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C ions based on first-principles calculationsSekikawa, 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
Times Cited Count：0 Percentile：0.44(Instruments & Instrumentation)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.
Hirata, Yuho; Kai, Takeshi; Ogawa, Tatsuhiko; Matsuya, Yusuke; Sato, Tatsuhiko
Nuclear Instruments and Methods in Physics Research B, 547, p.165183_1 - 165183_7, 2024/02
Times Cited Count：0 Percentile：0.02(Instruments & Instrumentation)The luminescence efficiency of the phosphors for swift ions is known to decrease because of the quenching effects. To obtain the precise dose distributions using phosphor detectors, understanding the mechanisms of quenching effects is mandatory. Here, we developed a new model for estimating the luminescence intensity of phosphors based on the track-structure modes for arbitrary materials implemented in PHITS. The developed model enabled the simulation of the quenching effects of the BaFBr detector and was verified by comparing the results to the corresponding measured data. The present model is expected to contribute to developing phosphor detectors worldwide.
Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke; Hirata, Yuho; Tezuka, Tomoya*; Tsuchida, Hidetsugu*; Yokoya, Akinari*
RSC Advances (Internet), 13(46), p.32371 - 32380, 2023/11
Times Cited Count：0 Percentile：0(Chemistry, Multidisciplinary)Although scientific knowledge of photolysis and radiolysis of water is widely used in the life sciences and other fields, the formation mechanism of the spatial distribution of hydrated electrons (spur) resulting from energy deposition to water is still not well understood. The chemical reaction times of hydrated electrons, OH radicals, and H
O
in the spur strongly depend on the spur radius. In our previous study, we elucidated the mechanism at a specific given energy (12.4 eV) by first-principles calculations. In the present study, we performed first-principles calculations of the spur radius at the deposition energies of 11-19 eV. The calculated spur radius is 3-10 nm, which is consistent with the experimental prediction (~4 nm) for the energy range of 8-12.4 eV, and the spur radius gradually increases with increasing energy. The spur radius is a new scientific knowledge and is expected to be widely used for estimating radiation DNA damage.
Hirata, Yuho; Kai, Takeshi; Ogawa, Tatsuhiko; Matsuya, Yusuke*; Sato, Tatsuhiko
Japanese Journal of Applied Physics, 62(10), p.106001_1 - 106001_6, 2023/10
Times Cited Count：2 Percentile：75.57(Physics, Applied)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.
Sato, Tatsuhiko; Matsuya, Yusuke*; Ogawa, Tatsuhiko; Kai, Takeshi; Hirata, Yuho; Tsuda, Shuichi; Parisi, A.*
Physics in Medicine & Biology, 68(15), p.155005_1 - 155005_15, 2023/07
Times Cited Count：2 Percentile：84.52(Engineering, Biomedical)In this study, we improved the microdosimetric function implemented in PHITS using the latest track-structure simulation codes. The improved function is capable of calculating the probability densities of not only the conventional microdosimetric quantities such as lineal energy but also the numbers of ionization events occurred in a target site, the so-called ionization cluster size distribution, for arbitrary site diameters from 3 nm to 1 um. As a new application of the improved function, we calculated the relative biological effectiveness of the single-strand break and double-strand break yields for proton irradiations using the updated PHITS coupled with the simplified DNA damage estimation model, and confirmed its equivalence in accuracy and its superiority in computational time compared to our previously proposed method based on the track-structure simulation.
