The Kinetics of Heminal Recombination in a Cavity

I. V. Grigor’ev*, Yu. A. Makhnovskii*, A. M. Berezhkovskii**, and V. Yu. Zitserman***

* Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences,
Leninskii pr. 29, Moscow, 117912 Russia

** Center for Information Technology, National Institutes of Health, Bethesda, Maryland, USA

*** Institute of High Temperatures Scientific Association (IVTAN), Russian Academy of Sciences,
Izhorskaya ul. 13/19, Moscow, 127412 Russia

Received September 6, 2002

Abstract—A theory of heminal recombination in a cavity containing a reaction center and an orifice that sto-
chastically opens and closes is suggested. A particle broken away from the reaction center diffuses in the cavity
until it either escapes through the orifice into the volume or recombines. The model qualitatively describes the
special features of several biologically important processes, in particular, the recombination of ligands in myo-
globin. It is shown that, at small reaction center and orifice sizes, diffusion process calculations reduce to solv-
ing simple kinetic equations, which allow the probability of recombination and the kinetics of the process to be
found in the form of explicit functions of model parameters.

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