Biomolecular Folding Rates As Understood From Single-Reaction-Coordinate Langevin Dynamics And Kramers’ Theory

Langevin dynamics was used to model the folding and unfolding of simple, hairpin-like biomolecules whose ends are attached to laser-trapped beads, as occurs in optical tweezers experiments. The Langevin process was evolved numerically, using parameters motivated by real experimental systems. Folding trajectories were generated and analyzed to extract the folding rate as a function of the force applied to the beads. The observed rate was compared to the analytical predictions of Kramers' theory. Strong discrepancies were noted. The failure of the Kramers' theory was attributed to the slow dynamical response of the beads, which it does not account for. The results of this work highlight the necessity to include in the modeling the experimental systems that mediate force along the length of the biomolecule.

Name thesis:degree_name

M.S. in Physics

Level thesis:degree_level

Thesis

Discipline thesis:degree_discipline

Physics and Astronomy

Year dc:date.available

2015

Author dc:creator

• Kabir, Md Adnan

Contributors dc:contributor

• Kevin Beach
• Cecille Labuda
• Luca Bombelli

• Biomolecular
• Kramers'
• Langevin Dynamics
• Protein
• Physics

Repository record dc:identifier

https://egrove.olemiss.edu/etd/1114

OAI identifier oai:identifier

oai:egrove.olemiss.edu:etd-2113