Theses and Dissertations
Date of Award
8-2017
Document Type
Thesis
Degree Name
Master of Science (MS)
Department
Physics
First Advisor
Dr. Andreas Hanke
Second Advisor
Dr. Ahmed Touhami
Third Advisor
Dr. Soumya Mohanty
Abstract
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.
Recommended Citation
Salimi, Ramin, "Molecular Dynamics Simulations of DNA Duplex Stretching" (2017). Theses and Dissertations. 385.
https://scholarworks.utrgv.edu/etd/385
Comments
Copyright 2017 Ramin Salimi. All Rights Reserved.
https://www.proquest.com/dissertations-theses/molecular-dynamics-simulations-dna-duplex/docview/1965463033/se-2?accountid=7119