Monte Carlo Simulation of Asymmetric Elastic Rod Model and Calculation of<br/>Probability of Loop Formation

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Monte Carlo Simulation of Asymmetric Elastic Rod Model and Calculation of
Probability of Loop Formation

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Type of Document: M.Sc. Thesis
Language: Farsi
Document No: 39892 (04)
University: Sharif University of Technology
Department: Physics
Advisor(s): Ejtehadi, Mohammad Reza
Abstract:
Sharply bent DNA plays an important role in many biological processes such as gene regulation, DNA replication and recombination. DNA cyclization experiments are well suited to study of sharply bent DNA, because they are sensitive to strongly bent conformations. Results of these experiments show that short length DNA molecules are more flexible than predicted by elastic rod model. Therefore, based on these experiments, the elastic rod model is not a suitable model for explaining elastic behavior of DNA at small lengths, although it can explain DNA elasticity at large length scales. Recently, it has been shown that a new model called asymmetric elastic rod model can explain high flexibility of DNA at small length scales. We will show that how one can simulate this model by using Monte Carlo method. Then the probability of loop formation will be calculated using umbrella sampling method and the results of simulation will be compared with the cyclization experiments
Keywords:
DNA ; Monte Carlo Method ; Loop Formation ; Asymmetric Elastic Rod Model ; Umbrella Sampling

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