Date of Award




Document Type


Degree Name

Doctor of Philosophy (PhD)


Department of Physics

Content Description

1 online resource (xix, 265 pages) : illustrations (some color)

Dissertation/Thesis Chair

Alan A Chen

Committee Members

Oleg Lunin, Paul Whitford, Jonathan Petruccelli, Matthew Szydagis


density functional theory, force field development, molecular dynamics simulations, molecular mechanics, quantum chemistry, RNA, Molecular dynamics, Computational chemistry

Subject Categories

Computational Chemistry | Numerical Analysis and Scientific Computing | Physics


Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would not have this reputation today without proper algorithms designed to replicate similar electronic structure phenomena from \textit{ab initio} computations instead at the molecular mechanics level.