In this thesis, a new robust modelling algorithm for estimating total flux densities of radio halo’s is presented. Radio halo’s are large scale (∼ 500 kpc in size) structures of extended diffuse...Show moreIn this thesis, a new robust modelling algorithm for estimating total flux densities of radio halo’s is presented. Radio halo’s are large scale (∼ 500 kpc in size) structures of extended diffuse emission consisting of relativistic electrons moving within magnetic fields in the intracluster medium (ICM). Their exact origin is still unknown. This new modelling method can contribute to solve this question by accurately measuring a fundamental characteristic of these objects. The algorithm combines the numerical power of Markov Chain Monte Carlo simulations and multiple theoretical models to enable us to estimate the total radio flux at a frequency of 144 MHz. Using this novel method, flux densities and radio powers of a total of 30 galaxy clusters with a mass range 0.8 − 11 × 1014 M⊙ are presented. Radio powers are calculated for every cluster at a frequency of 150 MHz assuming a spectral index of α = −1.2 (assuming Sν = να). Using our sample of clusters, existing mass-power scaling relations are tested. The radio halo’s are observed by the International LOFAR Telescope as part of the LOFAR Two Metre Sky Survey (LoTSS), observing at frequencies between 120-168 MHz.Show less
The DNA in eukaryotic organisms is largely stored in a compact wrap around histone proteins to form nucleosomes. The mechanics of the DNA play a major role in the biological processes for which the...Show moreThe DNA in eukaryotic organisms is largely stored in a compact wrap around histone proteins to form nucleosomes. The mechanics of the DNA play a major role in the biological processes for which the DNA is used. In this thesis we will computationally show that we can study the mechanics of the DNA with a simplified computational model. By parametrically constraining the DNA around a superhelical curve we can calculate the mechanical energy of the DNA by only the sequence of the DNA and the positions along the curve. We will demonstrate how, with Monte Carlo methods we can effectively estimate the sequence and position statistics of nucleosomal DNA.Show less
The aim of this study was to computationally resolve nucleosome dynamics and chromatin structure. To achieve this we ran Monte Carlo simulations of a base pair level model of a mononucleosome....Show moreThe aim of this study was to computationally resolve nucleosome dynamics and chromatin structure. To achieve this we ran Monte Carlo simulations of a base pair level model of a mononucleosome. Additionally, we developed a graphical user interface for generating a chromatin structure with realistic linker DNA, which enabled us to calculate linking number and writhe for different chromatin structures. The force extension curve of our simulated mononucleosome shows similar behaviour to force spectroscopy experiments.Show less
Accessibility to nucleosomal dna is an important factor in transcription and gene expression. During transcription, rna polymerase exerts a force on the nucleosome under which the nucleosome...Show moreAccessibility to nucleosomal dna is an important factor in transcription and gene expression. During transcription, rna polymerase exerts a force on the nucleosome under which the nucleosome unwraps, and, as recently shown experimentally, this can happen asymmetrically. In this thesis, we show, using computer simulations of sequence-dependent coarse-grained dna, what causes this asymmetry. We will also show a proof of concept that we can design dna sequences that unwrap in a predetermined way.Show less
