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Journal Articles

Changes in molecular conformation and electronic structure of DNA under $$^{12}$$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

 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.

Journal Articles

Clogging properties of HEPA filter induced by loading of soot from burned glove-box panel materials

Tashiro, Shinsuke; Ono, Takuya; Amano, Yuki; Yoshida, Ryoichiro; Watanabe, Koji*; Abe, Hitoshi

Nuclear Technology, 208(10), p.1553 - 1561, 2022/10

 Times Cited Count:0 Percentile:0.01(Nuclear Science & Technology)

To contribute to the confinement safety evaluation of the radioactive materials in the Glove box (GB) fire accident, combustion tests with the Polymethyl methacrylate (PMMA) and the Polycarbonate (PC) as typical panel materials for the GB have been conducted with a relatively large scale apparatus. As the important data for evaluating confinement safety, the release ratio and the particle size distribution of the soot generated from the burned materials were obtained. Furthermore, the rise of the differential pressure ($$Delta$$P) of the high efficiency particle air (HEPA) filter by the soot loading was also investigated. As results, the release ratio of the soot from the PC was about seven times as large as the PMMA. In addition, it was found that the behavior of the rise of the $$Delta$$P with soot loading could be represented uniformly regardless of kinds of combustion materials by considering effect of the loading volume of the soot particle in the relatively low loading region.

Journal Articles

Differential pressure changes of a high airflow-type HEPA filter during solvent fire in reprocessing facilities

Tashiro, Shinsuke; Uchiyama, Gunzo; Ono, Takuya; Amano, Yuki; Yoshida, Ryoichiro; Abe, Hitoshi

Nuclear Technology, 208(7), p.1205 - 1213, 2022/07

 Times Cited Count:0 Percentile:0.01(Nuclear Science & Technology)

A clogging behavior of a high-efficiency particulate air (HEPA) filter at solvent fire accidents for reprocessing facilities has been studied. In this study, the burning rates of 30% tri-butyl phosphate (TBP)/dodecane (DD) mixed solvent and DD solvent and the differential pressure ($$Delta$$P) of a high airflow typed HEPA filter applied in the actual facilities in Japan were measured. It was confirmed that the mainly burned was DD at the early stage of the mixed solvent burning and the TBP at the late stage. Furthermore, it was found that the $$Delta$$P rapidly rose at the late stage of the mixed solvent burning. The increase of the release ratio of the unburned particulate composition (TBP, its degraded solvent and inorganic phosphorus (P$$_{2}$$O$$_{5}$$)) was considered to contribute to the rapid rise. The correlating formulas with the $$Delta$$P and the mass of the loading particulates, except for the region of the rapid rise of $$Delta$$P, could be induced.

JAEA Reports

Effect of nitrous acid on migration behavior of gaseous ruthenium tetroxide into liquid phase

Yoshida, Naoki; Ono, Takuya; Yoshida, Ryoichiro; Amano, Yuki; Abe, Hitoshi

JAEA-Research 2021-011, 12 Pages, 2022/01

JAEA-Research-2021-011.pdf:1.49MB

In boiling and drying accidents involving high-level liquid waste in fuel reprocessing plants, emphasis is placed on the behavior of ruthenium (Ru). Ru would form volatile species, such as ruthenium tetroxide (RuO$$_{4}$$), and could be released to the environment with coexisting gases, including nitric acid, water, or nitrogen oxides. In this study, to contribute toward safety evaluations of these types of accidents, the migration behavior of gaseous Ru into the liquid phase has been experimentally measured by simulating the condensate during an accident. The gas absorption of RuO$$_{4}$$ was enhanced by increasing the nitrous acid (HNO$$_{2}$$) concentration in the liquid phase, indicating the occurrence of chemical absorption. In control experiments without HNO$$_{2}$$, the lower the temperature, the greater was the Ru recovery ratio in the liquid phase. Conversely, in experiments with HNO$$_{2}$$, the higher the temperature, the higher the recovery ratio, suggesting that the reaction involved in chemical absorption was activated at higher temperatures.

