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Nakagawa, Hiroshi; Yonetani, Yoshiteru*; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya*; Inamura, Yasuhiro; Kataoka, Mikio*; Kono, Hidetoshi*
JPS Conference Proceedings (Internet), 33, p.011101_1 - 011101_6, 2021/03
Hydration water dynamics were measured by quasi-elastic neutron scattering with Hn
O/DO contrast for two DNA dodecamers, 5'CGCG
CGCG'3 and 5'CGCG
CGCG'3, which have been computationally shown to be structurally rigid and flexible, respectively. The dynamical transitions of the hydration water as well as DNA were observed for both sequences at approximately 240 K. Above the transition temperature, the mean square displacements of the hydration water for the rigid sequence were smaller than those for the flexible one. Furthermore, the relaxation time of the hydration water was longer in the rigid DNA than in the flexible DNA. We suggest that hydration water dynamics on the picosecond timescale are associated with sequence-dependent deformability of DNA.
Nakagawa, Yosuke; Sukegawa, Hidetoshi; Naoi, Yosuke; Inoue, Naoko; Noro, Naoko; Okuda, Masahiro
Dai-41-Kai Nihon Kaku Busshitsu Kanri Gakkai Nenji Taikai Kaigi Rombunshu (Internet), 4 Pages, 2020/11
The physical protection exercise field, a facility equipped with various types of equipment such as sensors, cameras and fences that are used at nuclear facilities, is an effective tool for training on nuclear security at ISCN/JAEA, if it is carried out in-person. Due to the COVID-19 pandemic, the virtual tour of the facility is developed for the online training courses so that they could be more effective. The article explains the initial development of the virtual tour with some improvement inspired by using it on some occasions as well as a prospect of effective use of the virtual tour based on its characteristics.
Nakagawa, Hiroshi; Yonetani, Yoshiteru; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Inamura, Yasuhiro; Kataoka, Mikio; Kono, Hidetoshi
Physical Review E, 90(2), p.022723_1 - 022723_11, 2014/08
Times Cited Count：10 Percentile：55.34(Physics, Fluids & Plasmas)Molecular dynamics (MD) simulations and Quasi-Elastic Neutron Scattering (QENS) experiments were conducted on hydrated two DNA dodecamers with distinct deformability; 5'CGCGAATTCGCG3' and 5'CGCGTTAACGCG3'. The former is known to be rigid and the latter to be flexible. The mean-square displacements (MSDs) of DNA dodecamers exhibit so-called dynamical transition around 200-240 K for both sequences. To investigate the DNA sequence dependent dynamics, the dynamics of DNA and hydration water above the transition temperature were examined using both MD simulations and QENS experiments. The fluctuation amplitude of the AATT central tetramer is smaller, and its relaxation time is longer, than that observed in TTAA, suggesting that the AT step is kinetically more stable than TA. The sequence-dependent local base pair step dynamics correlate with the kinetics of breaking the hydrogen bond between DNA and hydration water. The sequence dependent DNA base pair step fluctuations appear above the dynamical transition temperature. Together with these results, we conclude that DNA deformability is related to the local dynamics of base pair step, themselves coupled to hydration water in the minor groove.
Yoshikawa, Hiroshi; Sakaki, Hironao; Sako, Hiroyuki; Takahashi, Hiroki; Shen, G.; Kato, Yuko; Ito, Yuichi; Ikeda, Hiroshi*; Ishiyama, Tatsuya*; Tsuchiya, Hitoshi*; et al.
Proceedings of International Conference on Accelerator and Large Experimental Physics Control Systems (ICALEPCS '07) (CD-ROM), p.62 - 64, 2007/10
J-PARC is a large scale facility of the proton accelerators for the multi-purpose of scientific researches in Japan. This facility consists of three accelerators and three experimental stations. Now, J-PARC is under construction, and LINAC is operated for one year, 3GeV synchrotron has just started the commissioning in this October the 1st. The completion of this facility will be next summer. The control system of accelerators established fundamental performance for the initial commissioning. The most important requirement to the control system of this facility is to minimize the activation of accelerator devices. In this paper, we show that the performances of each layer of this control system have been achieved in the initial stage.
Nakagawa, Hiroshi; Yonetani, Yoshiteru; Kono, Hidetoshi; Kataoka, Mikio; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Inamura, Yasuhiro
no journal, ,
no abstracts in English
Yonetani, Yoshiteru; Nakagawa, Hiroshi; Kono, Hidetoshi
no journal, ,
no abstracts in English
Nakagawa, Hiroshi; Yonetani, Yoshiteru; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Inamura, Yasuhiro; Kataoka, Mikio; Kono, Hidetoshi
no journal, ,
Molecular dynamics simulations and inelastic neutron scattering experiments were conducted on two hydrated DNA dodecamers with distinct deformability; CGCGAATTCGCG and CGCGTTAACGCG. The mean-square displacements of both DNA dodecamers exhibit so-called dynamical transition around 200-240 K and hydration water also exhibits the abrupt increase in the mean-square displacement at the same temperature. The fluctuation amplitude of the central tetramer AATT is smaller, and its relaxation time longer, than that observed on TTAA, suggesting that the AT step is kinetically more stable than the TA step. The sequence dependent DNA base pair step fluctuations appear above the dynamical transition temperature. Therefore, we concluded that the hydration water induces the DNA dynamical transition, and this enhanced motion by hydration is related to the deformability of DNA structure.
