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Research Advisor:
Dr. Nanjie Deng, PhD
Associate Professor, Department of Biochemistry and Molecular Biology
Dyson College of Arts and Sciences, Pace University

Document Type

Thesis

Abstract

This thesis relies on molecular dynamics (MD) simulations, which apply the AMBER software package to analyze the structural stability, energetics, and dynamics of Poly A - Poly T DNA duplexes. This work is mainly concerned with testing configurations of non-bonded interaction cutoffs (12 Å and 15 Å) on the Generalized Born solvation models (IGB1 and IGB2) to determine the most appropriate conditions regarding computation time and physical reliability in DNA molecular dynamics. The solvation models enable effective simulation of solvent effects, facilitating the calculation of simulation parameters to evaluate structural stability within different environmental conditions. Overall, the performance indicates that a 12 Å cutoff is ideal for retaining the DNA structure and its energetic stability since RMSD and potential energy showed low values, below 5 Å and fluctuations, respectively. Extending the cutoff to 15 Å did not introduce advantages, thus confirming the desirability of the 12 Å cutoff regarding both resource consumption and the precision of the simulation. It is clear that the IGB1 and IGB2 solvation models achieved DNA stabilization for simulations, and system stability between the two implicit solvent models was indistinguishable, likely meaning that there is flexibility in selecting a model depending on the objectives of the simulation experiments. This research presents a model simulation framework focusing on parameter optimization and providing insights into molecular dynamics simulations of the structural stability of DNA duplex.

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