UBC Theses and Dissertations
Atomistic and coarse-grained simulations of DNA electrostatics Ghanbarian Alavijeh, Shahzad
This thesis aims to understand the nanoscale effects of water as a structured solvent on the phenomenon of counterion-induced DNA condensation. We present results of molecular dynamics simulations of the electrostatic interaction between two DNA molecules in the presence of divalent counterions in different solvation models. We also develop a coarse-grained implicit solvent model for investigating the dynamics on long time and length scales. In the first project, we investigate the role of the solvation effects on the interaction between like-charged cylindrical rods as simplified model for DNA molecules. We obtain the average force between two parallel charged rods in simulations that differ only by their representation of water as a implicit or explicit solvent, but have otherwise identical parameters. We find that the presence of water molecules changes the structure of the counterions and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes. In the second project, we explore the importance of the DNA geometry on the electrostatic forces by considering two rigid helical models. The simulation results indicate that the DNA shape is an essential contributor to the interaction. A regime of attractive interaction, which disappeared in the cylindrical model, is recovered in the explicit solvent model in both types of helical models. The results also confirm that the behaviour of the interactions between two DNA molecules in the explicit solvent model are different from the implicit solvent models. In the third project, we develop a coarse-grained (CG) representation of these solvation effects. This CG model is constructed from explicit simulations and significantly reduces the computational expense. Short-ranged corrections are added to the pair-wise interaction potentials in the implicit solvent model such that the structure of counterions in the system is consistent with the results from the explicit solvent simulations. This CG model succeeds in reproducing the like-charge attraction effect between DNA molecules in explicit simulations. In a final project, we apply the CG model developed previously to study three DNA strands in the presence of divalent counterions as a starting point for investigating many-body effects in the mechanism of DNA bundling.
Item Citations and Data
Attribution-NonCommercial-NoDerivs 2.5 Canada