Description
- Abstract:
- Polymer folding and unfolding are fundamental processes in biology and materials science, presenting a long-standing challenge in understanding their underlying dynamics. Traditional methods for studying these processes in a landscape perspective often focus on local features of the energy landscape, such as local minima and saddle points. These approaches are limited in their ability to study intrinsically disordered proteins due to their lack of a well-defined native state. An alternative perspective for studying the potential energy landscape is to use the landscape ensemble and geodesic theory, which bridges the global topological information on the landscape with the system's dynamics. This approach is particularly useful for liquid systems with slow dynamics. In this work, we applied geodesic theory to investigate the folding and unfolding processes of dilute polymer solutions, using a model of a freely-jointed chain immersed in an explicitly modeled solvent. First, we design the interactions to allow the use of an energy parameter to suddenly switch between favoring the folded and the unfolded polymers. Molecular dynamics simulations were then conducted to explore the system's dynamics, revealing that the relaxation rates of the unfolding process are significantly slower than those of the folding process. By measuring and comparing the geodesic path lengths folding and unfolding, we find that the slowness comes from the longer and more complex geodesic paths that the polymer chain must navigate to reach the unfolded state. Additionally, calculations of the geodesic paths of the polymer chain both with and without the solvent demonstrate how the solvent significantly influences the polymer dynamics. The presence of the solvent extends the geodesic path and decelerates the process, with a more pronounced impact observed during the unfolding phase.
- Notes:
- Thesis (Ph. D.)--Brown University, 2024
Citation
Si, Dawei,
"Potential Energy Landscape Perspectives on Polymer Folding/Unfolding: Inherent Dynamics through Geodesic Paths"
(2024).
Chemistry Theses and Dissertations.
Brown Digital Repository. Brown University Library.
https://repository.library.brown.edu/studio/item/bdr:f3hbkrem/