Journal Articles

Consistent modelling of material weight loss and gas release due to pyrolysis and conducting benchmark tests of the model; A Case for glovebox panel materials such as polymethyl methacrylate

Ono, Takuya; Tashiro, Shinsuke; Amano, Yuki; Yoshida, Naoki; Yoshida, Ryoichiro; Abe, Hitoshi

PLOS ONE (Internet), 16(1), p.e0245303_1 - e0245303_16, 2021/01

 Times Cited Count:2 Percentile:11.76(Multidisciplinary Sciences)

It is necessary to consider how a glove box's confinement function will be lost when evaluating the amount of radioactive material leaking from a nuclear facility during a fire. In this study, we build a model that consistently explains the weight loss of glove box materials because of heat input from a flame and accompanying generation of the pyrolysis gas. The weight loss suggests thinning of the glove box housing, and the generation of pyrolysis gas suggests the possibility of fire spreading. The target was polymethyl methacrylate (PMMA), used as the glove box panel. Thermal gravimetric tests on PMMA determined the parameters to be substituted in the Arrhenius equation for predicting the weight loss in pyrolysis. The pyrolysis process of PMMA was divided into 3 stages with activation energies of 62 kJ/mol, 250 kJ/mol, and 265 kJ/mol. Furthermore, quantifying the gas composition revealed that the composition of the pyrolysis gas released from PMMA can be approximated as 100 percent methyl methacrylate. This result suggests that the released amount of methyl methacrylate can be estimated by the Arrhenius equation. To investigate the validity of such estimation, a sealed vessel test was performed. In this test, we observed increase of the number of gas molecules during the pyrolysis as internal pressure change of the vessel. The number of gas molecules was similar to that estimated from the Arrhenius equation, and indicated the validity of our method. Moreover, we also performed the same tests on bisphenol-A-polycarbonate (PC) for comparison. In case of PC, the number of gas molecules obtained in the vessel test was higher than the estimated value.

JAEA Reports

Effect of nitrogen oxides on decomposition behavior of gaseous ruthenium tetroxide

Yoshida, Naoki; Amano, Yuki; Ono, Takuya; Yoshida, Ryoichiro; Abe, Hitoshi

JAEA-Research 2020-014, 33 Pages, 2020/12

JAEA-Research-2020-014.pdf:3.66MB

Considering the boiling and drying accident of high-level liquid waste in fuel reprocessing plant, Ruthenium (Ru) is an important element. It is because Ru would form volatile compounds such as ruthenium tetroxide (RuO$$_{4}$$) and could be released into the environment with other coexisting gasses such as nitric oxides (NOx) such as nitric oxide (NO) and nitrogen dioxide (NO$$_{2}$$). To contribute to the safety evaluation of this accident, we experimentally evaluated the effect of NOx on the decomposition and chemical change behavior of the gaseous RuO$$_{4}$$ (RuO$$_{4}$$(g)). As a result, the RuO$$_{4}$$(g) decomposed over time under the atmospheric gasses with NO or NO$$_{2}$$, however, the decomposition rate was slower than the results of experiments without NOx. These results showed that the NOx stabilized RuO$$_{4}$$(g).

Journal Articles

Decomposition behavior of gaseous ruthenium tetroxide under atmospheric conditions assuming evaporation to dryness accident of high-level liquid waste

Yoshida, Naoki; Ono, Takuya; Yoshida, Ryoichiro; Amano, Yuki; Abe, Hitoshi

Journal of Nuclear Science and Technology, 57(11), p.1256 - 1264, 2020/11

 Times Cited Count:8 Percentile:71.58(Nuclear Science & Technology)

Emphasis has been placed on the behavior of ruthenium (Ru) in the evaporation to dryness accident due to the loss of cooling functions (EDLCF) of high-level liquid waste in fuel reprocessing plants. It is because Ru would form volatile compounds such as ruthenium tetroxide (RuO$$_{4}$$) and could be released into the environment with other coexisting gasses such as nitric acid (HNO$$_{3}$$), water (H$$_{2}$$O). To contribute to the safety evaluation of this accident, we experimentally evaluated the decomposition and chemical change behavior of the gaseous RuO$$_{4}$$ (RuO$$_{4}$$(g)) under the various atmospheric conditions: temperature and composition of coexisting gasses. As a result, the behavior of the RuO$$_{4}$$(g) was diverse depending on the atmospheric conditions. In the experiments with the dry air or H$$_{2}$$O vapor, decomposition of RuO$$_{4}$$(g) was observed. In the experiment with the mixed gas which containing HNO$$_{3}$$, almost no decomposition of the RuO$$_{4}$$(g) was observed, and chemical form of the RuO$$_{4}$$(g) was retained.

