Biophysical chaos: Bubbles in DNA molecules (Malcolm Hillebrand, 8/9/2022)
Channel: Academy of Athens
Date: 25/10/2022

Malcolm Hillebrand
Department of Mathematics and Applied Mathematics University of Cape Town

Abstract:
In this talk, I will discuss the investigation of the phenomenon of DNA “bubbles”, thermal openings in the double strand. This will be presented through numerical simulations of the dynamics of DNA in the coarse-grained nonlinear Peyrard-Bishop-Dauxois (PBD) model. With this, we have studied various aspects of these bubbles and the nonlinearity of the strand, using a rationally-determined definition for determining the open/closed state of a base pair. These aspects include the inherent lifetimes and occurrence probabilities of bubbles in random sequences as well as viral and bacterial promoters, and further timescale studies of out-of-equilibrium fluctuations in the double strand. These results will be discussed in the context of the chaotic dynamics inherent to the nonlinear model, including Lyapunov exponents and the deviation vector distribution.