Essential function of the N-termini tails of the proteasome for the gating mechanism revealed by molecular dynamics simulations

Ishida, Hisashi

Proteins: Structure, Function, and Bioinformatics, 82(9), p.1985 - 1999, 2014/09

https://doi.org/10.1002/prot.24553

Dependence of fracture geometry and spatial variation in pressure on hydraulic conductivity in rock fractures

Kishida, Kiyoshi*; Hosoda, Takashi*; Sawada, Atsushi; Sato, Hisashi; Nakashima, Shinichiro*; Yasuhara, Hideaki*

Harmonising Rock Engineering and the Environment, p.1327 - 1330, 2011/10

https://onepetro.org/isrmcongress/proceedings-abstract/CONGRESS12/All-CONGRESS12/ISRM-12CONGRESS-2011-239/100321?redirectedFrom=PDF

Although it is generally known that a natural rock fracture indicates a complex aperture distribution, the fracture is an ideal representation of the parallel plate model. The cubic law is applied to evaluate the hydraulic properties of fractured rock. From several previous research works, it is known that the cubic law can be applied when the Reynolds number is less than 1.0 and that the advection term can basically be ignored in such fracture flows. In this research work, two-dimensional seepage flow analyses, using the authors' proposed 2D model which is considered with the advection term, are carried out for single fracture hydro-conductivity experiments under conditions which allow for the application of the cubic law. From the numerical results, the validity of the 2D model is discussed along with the local Reynolds number and the application of the cubic law.

Branch migration of Holliday junction in RuvA tetramer complex studied by umbrella sampling simulation using a path-search algorithm

Ishida, Hisashi

Journal of Computational Chemistry, 31(12), p.2317 - 2329, 2010/09

Global conformational changes of ribosome observed by normal mode fitting for 3D cryo-EM structures

Matsumoto, Atsushi; Ishida, Hisashi

Structure, 17(12), p.1605 - 1613, 2009/12

https://doi.org/10.1016/j.str.2009.09.017

Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome

Ishida, Hisashi; Hayward, S.*

Biophysical Journal, 95(12), p.5962 - 5973, 2008/12

https://doi.org/10.1529/biophysj.108.134890

Alpha-ray detection with a MgB transition edge sensor

Okayasu, Satoru; Katagiri, Masaki; Hojo, Kiichi; Morii, Yukio; Miki, Shigenobu*; Shimakage, Hisashi*; Wang, Z.*; Ishida, Takekazu*

Physica C, 468(15-20), p.1998 - 2000, 2008/09

https://doi.org/10.1016/j.physc.2008.05.114

We have been investigating for neutron detection with the MgB transition edge sensor (TES). For the purpose, we have been developing a low noise measurement system for neutron detection. To confirm the usefulness of our detecting system, alpha-ray detection from an Am source was achieved. To improve the sensitivity, short meander samples with 35 m length and 1 m width is used. Samples are fabricated by the Kansai group. Superconducting transition temperature Tc is 23.3 K. The transition width is sharp enough less than 1 K. The detection was achieved under a constant current condition, and the resistivity changes at the sample due to the alpha-ray irradiation were detected. The bias current is 6 A.

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; Yura, Kei; Kano, Takuma; Matsumoto, Atsushi

Annual Report of the Earth Simulator Center April 2006 - March 2007, p.257 - 263, 2007/09

http://www.jamstec.go.jp/esc/publication/annual/annual2006/

The Earth Simulator has the highest power ever achieved to perform molecular dynamics simulation of large-scale supra-molecular systems. We are developing a molecular dynamics simulation system, called SCUBA, which is designed to run a system composed of more than a million particles efficiently on parallel computers. This fisical year, the arrays used in the program of SCUBA were intensively optimized to reduce the amount of memory use. This optimization enabled SCUBA to perform molecular dynamics simulations of large-scale supra-molecular systems comprised of more than a million atoms on the Earth Simulator. Moreover, the Martyna-Klein-Tuckerman algorithm was extended to utilize the multiple time step method, which increases the time step length significantly. Then, in order to elucidate the dynamics of the 70S ribosome, molecular dynamics simulation of the 70S ribosome including its explicit solvent, a system which is composed of about two million atoms, has been performed using SCUBA. A model of a nascent polypeptide was included in the system to investigate how the nascent polypeptide passes through the exit tunnel within the large subunit of the 70S ribosome. The ratchet-like motion of the 70S ribosome, which is thought to be important for the genetic translation, was successfully observed.

Conformational analysis of the structure of ribosome fit into electron microscopy density maps with normal mode analyses and molecular dynamics simulations

Ishida, Hisashi; Matsumoto, Atsushi; Tsutsumi, Yu*; Yura, Kei

Proceedings of 16th International Microscopy Congress (IMC 2006), P. 242, 2006/09

Supra-biomolecules, which contain numerous proteins and nucleic acids, function when the constituent molecules are assembled. Therefore, it is important to determine not only the 3D structures of the constituent molecules but also the 3D structure of the supra-biomolecule. Although X-ray crystallography can determine the atomic coordinates of biomolecules, it has difficulty in handling supra-biomolecules, because crystals of huge molecules cannot be made with ease. Single particle analysis using an electron microscope (EM) has been used to observe the structure of supra-biomolecules, but the resolution of the EM image has only achieve to the atomic level in a limited situation. Therefore, several attempts have been carried out to determine the 3D structure of supra-biomolecules in atomic resolution by fitting the constituent molecules, determined by X-ray crystallography, into an EM density map. In those attempts, each constituent molecule is usually fit into the EM density map manually, and the constituent molecules may have atomic collisions at their interfaces.

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

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

Annual Report of the Earth Simulator Center April 2003 - March 2004, p.175 - 179, 2004/07

http://www.jamstec.go.jp/esc/publication/annual/annual2003/

no abstracts in English

Advanced fusion technologies developed for JT-60 superconducting Tokamak

Sakasai, Akira; Ishida, Shinichi; Matsukawa, Makoto; Akino, Noboru; Ando, Toshinari*; Arai, Takashi; Ezato, Koichiro; Hamada, Kazuya; Ichige, Hisashi; Isono, Takaaki; et al.

Nuclear Fusion, 44(2), p.329 - 334, 2004/02

https://doi.org/10.1088/0029-5515/44/2/015

no abstracts in English