Bubble Statistics and Dynamics in Double-Stranded DNA

TL;DR

This study investigates the formation and dynamics of bubbles in double-stranded DNA using Langevin simulations, revealing how sequence and nonlinearity influence bubble lifetime and distribution.

Contribution

It introduces a detailed analysis of bubble statistics in DNA with a focus on the effects of sequence and nonlinearity on bubble lifetime and distribution.

Findings

Bubbles are more sharply peaked at active sites than thermodynamic predictions.

Bubble lifetime significantly influences distribution functions.

Certain sequences promote long-lived bubbles due to length scale competition.

Abstract

The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two probability functions describing coherently localized separations ("bubbles") of the double strand. We find that the resulting bubble distributions are more sharply peaked at the active sites than found in thermodynamically obtained distributions. Our analysis ascribes this to the fact that the bubble life-times significantly afects the distribution function. We find that certain base-pair sequences promote long-lived bubbles and we argue that this is due to a length scale competition between the nonlinearity and disorder present in the system.