Doctor of Philosophy (PhD)


Mechanical and Industrial Engineering

Document Type



Molecular dynamics (MD) simulations of interaction of DNA nucleotides with self-assembled monolayers (SAMs) provide valuable information that is critical to the development of a new DNA sequencing technique. We investigated the interactions and transport characteristics of mononucleotides moving through nanoslits with SAMs-covered surfaces. Our simulations focused on nanoslits in which the walls were composed of three different types of SAMs: methylformyl terminated, methyl terminated, and phenoxy terminated. The results demonstrated that the phenoxy terminated surfaces have the shortest required nanoslits length for nucleotides separation.

Using MD simulations, we also investigated the interaction of mono-lignin and oligo-lignols with lipid bilayers and small molecules. The simulations showed mono and dimer lignols have different affinity for the lipid bilayers interior and as such, depending on their molecular structure, they can penetrate deep into the bilayers or absorb at bilayer-water interface. When the lignols interaction with bilayers is strong they can affect various physical characteristics of the bilayers, including bilayers gel to fluid phase transition temperature. By focusing on three lignin dimers with different structure and hydrophobicity, our MD simulations provided atomistic insight into how the lignols affect the gel to fluid phase transition temperature in DPPC. Moreover, the magnitude of the values of phase transition temperature shift from MD simulations and differential scanning calorimetry experiments are in good agreement. The MD simulations of interaction of lignin dimer and its derivative with cyclodextrins show the formation of lignin-cyclodextrin association whose stability depend on the lignin dimer structure. The potential of mean force (free energy) for cyclodextrin-lignin dimer interaction was evaluated and used to investigate various characteristics, adsorption mechanism, and binding energy between lignin dimers and cyclodextrin. The characteristic properties include: molecular positioning during association, hydrogen bonding formation, distribution of dihedral angles, adsorption/desorption frequency, lipid tails order parameter, etc. The MD simulations of lignin tetramers in deep eutectic solvents in the presence of a microwave field show that in the externally applied time varying electric field cause stretching of certain interatomic bonds in lignin tetramers which in turn may increase the probability of bond breaking and therefore an increased rate of breakdown of lignin tetramers.

Committee Chair

Moldovan, Dorel

Available for download on Saturday, October 29, 2022