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Coarse Grained Molecular Dynamics Simulation of DNA Nanomechanics
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Khoei, Amir Reza (Co-Advisor)
Abstract
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...