Kai, Takeshi; Toigawa, Tomohiro; Ukai, Masatoshi*; Fujii, Kentaro*; Watanabe, Ritsuko*; Yokoya, Akinari*
Journal of Chemical Physics, 158(16), p.164103_1 - 164103_8, 2023/04
New insight into water radiolysis and photolysis is indispensable in the dramatic progress of sciences and technologies in various research areas. In the radiation field, reactive hydrated electrons are considerably produced along radiation tracks. Although the formation results from a transient dynamic correlation between ejected electrons and water, the individual mechanisms of electron thermalization, delocalization, and polarization are unknown. Using a dynamic Monte Carlo code, we show herein that the ejected electrons are immediately delocalized by molecular excitations in parallel with phonon polarization and gradually thermalized by momentum transfer with an orientation polarization in a simultaneous manner. Our results show that these mechanisms heavily depend on the intermolecular vibration and rotation modes peculiar to water. We expect our approach to be a powerful technique for connecting physical and chemical processes in various solvents.
Kai, Takeshi; Toigawa, Tomohiro; Matsuya, Yusuke*; Hirata, Yuho; Tezuka, Tomoya*; Tsuchida, Hidetsugu*; Yokoya, Akinari*
RSC Advances (Internet), 13(11), p.7076 - 7086, 2023/03
Times Cited Count：3 Percentile：81.33(Chemistry, Multidisciplinary)Scientific insights of water radiolysis are widely used in the life sciences and so on, however, the formation mechanism of radicals, a product of water radiolysis, is still not well understood. We are challenging to develop a simulation code to solve this formation mechanism from the viewpoint of radiation physics. Our first-principles calculations have revealed that the behavior of secondary electrons in water is governed not only by collisional effects but also by polarization effects. Furthermore, from the predicted ratio of ionization to electronic excitation, based on the spatial distribution of secondary electrons, we successfully reproduce the initial yield of hydrated electrons predicted in terms of radiation chemistry. The code provides us a reasonable spatiotemporal connection from radiation physics to radiation chemistry. Our findings are expected to provide newly scientific insights for understanding the earliest stages of water radiolysis.
-H2AX focus formation assay based on track-structure simulationYachi, Yoshie*; Matsuya, Yusuke*; Yoshii, Yuji*; Fukunaga, Hisanori*; Date, Hiroyuki*; Kai, Takeshi
International Journal of Molecular Sciences (Internet), 24(2), p.1386_1 - 1386_14, 2023/01
Times Cited Count：2 Percentile：75.46(Biochemistry & Molecular Biology)When living cells are irradiated with radiation and complex damage is formed within a few nanometers of DNA, it is believed to induce biological effects such as cell death. In general, complex DNA damage formed in cells can be detected experimentally by fluorescence microscopy, because the area around the damage site emits light like a focus point when a fluorophore is used. However, this detection method has not been able to analyze the degree of complexity of DNA damage. Therefore, in this study, we addressed on the measured focus size and evaluated the degree of complexity of DNA damage using a track structure analysis code. As a result, we found that as DNA damage becomes more complex, the focus size also increases. Our findings are expected to provide a new analytical method for elucidating the initial factors of radiation biological effects.
Sato, Tatsuhiko; Iwamoto, Yosuke; Hashimoto, Shintaro; Ogawa, Tatsuhiko; Furuta, Takuya; Abe, Shinichiro; Kai, Takeshi; Matsuya, Yusuke; Matsuda, Norihiro; Hirata, Yuho; et al.
Journal of Nuclear Science and Technology, 9 Pages, 2023/00
Times Cited Count：5 Percentile：98.08(Nuclear Science & Technology)The Particle and Heavy Ion Transport code System (PHITS) is a general-purpose Monte Carlo radiation transport code that can simulate the behavior of most particle species with energies up to 1 TeV (per nucleon for ions). Its new version, PHITS3.31, was recently developed and released to the public. In the new version, the compatibility with high-energy nuclear data libraries and the algorithm of the track-structure modes have been improved. In this paper, we summarize the upgraded features of PHITS3.31 with respect to the physics models, utility functions, and application software introduced since the release of PHITS3.02 in 2017.
Matsuya, Yusuke; Yoshii, Yuji*; Kusumoto, Tamon*; Akamatsu, Ken*; Hirata, Yuho; Sato, Tatsuhiko; Kai, Takeshi
Physics in Medicine & Biology, 19 Pages, 2023/00
Times Cited Count：0 Percentile：0.05(Engineering, Biomedical)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.
