Effects of the target aspect ratio and intrinsic reactivity onto diffusive search in bounded domains
- Westudy 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. TheoreticalWestudy 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.…
Author details: | Denis S. GrebenkovORCiD, Ralf MetzlerORCiDGND, Gleb OshaninORCiDGND |
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DOI: | https://doi.org/10.1088/1367-2630/aa8ed9 |
ISSN: | 1367-2630 |
Title of parent work (English): | New journal of physics |
Publisher: | IOP |
Place of publishing: | London |
Publication type: | Article |
Language: | English |
Date of first publication: | 2017/10/24 |
Publication year: | 2017 |
Publishing institution: | Universität Potsdam |
Release date: | 2017/11/16 |
Tag: | aspect ratio; cylindrical geometry; first passage time; protein search |
Volume: | 19 |
First page: | 1 |
Last Page: | 11 |
Funding institution: | Universität Potsdam, Publikationsfonds |
Funding number: | PA 2017_54 |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Physik und Astronomie |
DDC classification: | 5 Naturwissenschaften und Mathematik / 53 Physik / 530 Physik |
Peer review: | Referiert |
Grantor: | Publikationsfonds der Universität Potsdam |
Publishing method: | Open Access |
License (English): | Creative Commons - Namensnennung 3.0 Unported |
External remark: | Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 391 |