| Project/Area Number |
09640611
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Physical chemistry
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| Research Institution | KYUSHU INSTITUTE OF TECHNOLOGY |
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Principal Investigator |
KASHIWAGI Hiroshi Kyushu Institute of Technology, Department of Biochemical Engineering and Science, Professor, 情報工学部, 教授 (10000853)
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| Co-Investigator(Kenkyū-buntansha) |
SATO Fumitoshi Kyushu Institute of Technology, Department of Biochemical Engineering and Science, Research Associate, 情報工学部, 助手 (00235392)
OKAMOTO Masahiro Kyushu Institute of Technology, Department of Biochemical Engineering and Science, Associate Professor, 情報工学部, 助教授 (40211122)
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| Project Period (FY) |
1997 – 1999
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| Project Status |
Completed (Fiscal Year 1999)
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| Budget Amount *help |
¥3,200,000 (Direct Cost: ¥3,200,000)
Fiscal Year 1999: ¥600,000 (Direct Cost: ¥600,000)
Fiscal Year 1998: ¥600,000 (Direct Cost: ¥600,000)
Fiscal Year 1997: ¥2,000,000 (Direct Cost: ¥2,000,000)
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| Keywords | DENSITY FUNCTIONAL THEORY / PROTEINS / ALL-ELECTRON CALCULATIONS / LARGE SYSTEMS COMPUTATION / CONVERGENCE METHOD / BDS-I / PARALLEL CONTROL / オブジェクト指向による並列化 / 非局所補正法 / タンパク質内電子トンネリング / シトクロムc / オブジェクト指向プログラミング / ROKS法 / シトクロムc_3 / 大次元行列対角化の並列化 / 大次元逆行列計算の並列化 |
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| Research Abstract |
In order to understand the electronic properties of whole proteins, we developed a density functional (DF) theory program for all-electron calculations of proteins. In this study, we achieved all-electron calculation of small protein and developed system to investigate electron tunneling mechanism in proteins. The results were summarized as follows :
1. The parallel control of our DF program has been implemented to make calculations faster. The object oriented technology is useful to attain the safe and flexible parallel control of our program. The efficiency of parallel control with dozens of workstation clusters was over 80%.
2. We added the function removing the linear dependence of calculations into our DF program.
3. We newly introduced the restricted open-shell Kohn Sham (ROKS) method and adopted to the calculation of 4 active centers of cytochrome cィイD23ィエD2.
4. We improved the computational accuracies of electron tunneling calculations in proteins by using Feynman's path integral method.
5. The fast algorism to estimate non-local exchange-correlation potential, BLYP, was originally developed, and introduced into our DF program.
6. The electron transfer pathways in Ru-modified cytochrome c were simulated under model potential, and 3 main pathways were observed.
7. Some convergence techniques were originally developed for attaining the all-electron calculations of small proteins.
8. We achieved all-electron calculation of BDS-I which is 43 residues proteins. This is the first all-electron calculation of protein with DF method.
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