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Journal Articles

Design and actual performance of J-PARC 3 GeV rapid cycling synchrotron for high-intensity operation

Yamamoto, Kazami; Kinsho, Michikazu; Hayashi, Naoki; Saha, P. K.; Tamura, Fumihiko; Yamamoto, Masanobu; Tani, Norio; Takayanagi, Tomohiro; Kamiya, Junichiro; Shobuda, Yoshihiro; et al.

Journal of Nuclear Science and Technology, 32 Pages, 2022/02

In the Japan Proton Accelerator Research Complex, the purpose of the 3 GeV rapid cycling synchrotron (RCS) is to accelerate a 1 MW, high-intensity proton beam. To achieve beam operation at a repetition rate of 25 Hz at high intensities, the RCS was elaborately designed. After starting the RCS operation, we carefully verified the validity of its design and made certain improvements to establish a reliable operation at higher power as possible. Consequently, we demonstrated beam operation at a high power, namely, 1 MW. We then summarized the design, actual performance, and improvements of the RCS to achieve a 1 MW beam.

Journal Articles

A 3 MeV linac for development of accelerator components at J-PARC

Kondo, Yasuhiro; Asano, Hiroyuki*; Chishiro, Etsuji; Hirano, Koichiro; Ishiyama, Tatsuya; Ito, Takashi; Kawane, Yusuke; Kikuzawa, Nobuhiro; Meigo, Shinichiro; Miura, Akihiko; et al.

Proceedings of 28th International Linear Accelerator Conference (LINAC 2016) (Internet), p.298 - 300, 2017/05

We have constructed a linac for development of various accelerator components at J-PARC. The ion source is same as the J-PARC linac's, and the RFQ is a used one in the J-PARC linac. The beam energy is 3 MeV and nominal beam current is 30 mA. The accelerator has been already commissioned, and the first development program, laser-charge-exchange experiment for the transmutation experimental facility, has been started. In this paper, present status of this 3-MeV linac is presented.

Journal Articles

Development of a control system at a 3 MeV linac in J-PARC

Sawabe, Yuki*; Ishiyama, Tatsuya; Takahashi, Daisuke; Kato, Yuko; Suzuki, Takahiro*; Hirano, Koichiro; Takei, Hayanori; Meigo, Shinichiro; Kikuzawa, Nobuhiro; Hayashi, Naoki

Proceedings of 13th Annual Meeting of Particle Accelerator Society of Japan (Internet), p.647 - 651, 2016/11

In the J-PARC, a 3 MeV linac has been developed for the tests of beam scraper irradiation and charge exchange by high-power laser. To accomplish tests efficiently and safely, the control system for 3 MeV was designed and developed, and this system consists of four subsystems, personal protection system, machine protection system, timing system, and remote control system using the EPICS. In this paper, the details of control system for a 3 MeV linac are presented.

Journal Articles

Development of beam scrapers using a 3-Mev linac at J-PARC

Hirano, Koichiro; Asano, Hiroyuki; Ishiyama, Tatsuya; Ito, Takashi; Okoshi, Kiyonori; Oguri, Hidetomo; Kondo, Yasuhiro; Kawane, Yusuke; Kikuzawa, Nobuhiro; Sato, Yoshikatsu; et al.

Proceedings of 13th Annual Meeting of Particle Accelerator Society of Japan (Internet), p.310 - 313, 2016/11

We have used a beam scraper with the incident angle of 65deg to reduce the beam power deposition density in the MEBT between a 324 MHz RFQ and a 50-MeV DTL of the J-PARC linac. The 65$$^{circ}$$ scraper was irradiated by the H$$^{-}$$ beam up to particle number of 1.47E22. We observed a lot of surface projections with several hundred micrometers high in the beam irradiation damage on the scraper by using the laser microscope. In order to study the limits of scrapers, we constructed a new 3 MeV linac at J-PARC. We will conduct the scraper irradiation test at the end of this year.

