Abstract:
This thesis is divided into 5 chapters. In Chapter 1, the Introduction, we summarise
the necessary background to the work described in this thesis, including a discussion
of major features of nuclear architecture, the importance of non-equilibrium activity
for biophysical models of such architecture, and the background to understanding
gene regulation through DNA-binding proteins that associate to specific binding
sites. Chapter 2 provides details of our model for large-scale nuclear architecture
and a description of its computational implementation. In Chapter 3, we present
ab-initio simulation predictions of a number of features of large-scale nuclear archi-
tecture. In Chapter 4, we describe an algorithm, called THiCweed, for clustering
TFBS in ChIP-Seq data. This tool outperforms other existing tools in terms of its
speed and its ability to capture biologically significant motifs. Finally, in Chapter
5, we end with a conclusion and describe how these studies can be further extended.