Ogawa, Tatsuhiko; Hirata, Yuho; Matsuya, Yusuke; Kai, Takeshi
Isotope News, (784), p.13 - 16, 2022/12
Track-structure calculation, a method to simulate every secondary electron production reaction explicitly, has been extensively used as an important techniques in various fields such as radiation biology, material irradiation effect, and radiation detection. However, it requires the dielectric function of the target materials, which is not well known except for liquid water. Therefore we developed a model to perform track-structure calculation based on a systematic formula of secondary electron production cross section and that of stopping power. The model can therefore perform track-structure calculation regardless of the availability of dielectric function measurement data. Stopping range, and energy deposition radial distribution calculated by this model agreed well with the earlier experimental data and calculation by precedent codes. The lineal energy in tissue-equivalent gas calculated by this model agreed with measurement data taken from literature, showing distinct difference from that in liquid water. This model was implemented to PHITS Ver3.25, the general-purpose radiation transport simulation code of JAEA, being distributed to users as the first track-structure calculation model applicable to arbitrary materials available in general-purpose transport code.
Matsuya, Yusuke; Kai, Takeshi; Parisi, A.*; Yoshii, Yuji*; Sato, Tatsuhiko
Physics in Medicine & Biology, 67(21), p.215017_1 - 215017_13, 2022/11
Times Cited Count：5 Percentile：78.03(Engineering, Biomedical)Proton beam therapy allows to irradiate tumor volumes with reduced side effects on normal tissues with respect to X-ray radiotherapy. Biological effects such as cell killing after proton beam irradiations depend on the proton kinetic energy, which is intrinsically related in the early DNA damage induction. As such, the estimation of DNA damage yields based on Monte Carlo simulations is a research topic of worldwide interest. In this study, we investigate the possibility of applying a simple model developed for electron to proton without any modification. The yields of single-strand breaks (SSB), double-strand breaks (DSB) and the complex DSB were assessed as a function of the proton kinetic energy. The PHITS-based estimation accurately reproduced the experimental and simulated yields of various DNA damage types induced by protons with linear energy transfer (LET) up to about 30 keV/m. These results suggest that current DNA damage model implemented in PHITS is sufficient for estimating DNA lesion yields induced after protons irradiation except for lower energies than MeV.
Hirata, Yuho; Kai, Takeshi; Ogawa, Tatsuhiko; Matsuya, Yusuke; Sato, Tatsuhiko
Japanese Journal of Applied Physics, 61(10), p.106004_1 - 106004_6, 2022/10
Times Cited Count：5 Percentile：67.2(Physics, Applied)Some radiation effects such as pulse-height defects and soft errors can cause problems in silicon (Si) devices. Local energy deposition in microscopic scales is essential information to elucidate the mechanism of these radiation effects. We, therefore, developed an electron track-structure model, which can simulate local energy deposition down to nano-scales, dedicated to Si and implemented it into PHITS. Then, we verified the accuracy of our developed model by comparing the ranges and depth-dose distributions of electrons obtained from this study with the corresponding experimental values and other simulated results. As an application of the model, we calculated the mean energies required to create an electron-hole pair, the so-called epsilon value. We found that the threshold energy for generating secondary electrons reproducing the epsilon value is 2.75 eV, consistent with the corresponding data deduced from past theoretical and computational studies. Since the magnitudes of the radiation effects on Si devices largely depend on the epsilon value, the developed code is expected to contribute to precisely understanding the mechanisms of pulse-height defects and semiconductor soft errors.