Journal Articles

Ligand-induced protein responses and mechanical signal propagation described by linear response theories

Yang, L.-W.*; Kitao, Akio*; Huang, B.-C.*; Go, Nobuhiro*

Biophysical Journal, 107(6), p.1415 - 1425, 2014/09

 Times Cited Count:15 Percentile:55.96(Biophysics)

Journal Articles

Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses

Kai, Takeshi; Tokuhisa, Atsushi*; Moribayashi, Kengo; Fukuda, Yuji; Kono, Hidetoshi; Go, Nobuhiro*

Journal of the Physical Society of Japan, 83(9), p.094301_1 - 094301_5, 2014/09

 Times Cited Count:1 Percentile:13.18(Physics, Multidisciplinary)

no abstracts in English

Journal Articles

High-speed classification of coherent X-ray diffraction Patterns on the K computer for high-resolution single biomolecule imaging

Tokuhisa, Atsushi*; Arai, Junya*; Jochi, Yasumasa*; Ono, Yoshiyuki*; Kameyama, Toyohisa*; Yamamoto, Keiji*; Hatanaka, Masayuki*; Gerofi, B.*; Shimada, Akio*; Kurokawa, Motoyoshi*; et al.

Journal of Synchrotron Radiation, 20(6), p.899 - 904, 2013/11

 Times Cited Count:4 Percentile:27.21(Instruments & Instrumentation)

Journal Articles

Development of MLF-inhibit system for J-PARC

Ishiyama, Tatsuya; Ito, Yuichi; Kikuzawa, Nobuhiro; Suzuki, Takahiro; Oi, Motoki; Meigo, Shinichiro; Sakai, Kenji; Kato, Yuko

Proceedings of 9th Annual Meeting of Particle Accelerator Society of Japan (Internet), p.714 - 716, 2013/08

no abstracts in English

Journal Articles

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function; Resolution limit due to the quantum noise

Tokuhisa, Atsushi*; Taka, Junichiro*; Kono, Hidetoshi; Go, Nobuhiro*

Acta Crystallographica Section A, 68(3), p.366 - 381, 2012/05

 Times Cited Count:18 Percentile:82.22(Chemistry, Multidisciplinary)

Journal Articles

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding

Higuchi, Mariko; Fujii, Jumpei*; Yonetani, Yoshiteru; Kitao, Akio*; Go, Nobuhiro*

Journal of Structural Biology, 173(1), p.20 - 28, 2011/01

 Times Cited Count:2 Percentile:6.99(Biochemistry & Molecular Biology)

MutT distinguishes substrate 8-oxo-dGTP from dGTP and also 8-oxo-dGMP from dGMP despite small differences of chemical structures between them. In this paper we show by the method of molecular dynamics simulation that the transition between conformational substates of MutT is a key mechanism for a high resolution molecular recognition of the differences between the very similar chemical compounds. The native state MutT has two conformational substates with similar free energies, each characterized by either open or close of two loops surrounding the substrate binding active site. Between the two substates, the open substate is more stable in free MutT and in dGMP-MutT complex, and the closed substate is more stable in 8-oxo-dGMP-MutT complex. A hydrogen bond between H7 atom of 8-oxo-dGMP and the sidechain of Asn119 plays a crucial role for maintaining the closed substate in 8-oxo-dGMP-MutT complex.

Journal Articles

Progress in R&D efforts on the energy recovery linac in Japan

Sakanaka, Shogo*; Ago, Tomonori*; Enomoto, Atsushi*; Fukuda, Shigeki*; Furukawa, Kazuro*; Furuya, Takaaki*; Haga, Kaiichi*; Harada, Kentaro*; Hiramatsu, Shigenori*; Honda, Toru*; et al.

Proceedings of 11th European Particle Accelerator Conference (EPAC '08) (CD-ROM), p.205 - 207, 2008/06

Future synchrotron light sources based on the energy-recovery linacs (ERLs) are expected to be capable of producing super-brilliant and/or ultra-short pulses of synchrotron radiation. Our Japanese collaboration team is making efforts for realizing an ERL-based hard X-ray source. We report recent progress in our R&D efforts.

