TY - JOUR
T1 - Facilitated diffusion in a crowded environment
T2 - From kinetics to stochastics
AU - Meroz, Yasmine
AU - Eliazar, Iddo
AU - Klafter, Joseph
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=72149101003&partnerID=8YFLogxK
U2 - 10.1088/1751-8113/42/43/434012
DO - 10.1088/1751-8113/42/43/434012
M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???
AN - SCOPUS:72149101003
SN - 1751-8113
VL - 42
JO - Journal of Physics A: Mathematical and Theoretical
JF - Journal of Physics A: Mathematical and Theoretical
IS - 43
M1 - 434012
ER -