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| Fältnamn | Indikatorer | Metadata |
|---|---|---|
| 000 | 03970naa a2200481 4500 | |
| 001 | oai:lup.lub.lu.se:3864aa04-c460-4cf4-9d41-a9f80b20eb64 | |
| 003 | SwePub | |
| 008 | 160401s2015 | |||||||||||000 ||eng| | |
| 009 | oai:DiVA.org:umu-106367 | |
| 024 | 7 | a https://lup.lub.lu.se/record/74326532 URI |
| 024 | 7 | a https://doi.org/10.1088/1367-2630/17/4/0430362 DOI |
| 024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1063672 URI |
| 040 | a (SwePub)lud (SwePub)umu | |
| 041 | a engb eng | |
| 042 | 9 SwePub | |
| 072 | 7 | a art2 swepub-publicationtype |
| 072 | 7 | a ref2 swepub-contenttype |
| 100 | 1 | a Ahlberg, Sebastianu Umeå universitet,Institutionen för fysik4 aut |
| 245 | 1 0 | a Many-body effects on tracer particle diffusion with applications for single-protein dynamics on DNA |
| 264 | c 2015-04-17 | |
| 264 | 1 | b IOP Publishing,c 2015 |
| 520 | a 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. | |
| 650 | 7 | a NATURVETENSKAPx Biologix Biofysik0 (SwePub)106032 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Biological Sciencesx Biophysics0 (SwePub)106032 hsv//eng |
| 650 | 7 | a NATURVETENSKAPx Fysikx Annan fysik0 (SwePub)103992 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Physical Sciencesx Other Physics Topics0 (SwePub)103992 hsv//eng |
| 650 | 7 | a NATURVETENSKAPx Fysik0 (SwePub)1032 hsv//swe |
| 650 | 7 | a NATURAL SCIENCESx Physical Sciences0 (SwePub)1032 hsv//eng |
| 653 | a diffusion | |
| 653 | a crowding | |
| 653 | a biophysics | |
| 653 | a diffusion | |
| 700 | 1 | a Ambjörnsson, Tobiasu Lund University,Lunds universitet,Beräkningsbiologi och biologisk fysik - Genomgår omorganisation,Institutionen för astronomi och teoretisk fysik - Genomgår omorganisation,Naturvetenskapliga fakulteten,Computational Biology and Biological Physics - Undergoing reorganization,Department of Astronomy and Theoretical Physics - Undergoing reorganization,Faculty of Science4 aut0 (Swepub:lu)thep-tar |
| 700 | 1 | a Lizana, Ludvigu Umeå universitet,Institutionen för fysik4 aut0 (Swepub:umu)luli0012 |
| 710 | 2 | a Umeå universitetb Institutionen för fysik4 org |
| 773 | 0 | t New Journal of Physicsd : IOP Publishingg 17q 17x 1367-2630 |
| 856 | 4 | u http://dx.doi.org/10.1088/1367-2630/17/4/043036x freey FULLTEXT |
| 856 | 4 | u https://doi.org/10.1088/1367-2630/17/4/043036 |
| 856 | 4 | u https://doi.org/10.1088/1367-2630/17/4/043036y Fulltext |
| 856 | 4 | u https://umu.diva-portal.org/smash/get/diva2:841831/FULLTEXT01.pdfx primaryx Raw objecty fulltext:print |
| 856 | 4 8 | u https://lup.lub.lu.se/record/7432653 |
| 856 | 4 8 | u https://doi.org/10.1088/1367-2630/17/4/043036 |
| 856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-106367 |
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