| Project/Area Number |
15500201
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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 |
Bioinformatics/Life informatics
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| Research Institution | KANAZAWA INSTITUTE OF TECHNOLOGY (2005)
Waseda University (2003-2004) |
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Principal Investigator |
ICHIKAWA Kazuhisa Kanazawa Institute of Technology, Department of Brain and Bioinformation Science, Professor, 情報フロンティア学部, 教授 (20343626)
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| Project Period (FY) |
2003 – 2005
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| Project Status |
Completed (Fiscal Year 2005)
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| Budget Amount *help |
¥2,900,000 (Direct Cost: ¥2,900,000)
Fiscal Year 2005: ¥900,000 (Direct Cost: ¥900,000)
Fiscal Year 2004: ¥1,000,000 (Direct Cost: ¥1,000,000)
Fiscal Year 2003: ¥1,000,000 (Direct Cost: ¥1,000,000)
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| Keywords | stochastic simulation / deterministic simulation / localization of proteins / diffusion / biochemical reaction / 脳・神経系の情報処理 / 細胞情報・動態 / 計算論的神経科学 |
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| Research Abstract |
Theory and algorithm for stochastic biochemical reactions have constructed. Smoluchowski-Debye equation is well-known for the calculation of molecular level chemical reactions. However, this equation was found to be not suitable for the stochastic simulations, because an assumption in this equation is not consistent with the random walk simulations in a computer. Therefore, we constructed a new theory. This theory agrees with mass reaction theory in the limit of the infinite number of molecules. An algorithm for the computer simulation using this theory was developed. We tested various types of reactions, and found that the results of the stochastic simulation agreed well with the deterministic simulations when the number of molecules was large.
In addition, the localized activation of enzymes was found even in a small volume of a spine, using morphological modeling capability of A-Cell. The diffusion of molecules activated by Ca^<2+>, which flowed into a spine via glutamate receptor channels located at the spine head, enhanced the localization of kinase to the limited region within a spine head. This phenomenon, newly found by the simulation of this study, was robust for the change in parameters (i.e. rate constants, concentrations and diffusion constants) of two orders of magnitude. This suggested that the localized activation of enzyme was common in the cell, and would be crucial for its function.
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