Loading...

Elasticity of DNA Molecule The Role of Anisotropy, Asymmetry and Nonlocal Interactions

Eslami Mosallam, Behrouz | 2011

638 Viewed
  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 42228 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza
  7. Abstract:
  8. The DNA Molecule carries genetic information in almost all living organisms. The information coded on DNA is an instruction which organizes and conducts all living activities of the living organism. The role of DNA in biological processes is so fundamental that life, as we know, is not possible without DNA. Therefore, studying the biological properties of DNA is crucial for understanding the nature of life. In biological conditions, DNA molecule can be found in highly packed configurations. Since the DNA is a rather stiff molecule, the formation of these configurations cost a considerable amount of energy. The elasticity of DNA plays an important role here. The important question is: how much energy is required for the formation of these highly packed configurations? And where does this energy come from. Therefore, studying DNA elasticity is important for understanding its biological functions. One of the popular models to explain the elastic behavior of DNA is the wormlike chain model, which belongs to a larger group of models called “local harmonic coarsegrained models”. In these models DNA is considered as a flexible rod, which can be deformed in response of external forces and torques. Three translational degrees of
    freedom, as well as three rotational degrees of freedom, are assigned to each crosssection of the rod, and it is assumed that the elastic energy of the rod is a harmonic function of its degrees of freedom. It is also assumed that the elastic energy is local, i.e. each element of the rod only interacts with its nearest neighbors. The wormlike chain model is quite successful in explaining the elastic behavior of long DNA molecules. However, there are some experimental evidences indicating that short DNA molecules do not obey the wormlike chain model. Although there is some doubt about the results of some of these experiments, it is interesting to find alternative models which can explain the anomalous elastic behavior of short DNA molecules. The goal of this dissertation is to find generalizations for the wormlikechain model, which are more relevant to the real DNA. We especially concentrate on the structural properties of DNA. It is known that the DNA molecule has an asymmetric and anisotropic structure. These properties are not included in the wormlike chain model, but it is expected that they affect the elastic behavior of DNA. We introduce models which account for the asymmetric and anisotropic structure of DNA, and study the elastic behavior of DNA in these models. We show that, although these models are reduced to the wormlike chain model for long enough molecules, the asymmetric structure of DNA can significantly enhance its flexibility at small length scales. Comparing the predictions of the asymmetric elastic rod model with the experimental data, we show that this model can explain the anomalous elastic behavior of short DNA molecules, as observed in the experiments. We also study the role of nonlocal interactions in the elastic behavior of DNA. We show that the nonlocal interactions affect the elastic properties of DNA at small length scales, and contribute to the anomalous elastic behavior of DNA as observed in all-atom simulations.
  9. Keywords:
  10. Elasticity ; Anisotropy ; Asymmetry ; Coarse Grained Model ; Wormlike Chain Model ; Nonlocal Interaction

 Digital Object List

  • محتواي پايان نامه
  •   view

 Bookmark

No TOC