2005 Fiscal Year Final Research Report Summary
Parallel synthesis method of the electronic structures for proteins/nucleic acids and the development of the analytic system of their structures and functions
| Project/Area Number |
14340185
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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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 UNIVERSITY (2004-2005)
Hiroshima University (2002-2003) |
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Principal Investigator |
AOKI Yuriko Kyushu University, Faculty of Engineering Sciences, Professor, 大学院・総合理工学研究院, 教授 (10211690)
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| Co-Investigator(Kenkyū-buntansha) |
NAKA Kazunari Hiroshima University, Faculty of Science, Research associate, 大学院・理学研究科, 助手 (30314727)
TAKEDA Kunio Okayama Science University, Faculty of Engineering, Professor, 工学部, 教授 (10113193)
IMAMURA Akira Hiroshima Kokusaigakuin University, President, 学長 (70076991)
GU Feng Long Kyushu University, Faculty of Engineering Sciences, Researcher, 大学院・総合理工学研究院, 特任助教授 (80404036)
MAKOWSKI Marcin Kyushu University, Faculty of Engineering Sciences, Researcher, 大学院・総合理工学研究院, 特任助手 (90404045)
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| Project Period (FY) |
2002 – 2005
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| Keywords | Elongation method / parallel synthesis / Peptides / collagen triple helix / electronic states / Order-N method / total energy / quantum chemistry |
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| Research Abstract |
In this work, some new improvements of the elongation method will be addressed. The elongation calculations are demonstrated to be much more efficient compared to the conventional one with high accuracy. The elongation CPU time is shown as linear or sub-linear scaling for quasi-one-dimensional systems. Parallel calculations were also succeeded in our systems.
In the elongation method, after we obtain the electronic structure of the starting cluster, we localize the canonical molecular orbitals into regional localized molecular orbitals so that any polymer chain can be built up by adding a monomer unit to this starting cluster step by step. By this fashion, any random polymer can be theoretically synthesized by the elongation method using parallel CPUs.
One can see from our publications that the elongation method can reproduce very high accuracy in total energy with much of CPU time savings compared to the conventional one. The model systems cover non-bonded water chain, weakly bonded system (polyethylene), and very delocalized polymer (polyacetylene). It can be seen that all these models, the elongation method can provide chemical accuracy for the energy compared to the conventional one. The differences can be given to be less than 10^<-8>Hartree/atom.
The advantages of the elongation method are also highlighted for larger conducting polymers like polyparaphenylene, polydiacetylene, polythiophene and their substituted systems as well as polypeptides like collagen triple helix. As this system is very large for any conventional treatment and the elongation treatment guarantees the accuracy and also gains much CPU time saving.
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