Journal Articles

Rapid clogging of high-efficiency particulate air filters during in-cell solvent fires at reprocessing facilities

Ono, Takuya; Tashiro, Shinsuke; Amano, Yuki; Yoshida, Ryoichiro; Abe, Hitoshi

Nuclear Technology, 206(1), p.40 - 47, 2020/01

 Times Cited Count:2 Percentile:24.28(Nuclear Science & Technology)

Recent Japanese nuclear regulations have focused on the hazards of in-cell solvent fires at reprocessing facilities. In this work, a mixture of tributyl phosphate and dodecane-based solvents was burned to generate an aerosol composed of soot and unburned solvent that was then loaded onto a high-efficiency particulate air filter simulating the ventilation system of reprocessing facilities. A radical increase of differential pressure occurred in the filters during these tests after the dodecane burned out from the solvent in a phenomenon we named as rapid clogging, likely caused by the burnout of dodecane. This relationship provides valuable insight into the establishment of new regulations for reprocessing facilities. This work indicates that clogging of ventilation filters during solvent fires may occur more rapidly than previously estimated.

Journal Articles

Migration behavior of gaseous ruthenium tetroxide under boiling and drying accident condition in reprocessing plant

Yoshida, Naoki; Ono, Takuya; Amano, Yuki; Abe, Hitoshi

Journal of Nuclear Science and Technology, 55(6), p.599 - 604, 2018/06

 Times Cited Count:7 Percentile:52.79(Nuclear Science & Technology)

In the boiling and drying accident of high-level liquid waste in the fuel reprocessing plant, behavior of ruthenium (Ru) has attracted much attention because Ru could form volatile compounds such as ruthenium tetroxide (RuO$$_{4}$$) and could be released into the environment. To contribute towards safety evaluation of this accident, the migration behavior and the leak path factor of the gaseous ruthenium compound has been experimentally measured in this study. The experiment was proceeded by using the Ruthenium Migration Evaluating Apparatus, which partially simulates the atmospheric condition (temperature, flow rate, and composition of water vapor and gaseous nitric acid mixture) of migration pathway in the accident. Experiments with dry air and water vapor were also performed as the control experiment to discuss the effect of nitric acid. As a result, the experiment with dry air and the experiment with water vapor demonstrated that the majority of the ruthenium deposited along the migration pathway. On the other hand, the experiment with the water vapor containing gaseous nitric acid demonstrated that almost all of the ruthenium passed through the migration pathway without deposition. These results suggested that the migration behavior of gaseous ruthenium will be affected by the gas-phase composition.

Journal Articles

HEPA filter clogging and volatile material release under solvent fire accident in fuel reprocessing facility

Ono, Takuya; Watanabe, Koji; Tashiro, Shinsuke; Amano, Yuki; Abe, Hitoshi

Proceedings of 25th International Conference on Nuclear Engineering (ICONE-25) (CD-ROM), 7 Pages, 2017/07

After the Fukushima-Daiichi accident, countermeasures against the severe accident are newly required as regulatory items for nuclear facilities. Organic solvent fire in cell was defined as one of the accidents in the fuel reprocessing plant. When the solvent burns, aerosols including soot are released. The substances clog HEPA filters in the ventilation system and their breakthrough may happen because of differential pressure rising. Moreover, the fire can also release volatile radioactive gaseous species, which can pass through HEPA filters. These phenomena are important for evaluation of confinement capability of the facility and public exposure. We have investigated, in relating to the clogging behavior, release behavior of aerosols as well as of volatile materials from burnt solvent. In the presentation, we will report experimental data and evaluation results obtained from recent research.

