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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. Asimilar 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.Weanalyse 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. Asimilar 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.Weanalyse 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. Grebenkov, Ralf MetzlerORCiDGND, Gleb OshaninORCiDGND
URN:urn:nbn:de:kobv:517-opus4-403726
Publication series (Volume number):Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (391)
Publication type:Postprint
Language:English
Date of first publication:2017/11/16
Completion year:2017
Publishing institution:Universität Potsdam
Release date:2017/11/16
Tag:aspect ratio; cylindrical geometry; first passage time; protein search
Page number:11
Source:New journal of physics 19 (2017). - DOI: 10.1088/1367-2630/aa8ed9
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Physik und Astronomie
DDC classification:5 Naturwissenschaften und Mathematik / 53 Physik / 530 Physik
Peer review:Referiert
Publishing method:Open Access
License (English):License LogoCreative Commons - Namensnennung 3.0 Unported
External remark:Bibliographieeintrag der Originalveröffentlichung/Quelle