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- Type of Document: M.Sc. Thesis
- Language: Farsi
- Document No: 42469 (04)
- University: Sharif University of Technology
- Department: Physics
- Advisor(s): Ejtehadi, Mohammad Reza
- Abstract:
- Ejtehadi, M. R. (Mohammad Reza)All cells store their hereditary information in the same linear chemical code, DNA molecule. These information organize all activities of the cell. Therefore, studying various properties of DNA is a big step toward understanding life. Physicists are interested in elastic properties of DNA molecule. DNA is somehow a chain of successive atoms that have been arranged in a helical ladder shape. DNA is a stiff polymer so one has to use a large amount of energy to bend it. Interestingly, in most of the natural cases, DNA is highly packed into spaces that are much smaller that its total length. Cell’s nucleus and viral capsids are some examples. Virus maybe the simplest biological organism which consists of a protein capsid and a DNA chain confined in the capsid. Capsid’s size is up to a few tens of nanometer in diameter that is hundreds of times smaller than its DNA’s length. So a large amount of energy has been used to bend and condense DNA in the capsid. In this dissertation, we have developed a Monte Carlo simulation method to confine a long DNA chain in nanometer environment. We show that ordered rings appear in the capsid. We calculate persistence length which is a measure of DNA’s bending stiffness and show that correlation function of cosine of the end to end angle exhibits a oscillatory as well as exponential behavior in comparison to the free or 2 dimension confinements which only shows the exponential behavior
- Keywords:
- Viruses ; Monte Carlo Simulation ; Coarse Grained Model ; DNA Molecule Elastic Properties ; Bending Persistence Length
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