Paper Number
SM6 

Session
Polymer Solutions and Melts

Title
Relaxation dynamics of knotted polymers – knot swelling and end-to-end relaxation

Presentation Date and Time
October 9, 2017 (Monday) 1:30

Track / Room
Track 2 / Crystal B

Authors (Click on name to view author profile)

1. Narsimhan, Vivek (Massachusetts Institute of Technology, Chemical Engineering)
2. Klotz, Alexander R. (Massachusetts Institute of Technology, Chemical Engineering)
3. Doyle, Patrick S. (Massachusetts Institute of Technology)

Author and Affiliation Lines (in printed abstract book)
Vivek Narsimhan, Alexander R. Klotz, and Patrick S. Doyle
Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA

Speaker / Presenter 
Narsimhan, Vivek

Text of Abstract
In recent years, there has been interest in understanding the dynamics of knotted DNA due to the fact that such molecules have been observed in nanotechnology applications such as single-molecule gene-mapping and sequencing. In this talk, we discuss our latest experiments and simulations to characterize the relaxation behavior of knotted chains from a highly extended initial state. We examine two behaviors: (a) the swelling of the knot, and (b) how this swelling process alters the overall relaxation of the chain. Our single-molecule experiments repeatedly stretch and relax knotted DNA in an extensional electric field, which allows us to obtain an ensemble of knot swelling profiles vs. time. These studies plus Brownian dynamics simulations observe: (1) knots swell at a time scale that is comparable to the end-to-end relaxation of the polymer chain, (2) the swelling dynamics appear insensitive to the chain topology, at least for the complex knots we sample. In the second part of the talk, we discuss how knots modify the overall end-to-end relaxation of polymer chains, and how this behavior depends on the overall chain length and topology. For short polymer chains, our Brownian dynamics simulations show that knots hasten the relaxation of stretched chains, greater than what naïve scaling predictions would anticipate. We develop models to explain these trends and discuss what are the consequences of these effects on polymer rheology.