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.…
Verfasserangaben: | Denis S. GrebenkovORCiD, Ralf MetzlerORCiDGND, Gleb OshaninORCiDGND |
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DOI: | https://doi.org/10.1088/1367-2630/aa8ed9 |
ISSN: | 1367-2630 |
Titel des übergeordneten Werks (Englisch): | New journal of physics |
Verlag: | IOP |
Verlagsort: | London |
Publikationstyp: | Wissenschaftlicher Artikel |
Sprache: | Englisch |
Datum der Erstveröffentlichung: | 24.10.2017 |
Erscheinungsjahr: | 2017 |
Veröffentlichende Institution: | Universität Potsdam |
Datum der Freischaltung: | 16.11.2017 |
Freies Schlagwort / Tag: | aspect ratio; cylindrical geometry; first passage time; protein search |
Band: | 19 |
Erste Seite: | 1 |
Letzte Seite: | 11 |
Fördernde Institution: | Universität Potsdam, Publikationsfonds |
Fördernummer: | PA 2017_54 |
Organisationseinheiten: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Physik und Astronomie |
DDC-Klassifikation: | 5 Naturwissenschaften und Mathematik / 53 Physik / 530 Physik |
Peer Review: | Referiert |
Fördermittelquelle: | Publikationsfonds der Universität Potsdam |
Publikationsweg: | Open Access |
Lizenz (Englisch): | Creative Commons - Namensnennung 3.0 Unported |
Externe Anmerkung: | Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 391 |