Critical dynamics of DNA denaturation

TL;DR

This paper investigates the critical dynamics of DNA denaturation using molecular dynamics simulations of the Peyrard-Bishop model, revealing how spectral features change near the phase transition.

Contribution

It provides detailed spectral analysis of DNA denaturation dynamics, highlighting the behavior of displacement and force autocorrelation spectra near the critical point.

Findings

Spectra depend on wavelength relative to correlation length.

Single peak frequency approaches harmonic chain frequency near criticality.

Central peak remains temperature-independent.

Abstract

We present detailed molecular dynamics results for the displacement autocorrelation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is smaller than, or exceeds the correlation length. In the first case, the spectra are dominated by a single peak, whose frequency approaches the bare acoustic frequency of the harmonic chain, and whose linewidth approaches zero as $T_c-T$. In the second case, a central peak (CP) feature is dominant, accounting for most of the weight; the linewidth of the CP appears to be temperature-independent. We also present force autocorrelation spectra which may be relevant for analyzing the statistical properties of localized modes.