Anomalous diffusion in the presence of mobile obstacles

¹  Deutsches Krebsforschungszentrum - D-69120 Heidelberg, Germany, EU
²  Softmatter Lab, Department of Physics and ITPA, Xiamen University - Xiamen 361005, PRC
³  Leibniz-Institut für Polymerforschung Dresden - 01069 Dresden, Germany, EU

Corresponding author: a.wedemeier@googlemail.com

Received: 14 August 2009
Accepted: 13 October 2009

Abstract

In this letter a lattice model for the diffusional transport of binding proteins in a dynamic chromatin fiber network is proposed. Dynamic dense networks are created by a combined version of the bond fluctuation method and a Metropolis Monte Carlo algorithm. In the presence of binding affinities between protein and chromatin transient subdiffusion occurs for small particles. However, by comparing diffusion of binding particles in a static and a dynamic chain network, we demonstrate that binding properties do have a much stronger influence on particles in the static chain network than in the dynamic chain network: fluctuations of the chromatin fiber network weaken the effect of binding affinities on the diffusional transport of particles, i.e. in the presence of chromatin fluctuations the transport of small binding proteins is less anomalous. At the same time we show that dynamical fibers speed up the transport of binding proteins.