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Coarse Grained Molecular Dynamics Simulation of DNA Nanomechanics

Fathizadeh, Arman | 2013

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  1. Type of Document: Ph.D. Dissertation
  2. Language: Farsi
  3. Document No: 44556 (48)
  4. University: Sharif University of Technology
  5. Department: Institute for Nanoscience and Nanotechnology
  6. Advisor(s): Ejtehadi, Mohammad Reza; Khoei, Amir Reza
  7. Abstract:
  8. DNA is the most important biological molecule which contains all the genetic information of living organisms. The mechanical behavior of this molecule has a significant role on its functions. In this study, we introduce a model to for DNA nanomechanics. This model is called rigid base-pair chain in which every base pair is considered as a rigid object. The base-pairs only interact with their nearest neighbors via a harmonic potential. We have used this model to study the nanomechanical behavior of the DNA such as its bending, twisting, and stretching elasticity. Also the model was successful to predict the structure of DNA minicircles with extra amount of twist. After that we used the model in three important problems. First problem is about the definition of persistence length. We introduce a method which shows how to measure shear modulus of the DNA from AFM images. Second problem is about the sliding and positioning of a DNA chain in a nucleosome structure. With the sequence dependent elastic model we were able to explain the positiong of the DNA in a nucleosome. The third problem was about structure of a long DNA hcain which is confined in a nano spherical cavity. We showed that the structure is significantly depends on the dynamics of the system. Also it is found that the structures resemble the structure of nematic liquid crystals around spherical colloidal droplets. The different problems which we studied in this thesis, show that the harmonic rigid base-pair chain model is a powerful tool for study of DNA nanomechanics
  9. Keywords:
  10. Persistence Length ; DNA ; Rigid Base-Pair Model ; Rigid Body ; Nucleosome ; Viral Capsid ; Molecular Dynamic Simulation ; Coarse Grained Model

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