Effects of the target aspect ratio and intrinsic reactivity onto diffusive search in bounded domains

  • We study the mean first passage time (MFPT) to a reaction event on a specific site in a cylindrical geometry-characteristic, for instance, for bacterial cells, with a concentric inner cylinder representing the nuclear region of the bacterial cell. A similar problem emerges in the description of a diffusive search by a transcription factor protein for a specific binding region on a single strand of DNA. We develop a unified theoretical approach to study the underlying boundary value problem which is based on a self-consistent approximation of the mixed boundary condition. Our approach permits us to derive explicit, novel, closed-form expressions for the MFPT valid for a generic setting with an arbitrary relation between the system parameters. We analyse this general result in the asymptotic limits appropriate for the above-mentioned biophysical problems. Our investigation reveals the crucial role of the target aspect ratio and of the intrinsic reactivity of the binding region, which were disregarded in previous studies. TheoreticalWe study the mean first passage time (MFPT) to a reaction event on a specific site in a cylindrical geometry-characteristic, for instance, for bacterial cells, with a concentric inner cylinder representing the nuclear region of the bacterial cell. A similar problem emerges in the description of a diffusive search by a transcription factor protein for a specific binding region on a single strand of DNA. We develop a unified theoretical approach to study the underlying boundary value problem which is based on a self-consistent approximation of the mixed boundary condition. Our approach permits us to derive explicit, novel, closed-form expressions for the MFPT valid for a generic setting with an arbitrary relation between the system parameters. We analyse this general result in the asymptotic limits appropriate for the above-mentioned biophysical problems. Our investigation reveals the crucial role of the target aspect ratio and of the intrinsic reactivity of the binding region, which were disregarded in previous studies. Theoretical predictions are confirmed by numerical simulations.show moreshow less

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Metadaten
Author:Denis S. Grebenkov, Ralf MetzlerORCiD, Gleb Oshanin
DOI:https://doi.org/10.1088/1367-2630/aa8ed9
ISSN:1367-2630
Parent Title (English):New journal of physics : the open-access journal for physics
Publisher:IOP Publ. Ltd.
Place of publication:Bristol
Document Type:Article
Language:English
Year of first Publication:2017
Year of Completion:2017
Release Date:2020/04/20
Tag:aspect ratio; cylindrical geometry; first passage time; protein search
Volume:19
Pagenumber:11
Funder:French National Research Agency [ANR-13-JSV5-0006-01]; Deutsche Forschungsgemeinschaft; Potsdam University
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Physik und Astronomie
Peer Review:Referiert