Theses and Dissertations
Exploring Mechanical Properties and Configurational Energetics of Toxbox Using Molecular Dynamics Simulation
Date of Award
Master of Science (MS)
Dr. Ahmed Touhami
Dr. Andreas Hanke
Dr. Soumya Mohanty
All-atom Molecular Dynamics Simulations (MDS) have been performed to obtain 5 ns trajectory of the solvated, neutralized, and equilibrated toxbox system in NPT ensemble at 300 K. This trajectory data has been used to calculate the configurational entropy of toxbox by employing a quantum mechanical approach. The method is based on evaluating determinant of the covariance matrix, built from generalized coordinates of all atoms for each frame. The upper limit to the configurational entropy of toxbox has been calculated to be 30,030 J/mol-K. A preliminary investigation has been conducted to study the effects of sequence-dependent DNA conformation (DNA Crookedness) on the mechanical properties of toxbox by implementing constant force MDS. Results of this research may serve as the reference for studying ToxT – DNA interactions.
Mehdi, Shams, "Exploring Mechanical Properties and Configurational Energetics of Toxbox Using Molecular Dynamics Simulation" (2020). Theses and Dissertations. 511.
Copyright 2020 Shams Mehdi. All Rights Reserved.