Sharp DNA denaturation in a helicoidal mesoscopic model

TL;DR

This paper introduces a new 1D Hamiltonian model for DNA denaturation that incorporates helical twist, providing more realistic predictions of sharp melting transitions compared to traditional models.

Contribution

It develops a novel 1D Hamiltonian with twist dependence derived from a 3D model, validated for small angles, improving DNA melting simulations.

Findings

The model predicts sharp, first-order-like melting transitions for long DNA sequences.

Numerical comparisons confirm the model's validity in the small-angle regime.

It offers a more realistic description of DNA denaturation dynamics.

Abstract

The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other relevant molecular dimensions. Here, we start from a more realistic 3D model and work out several approximations to arrive at a new non-linear 1D Hamiltonian with a twist angle dependence. Our approximations were numerically compared to full 3D calculations, and established its validity in the regime of small angles. For long DNA sequences we obtain sharp, first-order-like melting, transitions.