umu.sePublications
Change search

Diffusion in fractal globules
Umeå University, Faculty of Science and Technology, Department of Physics.
2016 (English)Independent thesis Advanced level (professional degree), 300 HE creditsStudent thesisAlternative title
På spaning efter onormal diffusion av biomolekyler i DNA med hjälp av stokastisk simulering (Swedish)
Abstract [en]

Recent experiments suggest that the human genome (all of our DNA) is organised as a so-called fractal globule. The fractal globule is a knot--free dense polymer that easily folds and unfolds any genomic locus, for example a group of nearby genes. Proteins often need to locate specific target sites on the DNA, for instance to activate a gene. To understand how proteins move through the DNA polymer, we simulate diffusion of particles through a fractal globule. The fractal globule was generated on a cubic lattice as spheres connected by cylinders. With the structure in place, we simulate particle diffusion and measure how their mean squared displacement ($\langle R^2(t)\rangle$) grows as function of time $t$ for different particle radii. This quantity allows us to better understand how the three dimensional structure of DNA affects the protein's motion. From our simulations we found that $\langle R^2(t)/t\rangle$ is a decaying function when the particle is sufficiently large. This means that the particles diffuse slower than if they were free. Assuming that $\langle R^2(t) \rangle \propto t^\alpha$ for long times, we calculated the growth exponent $\alpha$ as a function of particle radius $r_p$. When $r_p$ is small compared to the average distance between two polymer segments $d$, we find that $\alpha \approx 1$. This means the polymer network does not affect the particle's motion. However, in the opposite limit $r_p\sim d$ we find that $\alpha<1$ which means that the polymer strongly slows down the particle's motion. This behaviour is indicative of sub-diffusive dynamics and has potentially far reaching consequences for target finding processes and biochemical reactions in the cell.

2016. , 23 p.
Keyword [en]
Fractal Globule, Anomalous Diffusion, Diffusion, DNA
National Category
Bioinformatics (Computational Biology)
Identifiers
OAI: oai:DiVA.org:umu-126570DiVA: diva2:1034087
Educational program
Master of Science Programme in Engineering Physics
Examiners
Available from: 2016-10-14 Created: 2016-10-11 Last updated: 2016-10-14Bibliographically approved

Open Access in DiVA

File information
File name FULLTEXT01.pdfFile size 1709 kBChecksum SHA-512
Type fulltextMimetype application/pdf
By organisation
Department of Physics
On the subject
Bioinformatics (Computational Biology)