Dynamics of proteins with different molecular structures under solution condition

Inoue, Rintaro*; Oda, Takashi*; Nakagawa, Hiroshi; Tominaga, Taiki*; Saio, Tomohide*; Kawakita, Yukinobu; Shimizu, Masahiro*; Okuda, Aya*; Morishima, Ken*; Sato, Nobuhiro*; et al.

Scientific Reports (Internet), 10, p.21678_1 - 21678_10, 2020/12

https://doi.org/10.1038/s41598-020-78311-4

Incoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, both low flux of neutron beam and absence of analytical procedure for extracting the internal dynamics from iQENS profile have been obstacles for studying it under physiological condition (in solution). Thanks to the recent development of neutron source, spectrometer and computational technique, they enable us to decouple internal dynamics, translational and rotational diffusions from the iQENS profile. The internal dynamics of two proteins: globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution were studied. It was found that the average relaxation rate of IDP was larger than that of GDP. Through the detailed analyses on their internal dynamics, it was revealed that the fraction of mobile H atoms in IDP was much higher than that in GDP. Interestingly, the fraction of mobile H atoms was closely related to the fraction of H atoms on highly solvent exposed surfaces. The iQENS study presented that the internal dynamics were governed by the highly solvent exposed amino acid residues depending upon protein molecular architectures.

Inspection and repair techniques in the reactor vessel of the experimental fast reactor Joyo; Development of cover gas recycling system with precise pressure control

Ushiki, Hiroshi*; Okuda, Eiji; Suzuki, Nobuhiro; Takamatsu, Misao; Nagai, Akinori

JAEA-Technology 2015-042, 37 Pages, 2016/02

JAEA-Technology-2015-042.pdf:16.51MB

The reactor vessel of a sodium-cooled fast reactor (SFR) is filled with sodium coolant and cover gas (argon gas). In case of a cover gas boundary open (ie., in-vessel repair), installation of a temporary cover gas boundary and controlling the cover gas pressure slightly positive are required to prevent the cover gas release and the contamination of impurities, and during upper core structure (UCS) replacement in the experimental SFR Joyo from March to December 2014, a vinyl bag was installed as a part of the temporary cover gas boundary. However, because it has inferior thermal resistance, supply a cooling gas too much was required to maintain proper temperature for two months. On the basis of this requirement, a cover gas recycling system with precise pressure control was developed and adopted for UCS replacement. The system has a good pressure controllability and recyclability. The successful results of this system contributed to the certain promotion of UCS replacement. In addition, the insights and the experience gathered in this development are expected to improve the in-vessel repair techniques in sodium-cooled fast reactors.

Spatial distributions of radionuclides deposited onto ground soil around the Fukushima Dai-ichi Nuclear Power Plant and their temporal change until December 2012

Mikami, Satoshi; Maeyama, Takeshi*; Hoshide, Yoshifumi*; Sakamoto, Ryuichi*; Sato, Shoji*; Okuda, Naotoshi*; Demongeot, S.*; Gurriaran, R.*; Uwamino, Yoshitomo*; Kato, Hiroaki*; et al.

Journal of Environmental Radioactivity, 139, p.320 - 343, 2015/01

https://doi.org/10.1016/j.jenvrad.2014.09.010

High speed eigenvalue solver on the Cell cluster system for controlling nuclear fusion plasma

Kushida, Noriyuki; Takemiya, Hiroshi; Tokuda, Shinji*

Proceedings of 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing (PDP 2010), p.482 - 488, 2010/02

In this study, we developed a high speed eigenvalue solver that is the necessity of plasma stability analysis system for International Thermo-nuclear Experimental Reactor (ITER) on Cell cluster system. According to our estimation, the most time consuming part of analysis system is eigensolver. However, current supercomputer is not applicable for such instantaneous calculation, because the overhead of network communication becomes dominant. Therefore, we employ Cell cluster system, whose processor has higher performance than current supercomputer, because we can obtain sufficient processing power with small number of processors. Furthermore, we developed novel eigenvalue solver with the consideration of hierarchical architecture of Cell cluster Finally, we succeeded to solve the block tridiagonal Hermitian matrix, which had 1024 diagonal blocks and the size of each block was 128 128 within a second.

