The dynamics of DNA denaturation
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- Institutt for fysikk 
Gaining knowledge and understanding of the structure and function of DNA, our genetic material, is crucial for dealing with diseases related to DNA. In 2004, the mapping of the complete human genome was accomplished, leading to an enormous progress in treating DNA-related diseases. The attention was for a long time directed at the DNA structure, specifically the sequence. However, the knowledge of the structure of DNA is not sufficient to understand biological processes. For this, we also need to understand how this structure affects the equilibrium properties and the dynamics of the DNA molecule. In fundamental genetic processes, such as transcription and replication, DNA must undergo dynamical changes. Both processes are highly complex, and due to the lack of detail insight, a satisfactory descriptive model is difficult to design. However, since these processes require a local opening of the DNA molecule, they resemble DNA denaturation, or DNA melting, which is a considerably simpler process to study theoretically and experimentally.Studying DNA denaturation is, besides that it is interesting by itself, also considered a well-grounded step towards the full comprehension of the mechanisms involved in transcription and replication.\newlineIn this work, the denaturation of DNA was explored by computer simulations applying the Peyrard-Bishop-Dauixous (PBD) model. DNA chains consisting of 33 \% AT base pairs and 66 \% GC base pairs were investigated, as well as a key secondary structure of DNA and RNA, the hairpin, which is involved in many important processes of DNA and RNA.Although DNA dynamics has gained increased interest during the last decades, there is still a need of more insight and knowledge within this field. This work contains the first quantitative study in which dynamical data, like denaturation rate constants, of the well-known PBD mesoscopic model has been compared with experiments. Our work will be valuable for improvements of these mesoscopic models.