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694 results on '"Nagashima, Umpei"'

153. 大規模分子の分子軌道計算 : Lysozyme とモデルDNA分子の分子軌道

Author

Watanabe, Toshio, Inadomi, Yuichi, Ishimoto, Takayoshi, Umeda, Hiroaki, Sakurai, Tetsuya, and Nagashima, Umpei

Abstract

フラグメント分子軌道（FMO）法に基づいた大規模系の分子軌道（FMO-MO）計算についての概要と、Lysozyme分子およびモデルDNA分子への適用結果を示す。FMO-MO法は、FMO計算によって得られた密度行列を基にFock行列を生成し、それを一度だけ対角化することによって近似的な分子軌道を得る方法である。本方法は巨大な分子全体に対する反復解法を行わずにすむため、従来の分子軌道法では非常に困難であった2000原子程度の大規模分子の分子軌道計算を、比較的短時間で行うことができる。また新たに開発した対角化法を用いると化学反応に重要なHOMO-LUMO付近のみの軌道エネルギーと軌道を得ることが可能であり、従来法に比較して大幅な時間短縮が可能である。Dual Opteron 246, 2GHz × 128台を用いた並列計算では、Lysozyme分子（129 アミノ酸残基, 1961 原子）と溶媒（8258原子、STO-3G 20758基底関数）に対するFMO-MO計算を、5時間程度で行うことができた。このとき、水分子の配置の仕方でHOMO-LUMOの位置が大きく変化することが確認された。また同じシステムを用いるとDNAのモデル（40核酸対、2636原子、STO-3G 10108基底関数）を1時間以内で計算可能であった。この場合、HOMOはDNAの中央に大きな振幅を持ち、LUMOはDNAの末端近くに大きな振幅を持っていた。

Published
2007

154. FMO-MO法における大規模分子軌道計算 : 解くべき固有値問題の特徴(<特集>行列・固有値問題における線形計算アルゴリズムとその応用)

Author

Inadomi, Yuichi, Umeda, Hiroaki, Watanabe, Toshio, Sakurai, Tetsuya, and Nagashima, Umpei

Abstract

Characters of generalized eigenvalue problem in FMO-MO method, which is one of the fastest methods to calculate molecular orbitals of large molecules such as proteins, are described in order to solve it efficiently. Fock matrix to solve looks dense, because 7.6% of elements have significant value even for a large molecule. The frontier orbital energies can be estimated from fragment and fragment-pair orbital energy distributions in FMO method, which is performed in FMO-MO calculation, and then the frontier orbitals can be obtained efficiently by the method to solve eigenvalue problem in a specific energy region.

Published
2005

155. FMO-MO法による大規模分子軌道計算(数値シミュレーション)

Author

Inadomi, Yuichi, Umeda, Hiroaki, Watanabe, Toshio, Sakurai, Tetsuya, and Nagashima, Umpei

Abstract

本論文では, フラグメント分子軌道(FMO)法に基づいた分子軌道(FMO-MO)計算についての概要と, 実際のタンパク分子への適用結果を示す.FMO-MO法では, 巨大な分子全体に対する反復解法を行わずにすむため, 従来の分子軌道法では非常に困難であった1,000原子を超える大規模分子の分子軌道計算を, 比較的短時間で行うことができる.大規模クラスタ計算機を用いた場合には, 卵白リゾチーム分子に対するFMO-MO計算を, 4時間半程度で行うことができた.また, 小さなサイズの分子軌道計算では見えなかった一般化固有値問題を解く時間が, 全計算時間の34%となり比較的大きなウェイトを占めることが明らかとなった.

Published
2005

156. Theoretical study of the H/D isotope effect on phase transition of hydrogen-bonded organic conductor κ-H3(Cat-EDT-TTF)2.

Author

Yamamoto, Kaichi, Kanematsu, Yusuke, Nagashima, Umpei, Ueda, Akira, Mori, Hatsumi, and Tachikawa, Masanori

Abstract

κ-H3(Cat-EDT-TTF)2 (H-TTF) is a hydrogen-bonded π-electron system which was found to reveal C2/c symmetry at 50–293 K, while its isotopologue, κ-D3(Cat-EDT-TTF)2 (D-TTF), showed the phase transition at 185 K from C2/c to P1̅. To elucidate the origin of such a difference, we calculated the potential energy curves (PECs) for the hydrogen transfer along the H-bonds in these conductors. We found that both the π-stacking and the hydrogen nuclear quantum effect drastically affected the hydrogen transfer energy. By taking account of both effects, we obtained a symmetric single-well effective PEC for H-TTF, which indicated that the hydrogen was always located at the center of the H-bond. By contrast, the effective PEC of D-TTF was a low-barrier double-well, indicating that the position of the H-bonded deuterium would change according to the temperature. We concluded that the π-stacking and the nuclear quantum effect were the key factors for the appearance of phase transition only in D-TTF. [ABSTRACT FROM AUTHOR]

Published
2016
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167. Eric: A Special-Purpose Processor for ERI Calculations in Quantum Chemistry Applications

Author

Nakamura, Kenta, Hatae, Hidenori, Harada, Muneyuki, Kuwayama, Yoji, Uehara, Masamitsu, Sato, Hisao, Obara, Shigeru, Honda, Hiroaki, Nagashima, Umpei, Inadomi, Yuichi, and Murakami, Kazuaki

Subjects
Ab initio molecular orbital calculation, application-specific processor, chip-multiprocessor architecture, electron repulsion integral
Abstract

Ab initio molecular orbital (MO) calculation is useful for solving many challenging problems regarding the development of new drugs, chemicals, polymers, materials, and so on. In the EHPC (Embedded High Performance Computing) project, we are now developing a special-purpose computer system for ab initio MO calculations in order to reduce the calculation time. The sequential execution time of ab initio MO is O( $ N^4 $) where $ N $ is the number of basis functions, the heaviest computation being the electron repulsion integrals (ERI's). In order to accelerate ab initio MO calculations, it is necessary to develop a special-purpose processor for ERI calculation. Using the characteristics of ERI in the Obara algorithm makes it possible to reduce the calculation time. In this work, we investigate a chip-multiprocessor (CMP) architecture, called Eric, for an application-specific processor able to perform fast ERI computations.

Published
2002

189. Mode-selective internal conversion of perylene

Author

Suganuma, Yoshitake, primary, Kowaka, Yasuyuki, additional, Ashizawa, Noritaka, additional, Nakayama, Naofumi, additional, Goto, Hitoshi, additional, Ishimoto, Takayoshi, additional, Nagashima, Umpei, additional, Ueda, Tadashi, additional, Yamanaka, Takaya, additional, Nishi, Nobuyuki, additional, and Baba, Masaaki, additional

Published
2011
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195. A Hybrid Data Base: Quantum Chemistry Literature Data Base II—New Concept and New Methodology—

Author

Takano, Keiko, primary, Koga, Nobuaki, additional, Matsushita, Toshio, additional, Hashimoto, Kenro, additional, Hosoya, Haruo, additional, Matsuzawa, Hidenori, additional, Nagashima, Umpei, additional, Nishikawa, Takeshi, additional, Wasada, Hiroaki, additional, Yamabe, Shinichi, additional, Tachikawa, Masanori, additional, and Hada, Masahiko, additional

Published
2010
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