| Project/Area Number |
22K03792
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Review Section |
Basic Section 17050:Biogeosciences-related
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| Research Institution | Institute of Science Tokyo |
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Principal Investigator |
SMITH Eric 東京科学大学, 地球生命研究所, 特任教授 (50770468)
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| Co-Investigator(Kenkyū-buntansha) |
Smith Harrison 東京科学大学, 地球生命研究所, 特任准教授 (50843934)
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| Project Period (FY) |
2022-04-01 – 2025-03-31
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| Project Status |
Completed (Fiscal Year 2024)
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| Budget Amount *help |
¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2024: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2023: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2022: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
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| Keywords | Reaction networks / Rule-based modeling / Chemical graph grammars / Information geometry / Systems chemistry / Thermochemical databases / Sugar metabolism / Cost of selection / Natural selection cost / Chemical networks / Rule-based systems / Evolution optimization / computational chemistry |
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| Outline of Research at the Start |
The most basic features of life are conserved across all living systems. Many are pathways of core metabolism, which all other living processes require. We will use computational chemistry to understand how uncontrolled chemical networks arise in nature and the way pathways are selected from them.
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| Outline of Final Research Achievements |
We aimed to understand how living organisms have come to use a small number of universal physiological reactions, when a very large number of alternative pathways are possible using the same reaction mechanisms. Our method of study combines a form of computational chemistry that models molecules as graphs, in order to use mathematical representations to make complete lists of possible reactions. We then used methods from statistical physics and probability theory to derive how complex, or how energetically costly, different pathways are that achieve the same chemical transformation.
Our results show that by a natural measure of simplicity and low cost, the biological Calvin Cycle for carbon fixation is a unique minimum, explaining why evolution has extracted this pathway from many possibilities. We were surprised to discover that the Calvin cycle is also a kind of "chemical program", which makes its discovery easier for evolution.
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| Academic Significance and Societal Importance of the Research Achievements |
We introduced new mathematical ways to connect elementary reaction mechanisms, which evolution can directly select, to the topology of reaction networks, which do work for organisms, and to the energy and matter flows on networks. Our methods can also be applied to metabolic pathway design.
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