Journal Articles

Physics and biology of protein

Go, Nobuhiro

Progress of Theoretical Physics Supplement, (170), p.198 - 213, 2008/01

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:90 Percentile:86.66(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

BAAQ; An Infrastructure for application integration and knowledge discovery in bioinformatics

Gong, X.*; Nakamura, Kensuke; Yura, Kei; Go, Nobuhiro

IEEE Transactions on Information Technology in Biomedicine, 11(4), p.428 - 434, 2007/07

 Times Cited Count:3 Percentile:28.56(Computer Science, Information Systems)

The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory. However, the development of grid applications is still a nightmare for general bioinformatics scientists, due to the lack of grid programming environments. Here, we present a system, which we named Bioinformatics: Ask Any Questions (BAAQ), to automate this development procedure as much as possible. BAAQ allows scientists to store and manage remote biological data and programs, to build analysis workflows that integrate these resources seamlessly, and to discover knowledge from available resources. This paper addresses two issues in building grid applications in bioinformatics: how to smoothly compose an analysis workflow using heterogeneous resources and how to efficiently discover and re-use available resources in the grid community. Correspondingly an intelligent grid programming environment and an active solution recommendation service are proposed.

Journal Articles

Analysis of the function of a large-scale supra-biomolecule system by molecular dynamics simulation system, SCUBA (Simulation Codes for hUge Biomolecular Assembly)

Ishida, Hisashi; Higuchi, Mariko; Yonetani, Yoshiteru*; Kano, Takuma; Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro

Annual Report of the Earth Simulator Center April 2005 - March 2006, p.237 - 240, 2007/01

no abstracts in English

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:17.86(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

Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction

Kim, O. T. P.*; Yura, Kei; Go, Nobuhiro

Nucleic Acids Research, 34(22), p.6450 - 6460, 2006/12

 Times Cited Count:87 Percentile:84.91(Biochemistry & Molecular Biology)

Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex three-dimensional (3D) structures has increased, it is now possible to statistically examine protein-RNA interactions based on 3D structures. We performed computational analyses of 86 representative protein-RNA complexes retrieved from the Protein Data Bank. Interface residue propensity was calculated for each amino acid residue type (residue singlet interface propensity). In addition to the residue singlet propensity, we introduce a new residue doublet interface propensity. The residue doublet interface propensity contains much more information than the sum of two singlet propensities alone. The prediction of the RNA interface using the two types of propensities plus a position-specific multiple sequence profile can achieve a specificity of about 80 percent.

Journal Articles

Hydration-coupled protein boson peak measured by incoherent neutron scattering

Nakagawa, Hiroshi; Kataoka, Mikio*; Jochi, Yasumasa*; Kitao, Akio*; Shibata, Kaoru; Tokuhisa, Atsushi*; Tsukushi, Itaru*; Go, Nobuhiro

Physica B; Condensed Matter, 385-386(2), p.871 - 873, 2006/11

 Times Cited Count:13 Percentile:53.84(Physics, Condensed Matter)

The boson peak of a protein was examined in relation to hydration using staphylococcal nuclease. Although the boson peak is commonly observed in synthetic polymers, glassy materials and amorphous materials, the origin of the boson peak is not fully understood. The motions that contribute to the peak are harmonic vibrations. Upon hydration the peak frequency shifts to a higher frequency and the effective force constant of the vibration increases at low temperatures, suggesting that the protein energy surface is modified. Hydration of the protein leads to a more rugged surface and the vibrational motions are trapped within the local minimum at cryogenic temperatures. The origin of the protein boson peak may be related to this rugged energy surface.

Journal Articles

Switch interactions control energy frustration and multiple flagellar filament structures

Kitao, Akio*; Yonekura, Koji*; Yonekura, Saori*; Samatey, F.*; Imada, Katsumi*; Namba, Keiichi*; Go, Nobuhiro

Proceedings of the National Academy of Sciences of the United States of America, 103(13), p.4894 - 4899, 2006/03

 Times Cited Count:44 Percentile:65.45(Multidisciplinary Sciences)

no abstracts in English

Journal Articles

Development of molecular dynamics simulation system for large-scale supra-biomolecules, PABIOS (PArallel BIOmolecular Simulator)

Ishida, Hisashi; Higuchi, Mariko; Yonetani, Yoshiteru*; Kano, Takuma; Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro

Annual Report of the Earth Simulator Center April 2004 - March 2005, p.241 - 246, 2005/12

no abstracts in English

82 (Records 1-20 displayed on this page)