Journal Articles

Use of fracture filling mineral assemblages for characterizing water-rock interactions during exhumation of an accretionary complex; An Example from the Shimanto Belt, southern Kyushu Japan

Ono, Takuya; Yoshida, Hidekazu*; Metcalfe, R.*

Journal of Structural Geology, 87, p.81 - 94, 2016/06

 Times Cited Count:4 Percentile:14.04(Geosciences, Multidisciplinary)

Fracture filling minerals were formed during the development of an accretionary complex. Each mineral formed under favourable geological conditions and can be used to estimate the conditions of accretion. Geological observations and analyses were made on fracture fillings from boreholes of ca. 140 m depth, in the Shimanto Belt of Kyushu. Results revealed that the minerals were formed in 5 stages distinguished by the textural relationships of the minerals. Filling minerals show that the studied rock formation has been subducted to several km depth and the temperature reached was ca. 200 - 300$$^{circ}$$C. After the subduction, the rock formation uplifted and surface acidic water penetrated up to 80 m beneath the present ground surface. The acid water dissolved calcite fillings to form the present groundwater flow-paths. The results shown here imply that filling minerals can be an effective tool to evaluate the environmental changes during accretionary complex formation.

Oral presentation

Design study for flow around pump shaft of Integrated IHX/pump of fast reactor JSFR, 2; Study of liquid sloshing caused by rotating pump shaft

Handa, Takuya; Enuma, Yasuhiro; Ono, Yukihiko*; Nakamura, Yuki*; Sakata, Nobuyasu*; Kushioka, Kiyonori*; Shimoji, Kuniyuki*; Inoue, Tomoyuki*; Matsumoto, Iwao*

no journal, , 

no abstracts in English

Oral presentation

Design study for flow around pump shaft of Integrated IHX/pump of fast reactor JSFR, 1; Study of pump shaft deformation by natural convection of cover gas

Enuma, Yasuhiro; Handa, Takuya; Shimazaki, Masanori*; Ono, Yukihiko*; Yoshida, Kazuhiro*; Hayakawa, Satoshi*; Inoue, Tomoyuki*

no journal, , 

no abstracts in English

Oral presentation

Characteristics and formation processes of water-conducting fractures in the Hyuga Group of the Shimanto Belt

Ono, Takuya; Yoshida, Hidekazu*

no journal, , 

Very few studies have been performed to reveal characteristics and evolutions of water-conducting fractures in sedimentary rocks of accretionary complexes. Accretionary complexes can be a proposed site for geological disposal in Japan. Because of such backgrounds, we investigated fractures in borehole cores excavated from the Hyuga Group of the Shimanto Belt in the south of the Kyushu Island. Microscopic observation, SEM observation, XRD analysis and XRF analysis of minerals in/around fractures revealed characteristics of water-conducting fractures in accretionary complex and a process of fracture sealing according to carbonate mineral precipitation.

Oral presentation

R&D on reduction technology of hydrogen generation in long-term waste storage containers, 8; Reaction mechanism of hydrogen recombination catalysts studied by synchrotron X-ray absorption spectroscopy

Matsumura, Daiju; Tsuji, Takuya; Nishihata, Yasuo; Hino, Ryutaro; Taniguchi, Masashi*; Takenaka, Keisuke*; Ono, Hitomi*; Kita, Tomoaki*; Tanaka, Hirohisa*

no journal, , 

no abstracts in English

Oral presentation

First-principles calculations of molecular structure and electronic state changes in DNA induced by radiation-induced holes

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

no journal, , 

Deoxyribonucleic acid (DNA) carries the genetic information of living organisms through various combinations of guanine, cytosine, adenine, and thymine, and radiation biological effects are mainly caused by damage to DNA. In this study, in order to theoretically investigate the transient molecular conformational changes that occur before DNA damage takes hold, we analyzed the behavior of the sites responsible for the conformational changes and chemical reactions by targeting the DNA that produced the holes using the first-principles calculation software OpenMX. As a result, it was confirmed that the holes reproduce the event of trapping in the guanine molecule of DNA, which reproduces the experimental results, and it was also newly found that the DNA sugar chain shows intense molecular fluctuation. The results of this study are expected to contribute to the elucidation of the first-phase process of radiation biological effects.

