 2023/11

JAEA-Data-Code-2023-011.pdf:0.93MB

Radioactive wastes generated from nuclear research facilities in Japan Atomic Energy Agency are planning to be buried in the near surface disposal field as trench and pit. Therefore, it is required to establish the method to evaluate the radioactivity concentrations of radioactive wastes until the beginning of disposal. In order to contribute to the study of radioactivity concentration evaluation methods for radioactive wastes generated from nuclear research facilities, we collected and analyzed concrete samples generated from JRR-3, JRR-4 and JAERI Reprocessing Test Facility. In this report, we summarized the radioactivity concentrations of 23 radionuclides (H, C, Cl, Ca, Co, Ni, Sr, Nb, Ag, Cs, Ba, Eu, Eu, Ho, U, U, U, Pu, Pu, Pu, Am, Am, Cm) which were obtained from radiochemical analysis of the samples in fiscal years 2021-2022.

Development of an electron track-structure mode for arbitrary semiconductor materials in PHITS

Hirata, Yuho; Kai, Takeshi; Ogawa, Tatsuhiko; Matsuya, Yusuke*; Sato, Tatsuhiko

Japanese Journal of Applied Physics, 62(10), p.106001_1 - 106001_6, 2023/10

https://doi.org/10.35848/1347-4065/ad00f4

Optimization of semiconductor detector design requires theoretical analysis of the process of radiation conversion to carriers (excited electrons) in semiconductor materials. We, therefore, developed an electron track-structure code that can trace an incident electron trajectory down to a few eV and simulate many excited electron productions in semiconductors, named ETSART, and implemented it into PHITS. The accuracy of ETSART was validated by comparing calculated electron ranges in semiconductor materials with the corresponding data recommended in ICRU Report 37 and obtained from another simulation code. The average energy required to produce a single excited electron (epsilon value) is an important value that describes the characteristics of semiconductor detectors. Using ETSART, we computed the epsilon values in various semiconductors and found that the calculated epsilon values cannot be fitted well with a linear model of the band-gap energy. ETSART is expected to be useful for initial and mechanistic evaluations of electron-hole generation in undiscovered materials.