Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

TL;DR

This paper models the thermal behavior of DNA near denaturation using an efficient PBD lattice dynamics approach, analyzing bubble formation, clustering, and melting profiles with new parametrization and statistical methods.

Contribution

It introduces a computationally efficient notation and a reparametrization of the PBD model for better analysis of DNA melting and bubble statistics.

Findings

Melting profiles for various DNA sequences are computed and discussed.

Statistics of open bubbles and bound clusters are formulated and analyzed.

The model provides insights into DNA denaturation mechanisms.

Abstract

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.