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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 details:Denis S. GrebenkovORCiD, Ralf MetzlerORCiDGND, Gleb OshaninORCiDGND
DOI:https://doi.org/10.1088/1367-2630/aa8ed9
ISSN:1367-2630
Title of parent work (English):New journal of physics : the open-access journal for physics
Publisher:IOP Publ. Ltd.
Place of publishing:Bristol
Publication type:Article
Language:English
Year of first publication:2017
Publication year:2017
Release date:2020/04/20
Tag:aspect ratio; cylindrical geometry; first passage time; protein search
Volume:19
Number of pages:11
Funding institution: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
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