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Updated: May 24, 2026

Single-Molecule Förster Resonance Energy Transfer Methods for Real-Time Investigation of the Holliday Junction Resolution by GEN1
Published on: September 18, 2019
Diffusion-mediated geminate reactions under excluded volume interactions
Kazuhiko Seki1, Mariusz Wojcik, M Tachiya
1National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8565 Japan.
Abstract:
In this paper, influence of crowding by inert particles on the geminate reaction kinetics is theoretically investigated. Time evolution equations for the survival probability of a geminate pair are derived from the master equation taking into account the correlation among all diffusing particles, and the results are compared with those obtained by Monte Carlo simulations. In general, excluded volume interactions by the inert particles slow down the diffusive motion of reactants. However, when the initial concentration of the inert particles is uniform and high, we show that additional influence of interference between reaction and correlated diffusion accelerates the transient decay of the survival probability in the diffusion-controlled limit. We also study the escape probability for a nonuniform initial distribution of the inert particles by taking the continuous limit in space. We show that reaction yield is increased when the reaction proceeds in the presence of a positive density gradient of the inert particles which inhibits the escape of reactants. The effect can be interpreted as a cage effect.
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