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Kawai, Hiroyuki*; Sekikawa, Takuya; Ozaki, Taisuke*; Ono, Yoshiaki*
Journal of the Physical Society of Japan, 94(12), p.124003_1 - 124003_15, 2025/12
Times Cited Count：1 Percentile：37.78(Physics, Multidisciplinary)OpenMX, a first-principles electronic structure calculation software, is a computational code based on density functional theory primarily used to determine the stable structure and electronic states of materials. This study attempted to develop a method for accelerating calculations using OpenMX by employing a GPU, Graphics Processing Unit, typically used for image processing. Test calculations on a 512-atom diamond structure silicon system achieved approximately double the speed compared to CPU-based calculations. Furthermore, for noncollinear calculations used in magnetic structure calculations, a 384-atom silicon system achieved 2.6 times faster speed than the CPU. Especially, GPU acceleration for noncollinear calculations is unprecedented. The results obtained in this study enable the handling of larger systems than previously possible in first-principles electronic structure calculations.
Ti
)
NiSe
Tsuchida, Shun*; Hirose, Yusuke; Sekikawa, Takuya; Ono, Yoshiaki*; Hirahara, Takuya*; Sano, Sumika*; Kawaguchi, Shogo*; Kobayashi, Shintaro*; Uwatoko, Yoshiya*; Settai, Rikio*
Journal of the Physical Society of Japan, 94(11), p.114703_1 - 114703_7, 2025/10
Times Cited Count：2 Percentile：37.78(Physics, Multidisciplinary)We investigated the carrier doping effect on an excitonic insulator TaNiSe by means of the electrical resistivity 
and Hall coefficient 
using single crystals of (TaTi)NiSe, and band calculation. The excitonic transition temperature 
is continuously suppressed to 83 K at 
= 0.104 while preserving the crystal structure. With increasing substitution concentration , a semiconducting increment of and is strongly suppressed and a metallic behavior is observed at > 0.06. Ti substitution can realize an excitonic correlated metallic state. This metallization is explained by the hole doping effect based on the band calculations. Applying pressure to the carrier doped (TaTi)NiSe, we found superconductivity above 2.6 GPa, which is much smaller than that of TaNiSe around 8 GPa. The carrier doping induced by Ti substitution favors superconductivity in this compound.
Sekikawa, Takuya; Takada, Kazuki*; Kai, Takeshi; Ono, Yoshiaki*
Journal of Applied Physics, 137(20), p.203901_1 - 203901_10, 2025/05
Times Cited Count：0 Percentile：0.00(Physics, Applied)no abstracts in English
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
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.
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：1 Percentile：22.55(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, 61(1), p.127 - 135, 2024/01
Times Cited Count：369 Percentile：99.98(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.
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.
Tsuchida, Shun*; Hirose, Yusuke*; Sekikawa, Takuya; Ono, Yoshiaki*; Settai, Rikio*
no journal, ,
The 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 Ta
NiSe
, which is one of the excitonic insulator candidates, but its synthesis itself is difficult and its physical properties have not yet been clarified. As a result, superconductivity was observed in (TaM
)NiSe at x = 0.08 in the high pressure region. The superconducting transition temperature was found to increase with increasing pressure. The phase transition shown in this study may provide new insight into the relationship between exciton insulators and superconductivity.
Kawai, Hiroyuki*; An, S.*; Ozaki, Taisuke*; Sekikawa, Takuya; Ono, Yoshiaki*
no journal, ,
X-ray photoemission spectroscopy (XPS) is one of the most widely used techniques to study the chemical composition and electronic structure of materials near the surface. The physical quantity measured by XPS is essentially the energy value of the core electrons. On the other hand, theoretical calculations of the core-electron energy require the pseudopotential, which is the interaction energy between the excited core electrons and the surrounding nuclei and other electrons (core-excitation pseudopotential). In this study, we optimized many parameters necessary to obtain the core-excitation pseudopotential for Se using a Monte Carlo method, and produced a high-precision core-excitation pseudopotential for Se. Using this core-excitation pseudopotential, we calculated core-electron energy values for four Se compounds and found that they reproduced XPS measurements with high accuracy. The results of this study are expected to become a standard for theoretical calculations of XPS measurements in the future.
