Theses and Dissertations

Date of Award


Document Type


Degree Name

Master of Science (MS)



First Advisor

Dr. Ahmed Touhami

Second Advisor

Dr. Andreas Hanke

Third Advisor

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.


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