Theses and Dissertations

Date of Award


Document Type


Degree Name

Master of Science (MS)



First Advisor

Dr. Andreas Hanke

Second Advisor

Dr. Ahmed Touhami

Third Advisor

Dr. Soumya Mohanty


Single-molecule DNA stretching experiments is a an extremely rigorous method to investigate mechanical properties of DNA and how DNA molecule binding to proteins, and other small molecules works. In these experiments, double-stranded DNA molecules are stretched by a force applied to opposite ends of the DNA, e.g., in an atomic force microscope or an optical tweezers instrument. Here we study the stretching behavior of the DNA duplex d(CGCAAAAAAGCG) 2 by molecular dynamics simulations. In particular, we calculate the change in free energy ∆F = ∆U − T ∆S as the DNA duplex is stretched. We seek to show that employing both the statistical mechanics, and also modeling of molecular systems(here, double stranded DNA molecule in water) aids us to better comprehend how the DNA molecule behaves under stretching conditions. In particular, we show how thermal fluctuations, and therefore, configurational entropies play role in the mechanical response and behaviour of the DNA molecule at the molecular level to fill in as much as possible the difference in the timescale of the experiment and of the simulation.


Copyright 2017 Ramin Salimi. All Rights Reserved.

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