Facilitated diffusion in a crowded environment: From kinetics to stochastics

Yasmine Meroz*, Iddo Eliazar, Joseph Klafter

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Facilitated diffusion is a fundamental search process used to describe the problem of a searcher protein finding a specific target site over a very large DNA strand. In recent years macromolecular crowding has been recognized to affect this search process. In this paper, we bridge between two different modelling methodologies of facilitated diffusion: the physics-oriented kinetic approach, which yields the reaction rate of the search process, and the probability-oriented stochastic approach, which yields the probability distribution of the search duration. We translate the former approach to the latter, ascertaining that the two approaches yield coinciding results, both with and without macromolecular crowding. We further show that the stochastic approach markedly generalizes the kinetic approach by accommodating a vast array of search mechanisms, including mechanisms having no reaction rates, and thus being beyond the realm of the kinetic approach.

Original languageEnglish
Article number434012
JournalJournal of Physics A: Mathematical and Theoretical
Issue number43
StatePublished - 2009


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