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Journal Articles

Martensitic transformation behavior of Fe-Ni-C alloys monitored by ${it in-situ}$ neutron diffraction during cryogenic cooling

Yamashita, Takayuki*; Harjo, S.; Kawasaki, Takuro; Morooka, Satoshi; Gong, W.; Fujii, Hidetoshi*; Tomota, Yo*

ISIJ International, 64(2), p.192 - 201, 2024/01

Journal Articles

Impacts of friction stir processing on irradiation effects in vacuum-plasma-spray coated tungsten

Ozawa, Kazumi; Tanigawa, Hiroyasu; Morisada, Yoshiaki*; Fujii, Hidetoshi*

Fusion Engineering and Design, 98-99, p.2054 - 2057, 2015/10

 Times Cited Count:1 Percentile:9.79(Nuclear Science & Technology)

Reduced activation ferritic/martensitic steel, as typified by F82H, is a promising candidate for structural material of DEMO fusion reactors. To prevent plasma sputtering, tungsten (W) coating was essentially required. This study aims to examine the irradiation effects on hardness and microstructure of vacuum-plasma-spray coated W-F82H steel, with a special emphasis on the impacts of grain-refining induced by frictional stir processing (FSP). It was revealed that the hardness of the VPS-FSP W after ion-irradiation to 5.4 dpa at 800$$^{circ}$$C were not remarkably changed, where bulk W usually exhibited significant irradiation hardening.

Journal Articles

Modification of vacuum plasma sprayed tungsten coating on reduced activation ferritic/martensitic steels by friction stir processing

Tanigawa, Hiroyasu; Ozawa, Kazumi; Morisada, Yoshiaki*; Noh, S.*; Fujii, Hidetoshi*

Fusion Engineering and Design, 98-99, p.2080 - 2084, 2015/10

 Times Cited Count:10 Percentile:64.82(Nuclear Science & Technology)

The vacuum plasma spray (VPS) technique has been investigated as the most practical method to form Tungsten (W) layer as a plasma facing material in fusion devices. The issues are the thermal conductivity and the strength of VPS-W, i.e., the thermal conductivity of VPS-W were significantly lower than that of the bulk W, and the hardness of VPS-W is much less than that of the bulk W. These are mainly caused by the porous structure of VPS-W. In order to solve these issues, friction stir processing (FPS) was applied on VPS-W in this study. It was suggested that FSP can contribute to significant improvement both in mechanical and thermal properties of VPS-W coating.

Journal Articles

Sequence-dependent DNA deformability studied using molecular dynamics simulations

Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*

Nucleic Acids Research, 35(18), p.6063 - 6074, 2007/09

 Times Cited Count:96 Percentile:86.58(Biochemistry & Molecular Biology)

Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base-pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base-pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base-pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

Journal Articles

DNA deformability and hydration studied by molecular dynamics simulation

Yonetani, Yoshiteru*; Kono, Hidetoshi; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro

Molecular Simulation, 33(1-2), p.103 - 107, 2007/01

 Times Cited Count:5 Percentile:16.64(Chemistry, Physical)

DNA tetramer sequences AATT and TTAA are known to be conformationally more rigid and flexible, respectively. In this study, we carry out molecular dynamics simulations of these two sequences, and investigate the characteristic hydration pattern. The rigid AATT is found to be more likely to construct the hydration spine in the minor groove than the flexible TTAA. The result suggests that the hydration water molecules play a critical role for determining the sequence dependent deformability of DNA conformation.

Journal Articles

Overview of national centralized tokamak program; Mission, design and strategy to contribute ITER and DEMO

Ninomiya, Hiromasa; Akiba, Masato; Fujii, Tsuneyuki; Fujita, Takaaki; Fujiwara, Masami*; Hamamatsu, Kiyotaka; Hayashi, Nobuhiko; Hosogane, Nobuyuki; Ikeda, Yoshitaka; Inoue, Nobuyuki; et al.

Journal of the Korean Physical Society, 49, p.S428 - S432, 2006/12

To contribute DEMO and ITER, the design to modify the present JT-60U into superconducting coil machine, named National Centralized Tokamak (NCT), is being progressed under nationwide collaborations in Japan. Mission, design and strategy of this NCT program is summarized.

Journal Articles

Overview of the national centralized tokamak programme

Kikuchi, Mitsuru; Tamai, Hiroshi; Matsukawa, Makoto; Fujita, Takaaki; Takase, Yuichi*; Sakurai, Shinji; Kizu, Kaname; Tsuchiya, Katsuhiko; Kurita, Genichi; Morioka, Atsuhiko; et al.

Nuclear Fusion, 46(3), p.S29 - S38, 2006/03

 Times Cited Count:13 Percentile:41.84(Physics, Fluids & Plasmas)

The National Centralized Tokamak (NCT) facility program is a domestic research program for advanced tokamak research to succeed JT-60U incorporating Japanese university accomplishments. The mission of NCT is to establish high beta steady-state operation for DEMO and to contribute to ITER. The machine flexibility and mobility is pursued in aspect ratio and shape controllability, feedback control of resistive wall modes, wide current and pressure profile control capability for the demonstration of the high-b steady state.

Journal Articles

Engineering design and control scenario for steady-state high-beta operation in national centralized tokamak

Tsuchiya, Katsuhiko; Akiba, Masato; Azechi, Hiroshi*; Fujii, Tsuneyuki; Fujita, Takaaki; Fujiwara, Masami*; Hamamatsu, Kiyotaka; Hashizume, Hidetoshi*; Hayashi, Nobuhiko; Horiike, Hiroshi*; et al.

