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Equilibrium States of Nano scaled DNA-loops in Different Elastic Models

Salari, Hossein | 2014

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 45862 (04)
  4. University: Sharif University of Technology
  5. Department: Physics
  6. Advisor(s): Ejtehadi, Mohammad Reza
  7. Abstract:
  8. DNA cyclization mechanism, has an important role in many biological processes such as gene regulation, DNA replication and recombination. In addition there are DNA-loops in Bacteria an around the Histones in Chromosomes in scale of 5-100 nm. We need to a appropriate model to study about bending and loop formationin in this important molecule which is able to describe elasticity properties of DNA.One of the most successful models, to describe the physical behaviour of a long DNA molecule, is the elastic rod model. In this model, DNA is considered as a  ixable rod that its bending energy is isotropic. Asymmetric elastic rod model is another model to describe elasticity properties of DNA. Predictions this model about long DNA is the same as elastic rod model, but for short DNA, it predicts dierent behaviors. Here we want to study and compare equilibrium cone guration of nano scale DNA-loops in this elastic models, by use of Monte Carlo simulation, and we will show that by considertion of temperature of system, these loops dier  om circle cone guration in elastic rod model, because of entropic eects, and choose other cone gurations. Also we shall show, there is kink in DNA-loops,in asymmetric elastic rod model by use of local mean curvature diagram.
  9. Keywords:
  10. Asymmetric Elastic Rod Model ; Monte Carlo Simulation ; DNA Molecule Elastic Properties ; Nanoscale DNA-Loops ; Symmetric Elastic Rod Model ; Anisotropic Elastic Rod Model

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