Department of Mathematics and Statistics
November 19, 2013
The Influence of Spatial Variation in Chromatin Density on the Time to Find DNA Binding Sites
We will describe our recent work investigating how volume exclusion due to the spatially varying density of DNA in the nucleus influences the time required for proteins to find DNA binding sites. A lattice master equation model will be derived to approximate the drift-diffusion process a protein undergoes as it searches for a binding site. Detailed three-dimensional simulations of the protein's search process will then be constructed using several different types of high-resolution imaging of the interior of mammalian cell nuclei. Using asymptotic expansions, we will develop a mathematical theory to explain our observed simulation results.