Bubble Statistics and Dynamics in Double-Stranded DNA

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.

References in corpus (1)

• Structurally specific thermal fluctuations identify functional sites for DNA transcription

Cited by in corpus (5)

• Probability distribution of bubble lengths in DNA
• Dependence on temperature and GC content of bubble length distributions in DNA
• Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
• Simple Combined Model for Nonlinear Excitations in DNA
• Bubble merging in breathing DNA as a vicious walker problem in opposite potentials