Tsuchida, Hidetsugu*; Majima, Takuya*; Kai, Takeshi
Oyo Butsuri, 91(9), p.553 - 557, 2022/09
In recent years, basic research has been conducted to understand the biological effects of radiation at the atomic level toward advancing particle beam cancer treatment. Here we show some recent results on the basic process of biomolecular damage caused by ion beams in liquid water. A biomolecular solution target was introduced to the vacuum by a liquid molecular beam or microdroplet method. Secondary ion mass spectrometry was applied to measure the fragments of biomolecules emitted from a target irradiated with an ion beam. For the simulation study using a PHITS code, physical nature of secondary electrons produced by ion beam in water was analyzed. The experimental and simulation research determined the energy range of secondary electrons involved in damaging biomolecules in liquid water caused by ion beams. The damage process by secondary electrons near the ion track is described.
Yachi, Yoshie*; Kai, Takeshi; Matsuya, Yusuke; Hirata, Yuho; Yoshii, Yuji*; Date, Hiroyuki*
Scientific Reports (Internet), 12, p.16412_1 - 16412_8, 2022/09
Times Cited Count：2 Percentile：47.19(Multidisciplinary Sciences)Recently, magnetic resonance-guided radiotherapy (MRgRT) which can visualize tumors in real time has been developed and installed in several clinical facilities. It is known that Lorentz force modulate macroscopic dose distribution by a charged particle, however, the impact by the force on microscopic radiation-track structure and early DNA damage induction remain unclear. In this study, we simulated the electron-track structure in a static magnetic field using a PHITS, and estimated features of biological effects. We indicated that the macroscopic dose distributions are changed by the force, while early DNA damage such as double strand breaks is attributed to the secondary electrons below a few tens of eV which are independent of the force. We expect that our insight significantly contributes to the MRgRT.
Matsuya, Yusuke; Kai, Takeshi; Sato, Tatsuhiko; Ogawa, Tatsuhiko; Hirata, Yuho; Yoshii, Yuji*; Parisi, A.*; Liamsuwan, T.*
International Journal of Radiation Biology, 98(2), p.148 - 157, 2022/02
Times Cited Count：15 Percentile：80.59(Biology)When investigating radiation-induced biological effects, it is essential to perform detailed track-structure simulations explicitly by considering each atomic interaction in liquid water (which is equivalent to human tissues) at sub-cellular and DNA scales. The Particle and Heavy Ion Transport code System (PHITS) is a Monte Carlo code which can be used for track structure calculations by employing an original electron track-structure mode (etsmode) and the world-famous KURBUC algorithms (PHITS-KURBUC mode) for protons and carbon ions. In this study, the physical features (i.e., range, radial dose and microdosimetry) of these modes have been verified by comparing to the available experimental data and Monte Carlo simulation results reported in literature. In addition, applying the etsmode to radiobiological study, we estimated the yields of single-strand breaks (SSBs), double-strand breaks (DSBs) and complex DSBs, and evaluated the dependencies of DNA damage yields on incident electron energy. As a result, the simulations suggested that DNA damage types are intrinsically related with the spatial patterns of ionization and electronic excitations and that approximately 500 eV electron can cause much complex DSBs. In this paper, we show the development status of the PHITS track-structure modes and its application to radiobiological research, which would be expected to identify the underlying mechanisms of radiation effects based on physics.
Ogawa, Tatsuhiko; Hirata, Yuho; Matsuya, Yusuke; Kai, Takeshi
Scientific Reports (Internet), 11(1), p.24401_1 - 24401_10, 2021/12
Times Cited Count：14 Percentile：76.83(Multidisciplinary Sciences)Track-structure calculation, a method to simulate every secondary electron production reaction explicitly, has been extensively used as an important techniques in various fields such as radiation biology, material irradiation effect, and radiation detection. However, it requires the dielectric function of the target materials, which is not well known except for liquid water. Therefore we developed a model to perform track-structure calculation based on a systematic formula of secondary electron production cross section and that of stopping power. The model can therefore perform track-structure calculation regardless of the availability of dielectric function measurement data. Stopping range, and energy deposition radial distribution calculated by this model agreed well with the earlier experimental data and calculation by precedent codes. The lineal energy in tissue-equivalent gas calculated by this model agreed with measurement data taken from literature, showing distinct difference from that in liquid water. This model was implemented to PHITS Ver3.25, the general-purpose radiation transport simulation code of JAEA, being distributed to users as the first track-structure calculation model applicable to arbitrary materials available in general-purpose transport code.
