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JAEA Reports

Evaluation of fundamental performance of JAEA's new supercomputer system

Sakamoto, Kensaku; Shimizu, Futoshi; Tsuruoka, Takuya*; Nemoto, Toshiyuki*; Ishikawa, Naota*

JAEA-Testing 2011-005, 88 Pages, 2011/11

JAEA-Testing-2011-005.pdf:5.16MB

A new supercomputer system was deployed at JAEA in March 2010. The system is mainly composed of a large scale Linux cluster system (PRIMERGY BX900: 200Tflops) and a lead off system of RIKEN's K computer (FX1: 12Tflops), whose purposes are to deliver a high-performance parallel computing environment and application code development environment for the K computer, respectively. In this report, we present results of the evaluation of fundamental performance of the system.

Journal Articles

An Approach to DNA crystallization using the thermal reversible process of DNA duplexes

Chatake, Toshiyuki*; Sazaki, Gen*; Kikko, Tatsuhiko*; Fujiwara, Satoru; Ishikawa, Takuya*; Matsumoto, Osamu*; Morimoto, Yukio*

Crystal Growth & Design, 10(3), p.1090 - 1095, 2010/03

 Times Cited Count:4 Percentile:48.38(Chemistry, Multidisciplinary)

We propose a technique for DNA crystallization using the thermal reversible process of DNA: a conversion between a double-stranded DNA (dsDNA) and two single-stranded DNAs (ssDNAs) with temperatures. We investigated the solubility of the crystals of a DNA hexamer d(CGCGCG) and their melting temperature, at which the thermal conversion occurs. The results obtained suggest that the conversion from a dsDNA to ssDNAs results in an increase in solubility. It was shown that using this temperature-controlled technique, high-grade single crystals of the DNA hexamer could be obtained from a small amount of DNA samples. This easy-to-apply technique would be superior to the conventional vapor diffusion technique in that it allows the solubility of DNA crystals to be controlled with no need for expensive setups.

Journal Articles

A Neutron crystallographic analysis of a cubic porcine insulin at pD 6.6

Ishikawa, Takuya*; Chatake, Toshiyuki*; Onishi, Yuki*; Tanaka, Ichiro*; Kurihara, Kazuo; Kuroki, Ryota; Niimura, Nobuo*

Chemical Physics, 345(2-3), p.152 - 158, 2008/04

 Times Cited Count:14 Percentile:44.73(Chemistry, Physical)

Oral presentation

Crystallization of $$beta$$-lactoglobulin, $$alpha$$-amylase, 2Zn-insulin, cubic-insulin and RNase a for neutron diffraction experiment

Yagi, Daichi*; Ebata, Toshinobu*; Ichige, Toshikatsu*; Kobayashi, Yoichiro*; Ishikawa, Takuya*; Yamashita, Masahiro*; Onishi, Yuki*; Tanaka, Ichiro*; Kurihara, Kazuo; Niimura, Nobuo*

no journal, , 

no abstracts in English

Oral presentation

Neutron diffraction study of cubic insulin at two different pDs

Ishikawa, Takuya*; Tanaka, Ichiro*; Chatake, Toshiyuki*; Kurihara, Kazuo; Onishi, Yuki*; Kusaka, Katsuhiro; Tamada, Taro; Kuroki, Ryota; Niimura, Nobuo*

no journal, , 

It is known that the protonation status of amino acid side chains can strongly affect the biological function and stability of a protein. It is often hard to estimate it because it depends also on the local environment of the side chain. Neutron diffraction is a powerful tool to observe hydrogen atoms because of its strong interaction with hydrogen. Thus, a neutron study of cubic insulin at pD 6 has been carried out using the BIX-4 diffractometer (JRR-3, JAEA) and the result was compared with the previous neutron study at pD 9 (Maeda, et al. 2004) and by X-ray at pH 6 (Diao, 2003). A large single crystal of cubic insulin was prepared based on the crystallization phase diagram. The crystal diffracted to 2.5 ${AA}$ resolution. It was found that only N$$_{pi}$$ of His 5 in the B-chain is protonated whereas both N$$_{pi}$$ and N$$_{tau}$$ of His10 in the B-chain is protonated at pD 6 and the results at pD 9 are also the same (the pK of histidine side chains in the free form is around 6.0). These indicate that neutron diffraction study is useful to determine the protonation status of a protein.

Oral presentation

In water observation of mock-up of the top of fuel pins using under sodium viewing system in the experimental fast reactor Joyo

Ishikawa, Takashi; Kawahara, Hirotaka; Yamashita, Takuya; Tagawa, Akihiro; Komai, Masafumi*

no journal, , 

no abstracts in English

Oral presentation

Development of the restoration support system for environment, 3; Verification of the system

Motohashi, Jun; Terauchi, Makoto; Yamashita, Takuya; Tagawa, Akihiro; Ishikawa, Satoshi*; Yamaguchi, Katsuyoshi*; Kosuge, Fumiaki*; Kinoshita, Naoki*; Homma, Ryohei*

no journal, , 

no abstracts in English

Oral presentation

Development of the restoration support system for environment, 1; Outline of the system

Yamashita, Takuya; Terauchi, Makoto; Motohashi, Jun; Tagawa, Akihiro; Ishikawa, Satoshi*; Yamaguchi, Katsuyoshi*; Kosuge, Fumiaki*; Kinoshita, Naoki*; Homma, Ryohei*

no journal, , 

The Restoration Support System for Environment "RESET" was developed to estimate the dose rate of post-decontamination and assist planning of the future decontamination by using a cloud computer installed on the Internet. This paper describes the outline of development of the system.

Oral presentation

Development of the restoration support system for environment, 2; Design of the system

Yamashita, Takuya; Tagawa, Akihiro; Terauchi, Makoto; Motohashi, Jun; Homma, Ryohei*; Ishikawa, Satoshi*; Yamaguchi, Katsuyoshi*; Kosuge, Fumiaki*; Kinoshita, Naoki*

no journal, , 

In order to support decontamination activities, the system which evaluates the reduction effect of the environmental dose rate before and after the decontamination for a wade area was developed.

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