Wang, Y.*; Sekikawa, Takuya; Ono, Yoshiaki*; Kai, Takeshi
no journal, ,
DNA (deoxyribonucleic acid) is a molecule that plays an essential role in the storage and transmission of genetic information, and its structure and electronic state are deeply involved in its biological functions. The effects of radiation-induced DNA damage and hole generation on the electronic structure of nucleotide molecules have been the focus of much attention in recent years. In this study, the electronic states of nucleotide molecules in water and in the vacuum environment were analyzed in detail using the first-principles calculation software OpenMX. In particular, the electronic state changes in the neutral, one-electron-lost, and two-electron-lost states of the molecule were calculated, indicating that the shape of the chemical reaction region of the nucleotide molecule changes in the aqueous solution environment and when the molecule includes hole, resulting in a significant change in the physical properties of the molecule. The results of this study will contribute to the elucidation of the initial process of radiation biological effects.
Ikaida, Riku*; Sekikawa, Takuya; Toigawa, Tomohiro; Ono, Yoshiaki*; Kai, Takeshi
no journal, ,
The organic molecule called Tetra-Octyl-DiGlycol-Amide (TODGA) is used to extract minor actinides (MA) and rare earth elements (RE) from high-level radioactive liquid waste. In the actual extraction process, MAs and REs bound to TODGA are extracted from the organic layer by stirring an oily organic solvent in which TODGA is dissolved and a high-level liquid waste. However, it has been reported that the extraction performance of TODGA decreases after prolonged use due to 
-radiolysis. In addition, the physical and physicochemical processes related to radiolysis of TODGA have not been fully elucidated. In this study, we used the first-principles calculation software OpenMX to calculate the molecular structural changes in the physical and physicochemical processes of TODGA induced by ionization. As a result, we found molecular conformational changes and intramolecular proton transfer corresponding to the degradation products obtained experimentally. The elucidation of this process will lead to the clarification of the degradation behavior of TODGA and the mechanism of -ray induced hydrogen evolution.
based on the first-principles calculations; Analysis using Tetrahedron Method IIIkaida, Riku*; Sekikawa, Takuya; Ono, Yoshiaki*; Sano, Kazuhiro*; Masuda, Yoshimi*
no journal, ,
The SrTiO, a dilute mixture of Nb and other elements, has been studied as one of the most dilute free electron superconductors. At the same time, SrTiO has a huge dielectric constant at low temperatures, and ferroelectric transition occurs due to the substitution of O18 for O16 and Ca for Sr. Furthermore, an increase in the superconducting transition temperature Tc has been observed at substitution concentrations near where the ferroelectric transition occurs. However, the relationship between ferroelectricity and superconductivity is not clarified. In this study, we calculated the physical quantities related to ferroelectricity and superconductivity in the free electron density region near the highest superconducting transition temperature using the first-principles calculation software Quantum ESPRESSO. In the result, we found that the frequency of crystal oscillation decreases with decreasing free electron density, which is an indication of the ferroelectric transition. Furthermore, we found that Tc increases with decreasing free electron density. These results lead to a theoretical clarification of the relationship between ferroelectricity and superconductivity in SrTiO.
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 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.
NiSeTsuchida, 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.
Sekikawa, Takuya; Matsuya, Yusuke; Kawai, Hiroyuki*; Hwang, B.*; Ishizaka, Masato*; 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, we simulated ionization distributions induced within a DNA by carbon ion beam, and evaluated the molecular conformational changes in the DNA. We first calculated the numbers of ionizations in the DNA induced by carbon ion using Particle and Heavy-Ion Transport code System (PHITS). Second, the stable structure and wave function of the DNA under the condition that one and two electrons are ionized by radiation were calculated using a first-principles calculation software OpenMX. As a result, we found that a small number of holes can reproduce the experimental results in which the holes spread to the base molecules (that carry genetic information in DNA), while a large number of holes can be trapped in the hybrid orbit of the sugar chain molecules (that support the overall structure of DNA) and base molecules. Our results are expected to contribute to the deeper understanding of the ionized DNA molecules.
Sekikawa, Takuya; Inokuma, Yusuke*; Ono, Yoshiaki*; Tokunaga, Yo; Kai, Takeshi
no journal, ,
Deoxyribonucleic acid (DNA), which carries the genetic information of living organisms through the diverse arrangement of guanine-cytosine and adenine-thymine base pairs, has been discussed as a stage of solid state physics as well as various possibilities including magnetism and superconductivity. In this study, we calculated the structural changes and band dispersion of DNA hole-doped by irradiation and other processes using the first-principles calculation software OpenMX. As a result, it was found that the relatively large molecular orbitals of base pairs, which carry genetic information, and the very narrow molecular orbitals of the sugar chain, which support the structure of DNA, hybridize, especially in the region where many electrons are lost above 10 valence, and an electronic state similar to the heavy electron system observed in rare earth compounds is developed. The discussion will also incorporate strong correlation effects such as the effective mass of electrons traveling DNA. The results of this research will contribute to the elucidation of the electronic structure of DNA and the heavy fermion state.
