||As DNA contains the blue print of life, it is the subject of many studies. Comprehending DNA has
lead to breakthroughs in both medical and scientific understanding. In medicine, DNA presents
the possibility to make early diagnoses and find treatment; in science, genetic engineering has
led to great advancements in agriculture, biology and nanotechnology. DNA is build up out of
base pairs. The sequences of these base pairs store the essential genetic information for life to
function. As such understanding the mechanical rules that govern the positioning of these base
pairs is of paramount importance.
This thesis aims to study the sequence dependence of the cyclization of small DNA rings
by Monte Carlo simulation. Chapter one introduces the key concepts behind DNA rings and
summarizes the paper that inspired this project. In chapter two we introduce our model in the
context of Metropolis Monte Carlo simulations. Finally, we will present and discuss our results in
chapter 3. This last chapter is divided into three parts. The first part discusses the initial tests and
simulations performed with the different Monte Carlo moves. In the second part, the results of
our simulation of the Rosanio et al. cyclization experiment are presented. The chapter concludes
with a discussion of several simulations that were designed to generate interesting new results
that might be hard to come by experimentally.