2019 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, 准教授 (20378532)
好村 滋行 首都大学東京, 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 |
The mathematical multi-particle model of an active crowded colloid, consisting of the dumbbell particles that cyclically change their shapes, was constructed. Its parameter values, characteristic for cytoplasm of bacterial cells, were determined. Computer simulation methods for this model were developed. First numerical simulations for systems with a relatively small numbers of particles were undertaken. They have shown that, in absence of conformational activity, the colloids behaved as glasses where diffusion and relaxation processes were slowed down very much; large deviations from Gaussian statistics were also observed. A strong increase in diffusion was found when conformational activity was introduced and gradually increased. This was accompanied by a rapid decrease in the relaxation time and disappearance of non-Gaussian statistical effects. Therefore, non-equilibrium fluidization of the colloid, similar to that seen in the experiments with biological cells, could be seen in the simulations. The results were published as a rapid communication in EPL. Considering non-equilibrium hydrodynamic effects of enzyme, we performed an analytical and numerical study of hydrodynamic force dipoles in the minimal active dimer model of a mechanochemical enzyme. The findings of the study were used to improve quantitative estimates for diffusion enhancement in solutions of catalytically active enzymes. Moreover, we demonstrated that conformational activity in colloids can lead to a decrease in viscosity of such polymer solutions. These results were published in Physical Review E.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
As shown above, we have studied on the conformationally active colloids and hydrodynamical effects of enzymes, and published the results in EPL. Thus, we consider our project is proceeding as scheduled.
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| Strategy for Future Research Activity |
The computer for numerical calculations was planned to be bought at the Kanazawa university. But the computer will be mainly used by Dr. Koyano at the Tohoku university. It is convenient to have the computer at the Tohoku university, so the distribution of money will be changed.
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| Causes of Carryover |
We have spent less money than expeceted because we could use the computer for numerical calculation in the institute. Moreover, the amount of travel fee was also less than expected. In the next project year, we are planning to buy a computer for the numerical calculation, which will be equipped at Tohoku university, since Koyano will mainly perform the numerical calculation.
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