Observation of itinerant Ce 4 electronic states in CeIrSi studied by angle-resolved Ce 3 resonance photoemission spectroscopy

Okochi, Takuo*; Toshimitsu, Takafumi*; Yamagami, Hiroshi; Fujimori, Shinichi; Yasui, Akira; Takeda, Yukiharu; Okane, Tetsuo; Saito, Yuji; Fujimori, Atsushi; Miyauchi, Yuichiro*; et al.

Journal of the Physical Society of Japan, 78(8), p.084802_1 - 084802_6, 2009/08

https://doi.org/10.1143/JPSJ.78.084802

We have applied angle-resolved Ce 34 resonance photoemission spectroscopy to the non-centrosymmetric pressure-induced superconductor CeIrSi and obtained the 4 band-structure and Fermi surfaces. We have found that the Ce 4 states are located mainly near the Fermi level and that the photoemission intensity derived from the dispersive conduction bands across the Fermi level shows considerable resonant enhancement. In addition, the band structure and Fermi surfaces of CeIrSi are different from those of the non- reference compound, LaIrSi and the difference is well explained by the band structure calculated within the local density approximation (LDA). These results strongly suggest that the Ce 4 electrons in CeIrSi are well hybridized with conduction bands and form itinerant electronic states.

Optimization of the parallel finite element method for the earth simulator

Kushida, Noriyuki; Okuda, Hiroshi*

Journal of Computational Science and Technology (Internet), 2(1), p.81 - 91, 2008/00

https://doi.org/10.1299/jcst.2.81

Since the earth simulator consists of 640 SMP nodes, each of which has eight vector processors, there are three levels of hierarchical parallelization methods: inter-node, intra-node, and vectorization. In the present study, intra-node and vectorization were added on the inter-node parallelized FEM code, and the performance was examined. As a result, we achieved 30 times acceleration at maximum. Additionally, we achieved 10 TeraFLOPS, which was approximately 30% of peak performance, when we used 4,096 processors.

Convergence acceleration of parallel CG-FEM with controlled domain decomposition for singularity problems

Kushida, Noriyuki; Okuda, Hiroshi*

Journal of Computational Science and Technology (Internet), 1(1), p.2 - 13, 2007/00

https://doi.org/10.1299/jcst.1.2

Stress singularity is usually observed in practical stress analysis, and it may lead to the deterioration of the convergence rate of the preconditioned conjugate gradient method(PCG). Until now, parallel PCG has been used without considering the practical issues; therefore, the deterioration was induced in the problem in which stress singularity was observed. The convergence acceleration method was developed in parallel PCG based on controlled domain decomposition. The acceleration method can be achieved by considering the spatial locality of stress singularity and preconditioning of conjugate gradient method. The convergence acceleration method reduces the 15 % of iteration of PCG as a maximum, where the singular area is included in one domain.

Pipe shape optimization by using adjoint variable method

Shinohara, Kazunori; Okuda, Hiroshi*; Ito, Satoshi*; Nakajima, Norihiro; Ida, Masato

Nihon Oyo Suri Gakkai 2006-Nendo Nenkai Koen Yokoshu, p.268 - 269, 2006/09

no abstracts in English

Shape optimization technique using adjoint variable method

Shinohara, Kazunori; Okuda, Hiroshi*; Ito, Satoshi*; Nakajima, Norihiro; Ida, Masato

Dai-19-Kai Suchi Ryutai Rikigaku Shimpojiumu Koen Yoshishu, P. 214, 2005/12

no abstracts in English

Nonlinear behaviour of collisionless double tearing mode induced by electron inertia

Matsumoto, Taro; Naito, Hiroshi*; Tokuda, Shinji; Kishimoto, Yasuaki*

Nuclear Fusion, 45(11), p.1264 - 1270, 2005/11

https://doi.org/10.1088/0029-5515/45/11/006

A gyrokinetic particle simulation is executed to clarify the effect of the electron inertia on the MHD phenomena in the reversed shear configuration (RSC) of a cylindrical tokamak plasma. It is found that the collisionless (kinetic) double tearing modes grow up at the Alfvn time scale, and nonlinearly induce the internal collapse when the helical flux at the magnetic axis is less than that at the outer resonant surface. After the internal collapse, the secondary reconnection is induced by the current concentration due to the convective flow. It is also clarified that a nonlinear dynamics accompanied with the elementary processes caused by the flow can generate a new RSC with resonant surfaces. In the presence of the density gradient, after the full reconnection induced by the mode, the radial electric field is found to be generated due to the difference of the motion between ions and electrons. However, the intensity of the radial field is not so large as that induced by the collisionless kink mode.