Matsuya, Yusuke; Kai, Takeshi; Ogawa, Tatsuhiko; Hirata, Yuho; Sato, Tatsuhiko
Hoshasen Kagaku (Internet), (112), p.15 - 20, 2021/11
Particle and Heavy Ion Transport code System (PHITS) is a general-purpose Monte Carlo code enabling radiation kinetics, which is often used in diverse research fields, such as atomic energy, engineering, medicine and science. After released in 2010, the PHITS code has been developed to expand its functions and to improve its convenience. In the few years, track-structure mode has been introduced in PHITS that can simulate each atomic interaction by electrons, positions, protons and carbon ions in liquid water. Thanks to the development of track-structure mode, the latest PHITS code enables microscopic dose calculations by decomposing it to the scale of DNA. Aiming at realizing the track-structure mode with high precision, the further developments of electron and ion track-structure mode for arbitrary materials are recently ongoing. This review shows the development history and future prospect of PHITS track-structure mode, which can expect to be further applied to the research fields of atomic physics, radiation chemistry, and quantum life science.
Matsuya, Yusuke; Kai, Takeshi; Sato, Tatsuhiko; Liamsuwan, T.*; Sasaki, Kohei*; Nikjoo, H.*
Physics in Medicine & Biology, 66(6), p.06NT02_1 - 06NT02_11, 2021/03
Times Cited Count：17 Percentile：90.49(Engineering, Biomedical)A general-purpose Monte Carlo radiation transport simulation code, Particle and Heavy Ion Transport code System (PHITS), has the ability to handle diverse particle types over a wide range of energy. In PHITS version 3.20, ion track structure mode has been developed based on the algorithms in the KURBUC code, which enables to simulate the atomic interactions by primary ion and secondary particles (named as PHITS-KURBUC mode). In this study, we compared the range, radial dose distributions, and microdosimetric distributions calculated using the PHITS-KURBUC mode to the corresponding data obtained from the original KURBUC and from other studies. These comparative studies confirm the successful inclusion of the KURBUC code in the PHITS code. As results of the synergistic effect between the macroscopic and microscopic radiation transport codes, this implementation enabled the detailed calculation of the microdosimetric and nanodosimetric quantities under complex radiation fields, such as proton beam therapy with the spread-out Bragg peak. This PHITS-KURBUC mode is expected to pave the way for next-generation radiation researches, such as radiation physics, radiological protection, medical physics, and radiation biology.
Toigawa, Tomohiro; Tsubata, Yasuhiro; Kai, Takeshi; Furuta, Takuya; Kumagai, Yuta; Matsumura, Tatsuro
Solvent Extraction and Ion Exchange, 39(1), p.74 - 89, 2021/00
Times Cited Count：2 Percentile：10.1(Chemistry, Multidisciplinary)Absorbed-dose estimation is essential for evaluation of the radiation feasibility of minor-actinide-separation processes. We propose a dose-evaluation method based on radiation permeability, with comparisons of heterogeneous structures seen in the solvent-extraction process, such as emulsions forming in the mixture of the organic and aqueous phases. A demonstration of radiation-energy-transfer simulation is performed with a focus on the minor-actinide-recovery process from high-level liquid waste with the aid of the Monte Carlo radiation-transport code PHITS. The simulation results indicate that the dose absorbed by the extraction solvent from alpha ray depends upon the emulsion structure, and that from beta and gamma ray depends upon the mixer-settler-apparatus size. Non-negligible contributions of well-permeable gamma rays were indicated in terms of the plant operation of the minor-actinide-separation process.