Fusion Engineering and Design, 81(8-14), p.1599 - 1605, 2006/02

 Times Cited Count:1 Percentile:9.98(Nuclear Science & Technology)

no abstracts in English

Journal Articles

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations; Toward understanding the indirect readout mechanism in protein-DNA recognition

Ara$'u$zo-Bravo, M. J.*; Fujii, Satoshi*; Kono, Hidetoshi; Ahmad, S.*; Sarai, Akinori*

Journal of the American Chemical Society, 127(46), p.16074 - 16089, 2005/11

 Times Cited Count:46 Percentile:73.07(Chemistry, Multidisciplinary)

no abstracts in English

Journal Articles

Prediction of material behavior by database and neural network model within Bayesian framework

Tsuji, Hirokazu; Fujii, Hidetoshi*

Proceedings of 10th German-Japanese Workshop on Chemical Information, p.127 - 130, 2002/00

A neural network model within a Bayesian framework was adopted based on the material database constructed by JAERI for prediction of creep rupture properties of irradiated type 304 stainless steel. Stress level was modeled as a function of 18 variables, including rupture life, creep test temperature, chemical compositions; 10 elements, heat treatment temperature, heat treatment duration, neutron irradiation temperature, fast neutron fluence, thermal neutron fluence, irradiation time, based on JAERI material database in which 347 creep rupture data sets of type 304 stainless steels were stored. The Bayesian method puts error bars on the predicted values of the rupture strength and allows the significance of each individual factor to be estimated.

Journal Articles

Application of multivariables analysis method to prediction of material behaviors

Tsuji, Hirokazu; Fujii, Hidetoshi*

Tahenryo Kaiseki Jitsurei Handobukku, p.107 - 114, 2002/00

no abstracts in English

Oral presentation

Balance of direct readout and indirect readout contributions to protein-DNA recognition

Kono, Hidetoshi; Kumar, S.*; Ahmad, S.*; Ara$'u$zo-Bravo, M. J.*; Fujii, Satoshi*; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Oral presentation

Indirect readout by DNA binding proteins; Analysis of sequence dependent conformation by molecular dynamics simulation

Fujii, Satoshi*; Ara$'u$zo-Bravo, M. J.*; Takenaka, Shigeori*; Kono, Hidetoshi; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Oral presentation

Analysis of sequence-dependent conformation of DNA backbone torsion angles by molecular dynamics simulations

Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Oral presentation

Sequence context dependent flexibility of DNA studied by molecular dynamics simulation

Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Oral presentation

DNA sequence-dependent deformability associated with hydration; Implication for indirect readout in protein-DNA interactions

Kono, Hidetoshi; Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro

no journal, , 

Proteins recognize specific DNA sequences not only through direct contact between amino acids and base-pairs, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetramericsequences sandwiched between CGCG sequences. We found that the average conformation and deformability of the tetramers can be highly sequence dependent. Even the tetrameric sequences having the same dimeric sequence at the center showed the distinct deformabilities dependent on the bases on either end of the tetramers. Such conformations of tetramers were found to be associated with hydration. The tetrameric sequences with AT at their center, for instance, generally were rigid and highly hydrated. The rigidity among the tetramers was affected by the flanking bases and also correlated with the amount of hydration which we defined as number of water molecules bridging two bases belonging to different chains in minor groove. These results suggest that hydration of DNA is responsible for the mechanism of indirect readout during protein-DNA recognition. We also show that the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

Oral presentation

The Role of the sequence-dependent DNA backbone conformation on the parotein-DNA recognition

Fujii, Satoshi*; Kono, Hidetoshi; Takenaka, Shigeori*; Go, Nobuhiro; Sarai, Akinori*

no journal, , 

no abstracts in English

Oral presentation

Sequence-dependent DNA deformability and hydration

Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Kono, Hidetoshi; Go, Nobuhiro

no journal, , 

no abstracts in English

Oral presentation

DNA sequence specific hydration responsible for conformational flexibility; Molecular dynamics simulation on all possible tetramer sequences

Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Kono, Hidetoshi; Go, Nobuhiro

no journal, , 

DNA conformation and deformability depend on sequence composition. For example, it is known that a sequence containing contiguous AT steps is more deformable. The variability in DNA conformation and deformability has been believed to be one of important factors in specific recognition of DNA sequence by regulatory proteins. Several factors can be considered to yield the difference in DNA conformation and deformability among distinct DNA sequences. One is the mechanical stiffness inherent in the DNA itself, which is originated from base-pairing hydrogen interactions and base-stacking interactions. Another important factor affecting the DNA conformation and deformability is the hydration. The hydration effect is inevitable when discussing the structural properties of DNA, since DNA is physiologically surrounded by water molecules, and the structure cannot be maintained without water. A characteristic hydration pattern observed for DNA is the spine of water, which is composed of the highly ordered water molecules aligned along the floor of the minor groove. Such a hydration pattern as well as the conformation of DNA is dependent on the sequence. Consequently, the following question arises: How and to what extent does the hydration affect the sequence-dependent deformability of DNA ? To address this question, a comparative study of various DNA sequences is required. Recently, the sequence dependence of DNA conformation and deformability has been studied by MD simulations, where all possible 136 patterns for tetramer were examined. In the present work, we report further analysis of these 136 MD trajectories focused on the hydration water. We compared the both properties of DNA hydration and deformation, and found a possible relationship between them.

Oral presentation

DNA sequence-dependent deformability and hydration

Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Kono, Hidetoshi; Go, Nobuhiro

no journal, , 

no abstracts in English

35 (Records 1-20 displayed on this page)