2020 Fiscal Year Research-status Report
Enzymes as Active Matter at Nanoscales
| Project/Area Number |
19K03765
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| Research Institution | Kanazawa University |
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Principal Investigator |
Mikhailov Alex.S 金沢大学, ナノ生命科学研究所, リサーチ・プロフェッサー (00817364)
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| Co-Investigator(Kenkyū-buntansha) |
北畑 裕之 千葉大学, 大学院理学研究院, 教授 (20378532)
好村 滋行 東京都立大学, 理学研究科, 准教授 (90234715)
小谷野 由紀 東北大学, 理学研究科, JSPS特別研究員(PD) (50849643)
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| Project Period (FY) |
2019-04-01 – 2022-03-31
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| Keywords | enzymes / colloids / glasses / nonequilibrium transport |
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| Outline of Annual Research Achievements |
Analytical and numerical investigations for hydrodynamic force dipoles of enzymes were performed for the simplified dimer model of a catalytically active enzyme. Based on this, diffusion enhancement for passive tracer particles in experiments and in multi-particle computer simulations was discussed. The results of this study were published in the journal Soft Matter of the Royal Chemical Society in UK. We have also examined possible hydrodynamic mechanisms for diffusion enhancement in active enzymes themselves, caused by reaction-induced conformational changes in such proteins; a publication is currently being prepared. Numerical simulations for active crowded colloids were scaled up by us to the larger systems and performed on a new high-performance computer purchased from this grant. Our focus was on checking the fluctuation-dissipation theorem and determining the effective temperature for the particles of different sizes in active colloids. We intend to reproduce in computer simulations the experimental active micro-rheology measurement set-up. Additionally, diffusion enhancement for levitated droplets, caused by oscillatory deformations within them, was experimentally and numerically studied by us; the results are published in Physical Review E. A model of an autonomous three-bead elastic microswimmer was proposed and analyzed in different dynamical regimes. For this model, the propulsion velocity is determined and the bifurcation diagram is examined. The results are reported as a rapid communication in Europhysics Letters.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
Because of the COVID-19 pandemy, collaboration between the PI and co-PIs was more difficult to implement. The PI, prof. A. Mikhailov, remained in Germany and could not come to Japan until November 2020.
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| Strategy for Future Research Activity |
We shall proceed according to the work schedule formulated in the original grant proposal. The theoretical study of single-molecule diffusion enhancement (or boosting) for active enzymes will be completed. Its results will allow to provide theoretical interpretation for a large volume of data, obtained by means of various experimental methods in the group of prof. S. Granick in his Center for Soft and Living Matter in the Ulsan National Institute for Science and Technology in South Korea. We shall finish our large-scale multi-particle computer simulations for active crowded colloids. Extensive theoretical analysis of their data will be undertaken, with special emphasis on the implications for living biological cells. At least two publications will be prepared to report the results.
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| Causes of Carryover |
The amount of travel fee was less than expected due to the COVID-19 pandemy. The unused money that is carried over for FY2021 will be used as travel fee for the discussion with Co-PIs and other researchers and for the consumables like storages for numerical calculation. Moreover, we are planning to buy a computer for the numerical calculation, which will be equipped at Chiba university, since Kitahata will perform the numerical calculation.
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