Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA
Umeå University, Faculty of Science and Technology, Department of Physics.
Umeå University, Faculty of Science and Technology, Department of Physics.
2015 (English)In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 17, 043036Article in journal (Refereed) Published
Abstract [en]

30% of the DNA in E. coli bacteria is covered by proteins. Such a high degree of crowding affects the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc) in ways that are not yet fully understood. In this paper, we theoretically address the diffusion constant of a tracer particle in a one-dimensional system surrounded by impenetrable crowder particles. While the tracer particle always stays on the lattice, crowder particles may unbind to a surrounding bulk and rebind at another, or the same, location. In this scenario we determine how the long time diffusion constant D (after many unbinding events) depends on (i) the unbinding rate of crowder particles k(off), and (ii) crowder particle line density rho, from simulations (using the Gillespie algorithm) and analytical calculations. For small k(off), we find D similar to k(off)/rho(2) when crowder particles do not diffuse on the line, and D similar to root Dk(off)/rho when they are diffusing; D is the free particle diffusion constant. For large k(off), we find agreement with mean-field results which do not depend on k(off). From literature values of k(off) and D, we show that the small k(off) -limit is relevant for in vivo protein diffusion on crowded DNA. Our results apply to single-molecule tracking experiments.

Place, publisher, year, edition, pages
2015. Vol. 17, 043036
Keyword [en]
diffusion, crowding, biophysics
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:umu:diva-106367DOI: 10.1088/1367-2630/17/4/043036ISI: 000354021400003OAI: oai:DiVA.org:umu-106367DiVA: diva2:841831
Available from: 2015-07-15 Created: 2015-07-14 Last updated: 2017-12-04Bibliographically approved

Open Access in DiVA

fulltext(2797 kB)97 downloads
File information
File name FULLTEXT01.pdfFile size 2797 kBChecksum SHA-512
2f3affb64a97e930729a4d311a5a40a3d12cb1cc1af37d43d7191d8eaeea20e487871403f6d50b1fbc652899cc4cd69c5c1a4d4da7913fd060da48bd5ab23fde
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
Ahlberg, SebastianLizana, Ludvig
By organisation
Department of Physics
In the same journal
New Journal of Physics
Physical Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 97 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 239 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf