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.

Development of a model for evaluating the luminescence intensity of phosphors based on the PHITS track-structure simulation

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

https://doi.org/10.1016/j.nimb.2023.165183

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.

Development of an areal density imaging for boron and other elements

Tsuchikawa, Yusuke; Kai, Tetsuya; Abe, Yuta; Oikawa, Kenichi; Parker, J. D.*; Shinohara, Takenao; Sato, Ikken

Journal of Physics; Conference Series, 2605, p.012022_1 - 012022_6, 2023/10

https://doi.org/10.1088/1742-6596/2605/1/012022

We developed a method to obtain the areal density distribution of boron, which has a large neutron cross section, by means of an energy resolved neutron imaging. Commonly in a measurement of elements with very high neutron sensitivity, the quantitative measurement becomes more difficult with the amount of element due to the neutron self-shielding effect. To avoid this effect, an energy-resolved method using known cross section data was attempted, and a quantitative imaging of such elements was demonstrated at the MLF of J-PARC. This presentation introduces a measurement of melted simulated-fuel assemblies obtained in the research of the Fukushima Daiichi Nuclear Power Plant after the severe accident. Energy-dependent neutron transmission rates of the samples were measured by a neutron imaging detector, and were analyzed to obtained the areal density of boron at each position.

Improvement of the hybrid approach between Monte Carlo simulation and analytical function for calculating microdosimetric probability densities in macroscopic matter

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

https://doi.org/10.1088/1361-6560/ace14c

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.

Assessment of the infiltration behaviour of buffer material in seawater-type groundwater environments using a coupled THMC analysis model (Contract research)

Suzuki, Hideaki*; Takayama, Yusuke; Sato, Hisashi*; Watahiki, Takanori*; Sato, Daisuke*

JAEA-Research 2022-013, 41 Pages, 2023/03

JAEA-Research-2022-013.pdf:3.99MB

It is anticipated that the coupled thermal-hydraulic-mechanical and chemical (THMC) processes will occur, involving an interactive process with radioactive decay heat arising from the vitrified waste, infiltration of groundwater from the host rock into the buffer material, swelling pressure of buffer material due to its saturation and chemical reaction between bentonite and pore-water in the near-field of a geological disposal system for high-level radioactive waste repository. In order to evaluate these phenomena in the near-field, the THMC model has been developed. In this study, For the purpose of evaluating the near-field infiltration behavior in seawater-type groundwater environment, a hydraulic model was set in which the permeability of the buffer material change depending on the salt concentration in the pore-water. In order to evaluate the drying phenomenon of the buffer material due to waste heat, a temperature gradient water transfer model was set in consideration of the dependence of temperature and pore-water saturation. The THMC analysis of the in-situ experiment of engineered barrier system (EBS) experiment at the Horonobe Underground Research Laboratory was carried out. The validity of the model was then checked through comparison with measured data.

Recent improvements of the Particle and Heavy Ion Transport code System; PHITS version 3.33

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

https://doi.org/10.1080/00223131.2023.2275736

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.

Translational study for stereotactic body radiotherapy against non-small cell lung cancer, including oligometastases, considering cancer stem-like cells enable predicting clinical outcome from data

Saga, Ryo*; Matsuya, Yusuke; Sato, Hikari*; Hasegawa, Kazuki*; Obara, Hideki*; Komai, Fumio*; Yoshino, Hironori*; Aoki, Masahiko*; Hosokawa, Yoichiro*

Radiotherapy and Oncology, p.109444_1 - 109444_9, 2023/00

https://doi.org/10.1016/j.radonc.2022.109444

When treating non-small cell lung cancer (NSCLC), stereotactic body radiotherapy (SBRT) with high-dose irradiation is often utilized. The fractionation schemes and curative effects can be evaluated by mathematical models for predicting cell survival curve. Such model parameters can be determined from in vitro experiment, but they are empirically determined based on experiences in clinics. As such, there is a large gap between in vitro and clinical study. As such background, translational study between in vitro cell survival and clinical curative effects is necessary. In this study, explicitly considering existence of cancer stem-like cells (CSCs), we developed an all-in-one model for predicting both in vitro cell survival and clinical curative effects (integrated microdosimetric-kinetic (IMK) model) and performed retrospective evaluation of clinical outcomes following SBRT for NSCLC in Hirosaki University Hospital. As a result, the IMK model successfully reproduced both in vitro cell survival and the tumor control probability with various fractionation schemes (i.e., 6-10 Gy per fraction). The developed model would contribute on precisely understanding the impact of CSCs on curative effects after SBRT for NSCLC with high precision.

Application of a simple DNA damage model developed for electrons to proton irradiation

Matsuya, Yusuke; Kai, Takeshi; Parisi, A.*; Yoshii, Yuji*; Sato, Tatsuhiko

Physics in Medicine & Biology, 67(21), p.215017_1 - 215017_13, 2022/11

https://doi.org/10.1088/1361-6560/ac9a20

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.

Partial breakdown of translation symmetry at a structural quantum critical point associated with a ferroelectric soft mode

Ishii, Yui*; Yamamoto, Arisa*; Sato, Naoki*; Nambu, Yusuke*; Kawamura, Seiko; Murai, Naoki; Ohara, Koji*; Kawaguchi, Shogo*; Mori, Takao*; Mori, Shigeo*

Physical Review B, 106(13), p.134111_1 - 134111_7, 2022/10

https://doi.org/10.1103/PhysRevB.106.134111

Development of the DICOM-based Monte Carlo dose reconstruction system for a retrospective study on the secondary cancer risk in carbon ion radiotherapy

Furuta, Takuya; Koba, Yusuke*; Hashimoto, Shintaro; Chang, W.*; Yonai, Shunsuke*; Matsumoto, Shinnosuke*; Ishikawa, Akihisa*; Sato, Tatsuhiko

Physics in Medicine & Biology, 67(14), p.145002_1 - 145002_15, 2022/07

https://doi.org/10.1088/1361-6560/ac7998

Carbon ion radiotherapy has an advantage over conventional radiotherapy such that its superior dose concentration on the tumor helps to reduce unwanted dose to surrounding normal tissues. Nevertheless, a little dose to normal tissues, which is a potential risk of secondary cancer, is still unavoidable. The Monte Carlo simulation is a good candidate for the tool to assess secondary cancer risk, including the contributions of secondary particles produced by nuclear reactions. We therefore developed a new dose reconstruction system implementing PHITS as the engine. In this system, the PHITS input is automatically created from the DICOM data sets recorded in the treatment planning. The developed system was validated by comparing to experimental dose distribution in water and treatment plan on an anthropomorphic phantom. This system will be used for retrospective studies using the patient data in National Institute for Quantum and Science and Technology.