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Thursday, May 23

Unknotting Challenging Questions in Protein Physics using Wang-Landau Sampling

Thomas Wuest, Swiss Federal Research Institute WSL,
National Center for Computational Sciences Seminar
10:00 AM — 11:00 AM, Joint Institute for Computational Sciences (Building 5100) Auditorium (Room 128)
Contact: Markus Eisenbach ( ), 865.241.1342


Knots are abundant in globular homopolymers but rare in proteins. To shed new light on this long-standing conundrum, I will present a computational study of knotting within the hydrophobic/polar (HP) model of protein folding. In globular, low energy structures of random HP heteropolymers, knots are still abundant on average, but sequence introduces variability in the degree of self-entanglements. It is possible to design sequences which are either almost always or almost never knotted. This serves as proof of concept that the introduction of just one additional degree of freedom (in our case sequence) facilitates evolution towards unknotted proteins. Through the presentation of this study and several other examples, I will demonstrate that Wang-Landau (WL) sampling provides a powerful means to investigate generic questions in protein folding and polymer physics. Our recently introduced parallel WL procedure incorporating replica exchange Monte Carlo has the potential to further raise the bar towards larger treatable, and thus more representative, system sizes.