Oral presentation

Carrier doping effect of excitonic insulator candidate Ta$$_{2}$$NiSe$$_{5}$$, 4

Tsuchida, Shun*; Hirose, Yusuke*; Sekikawa, Takuya; Ono, Yoshiaki*; Settai, Rikio*

no journal, , 

Exciton insulators have the property that the entire crystal becomes an insulator due to the collective behavior of electrons and holes bound together in the crystal, and they are beginning to attract attention as a new physical property. In this study, we focused on Ta$$_{2}$$NiSe$$_{5}$$, which is one of the excitonic insulator candidates, but its synthesis itself is difficult and its physical properties have not yet been clarified. Furthermore, when titanium is substituted for tantalum (M = Ti), the electrical resistivity of the sample with composition ratio x less than 0.06 is semiconducting, while the electrical resistivity of the high-temperature phase behaves metallic when x = 0.06 or higher. The phase transition shown in this study may be a new insight into the realization of excitonic insulators.

Oral presentation

First-principles calculations of DNA irradiated with a proton and a carbon ion beam

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

no journal, , 

Deoxyribonucleic acid (DNA) carries the genetic information of living organisms through various combinations of guanine, cytosine, adenine, and thymine, and radiation biological effects are mainly caused by damage to this DNA. In this study, we theoretically investigated the transient molecular conformational changes that occur before DNA damage takes hold, using the heavy particle and ion transport code PHITS and the first-principles calculation software OpenMX. As a result, it was clarified that the chemical reaction site of DNA shifts from guanine and cytosine, which carry genetic information, to the sugar chain, which supports the entire DNA, and that the new DNA sugar chain shows intense molecular fluctuations. The results of this study will contribute to the elucidation of the initial process of radiation biological effects.

Oral presentation

Computer simulation of the first stage of radiation biological effects; Effects of radiation damage on the electronic state of DNA

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

no journal, , 

Deoxyribonucleic acid (DNA) carries the genetic information of living organisms through various combinations of guanine, cytosine, adenine, and thymine, and biological effects of radiation are mainly caused by damage to this DNA. In this study, in order to theoretically investigate the transient changes in molecular structure until DNA damage is established, the number of holes produced by radiation-induced carbon beams was calculated using the Particle and Heavy Ion Transport code System (PHITS), and the number of holes produced by the first The first principle calculation software OpenMX was used to calculate the sites responsible for conformational changes and chemical reactions by targeting the DNA that produced the holes. As a result, the experimental result that a small number of holes are trapped in the guanine molecule of DNA is reproduced, while a large number of holes are trapped in the hybrid orbital of the sugar chain and guanine molecule of DNA. The results of this study are expected to contribute to the elucidation of the initial processes of radiation biological effects.

Oral presentation

GPU acceleration of first-principles electronic structure calculation software OpenMX and its application to modified-DNA

Kawai, Hiroyuki*; Sekikawa, Takuya; Ozaki, Taisuke*; Furuya, Shinnosuke*; Ono, Yoshiaki*

no journal, , 

First-principles electronic structure calculation software OpenMX is a calculation code based on density functional theory, and is mainly used to obtain the most stable structures and electronic states of materials. In this study, we attempted to develop a method to accelerate OpenMX calculations using a GPU (Graphics Processing Unit), which is usually used for image processing, and succeeded in reducing the calculation time to about one-half of that using the same number of CPUs in a benchmark calculation on DNA. The benchmark calculation on DNA succeeded in reducing the calculation time by about one-half compared to the same number of CPUs. We then applied the method developed in this study to modified-DNA (DNA in which some of the atoms constituting a base pair are replaced with transition metals or organic molecules), which has been investigated using OpenMX, and verified the degree of speed-up. Details of the obtained modified-DNA, including its electronic state, will be presented on the day.

23 (Records 1-20 displayed on this page)