Simulating the sequence dependence of DNA cyclization by Monte Carlo methods

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Simulating the sequence dependence of DNA cyclization by Monte Carlo methods

Type: Master thesis
Title: Simulating the sequence dependence of DNA cyclization by Monte Carlo methods
Author: Wondergem, A.J.
Issue Date: 2016-02-12
Abstract: 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.
Supervisor: Schiessel, Helmut
Faculty: Faculty of Science
Department: Physics (Master)
Specialisation: Physics Experimental
ECTS Credits: 3
Handle: http://hdl.handle.net/1887/40650
 

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