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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：0.19(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.
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：8 Percentile：99.12(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.
Sato, Tatsuhiko; Matsuya, Yusuke; Kai, Takeshi; Ogawa, Tatsuhiko; Hirata, Yuho; Sekikawa, Takuya
no journal, ,
DNA damage calculation using the track-structure mode of PHITS will be discussed at the meeting.
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.
NiSe
, 4Tsuchida, 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 TaNiSe, 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.
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.
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.
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.
NiSe
Tsuchida, Shun*; Hirose, Yusuke*; Sekikawa, Takuya; Ono, Yoshiaki*; Settai, Rikio*
no journal, ,
Excitonic 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 have begun to attract attention as a new physical property. In this study, we focused on TaNiSe, which is one of the excitonic insulator candidates, but its synthesis itself is difficult and its physical properties have not yet been clarified. The electrical resistivity of M=Ti, Zr, and Hf at low temperatures is 5 to 6 orders of magnitude lower than that of the parent material. Furthermore, when titanium is substituted for tantalum (M=Ti), the electrical resistivity of samples 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.
Sekikawa, Takuya; Kai, Takeshi; Onuma, Sota*; Haga, Yoshinori; Yokoya, Akinari*
no journal, ,
Uracil is a base of ribonucleic acid (RNA), which is responsible for copying genetic information from deoxyribonucleic acid (DNA) and transporting it to ribosomes, where protein synthesis takes place. The radiation sensitizing effect of uracil bromide, in which bromine is substituted for a part of uracil, has been expected to be effective. In this study, we used the first-principles calculation software OpenMX to investigate the effect of partial substitution of halogen for uracil. The results of calculations targeting molecules with uracil partially substituted with fluorine and bromine showed that the electrons in uracil halide are easily ionized in the order of fluorine and bromine. The results of this study are expected to contribute to the development of radiosensitizers for radiotherapy.
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, in order to theoretically investigate the transient molecular conformational changes until DNA damage is established, we used the first-principles calculation software OpenMX to perform calculations targeting DNA that produces 1
20 holes, where the holes are trapped in the guanine bases of the DNA when there are few holes and the DNA with many holes In the case of DNA, it was found that the main strand mainly contributes to the chemical reaction. The results of this study will contribute to the elucidation of the first-phase processes of radiation biological effects.
NiSe, 5Tsuchida, 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 are attracting attention as a novel physical property. In this study, we succeeded in growing an element-substituted sample (Ta1-xMx)NiSe (M=Ti, Zr, Hf) and found that the electrical resistivity of the high-temperature phase of the sample with a Ti content of 0.06 or more exhibits a metallic behavior. The electrical resistivity of the high-temperature phase behaves metallurgically for samples with a titanium (Ti) content of 0.06 or more. This is in contrast to the pressure effect, which changes from an insulator to a metallic phase discontinuously. Therefore, we also report the results of the electrical resistivity measurement under pressure of (Ta1-xTix)NiSe, in which the element substitution effect and the pressure effect exist simultaneously. The phase transition shown in this study is a new insight into the realization of excitonic insulators.
