Diffusion-influenced controlled reaction in an inhomogeneous medium: Small concentration of reagents

Abstract

We report a computer simulation study of diffusion influenced reactions in a disorder medium constituting by immobile spherical obstacles when the concentration of reagents is smaller than the concentration of obstacles. We found that the compartmentalization of the embedding medium leads to a strong decrease of the rate of the first collision between reagents and a strong increase of the rate of recollision after a no-reactive encounter. The behavior of the full rate of reaction depends on the probability that a collision leads to reaction (value of the activation energy) and on the relationship between the decrease of the rate of collision and the increase of the rate of recollision. Thus, totally diffusion controlled reactions are always unfavored in these mediums, while partially diffusion controlled reactions with very high activation energy are more favored in mediums with a bigger degree of compartmentalization.

Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study

“…12). It is also interesting that the rate constant does not vanish even for f ¼ 0.40, contrary to the case of immobilized obstacles where the reaction rate decays to zero for f ¼ 0.20 (24).…”

“…There have been simulation studies on the related problem of reaction rates in random media (24)(25)(26)(27). Buján-Nuñez et al (24) investigated the effect of immobile obstacles on the rates of association reaction.…”

“…There have been simulation studies on the related problem of reaction rates in random media (24)(25)(26)(27). Buján-Nuñez et al (24) investigated the effect of immobile obstacles on the rates of association reaction. The presence of immobilized obstacles are often referred to as confinement effects and are distinct from crowding effects imposed by mobile crowding agents (5,8).…”

Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects

“…This size effect has been investigated by Bujan-Nunez et al 51 through BD simulations with the Cichocki-Hinsen method, but all the crowding molecules were held fixed in space. The same is true for the binary hard sphere system where the crowding particle is larger than the tracer, although the reduction in diffusion is dependent on the size ratio.…”

“…17,51 We repeated all the simulations with the radius of crowding molecules set to 4 and 6 nm while keeping the tracer at 2 nm. 17,51 We repeated all the simulations with the radius of crowding molecules set to 4 and 6 nm while keeping the tracer at 2 nm.…”