Scaling in DNA unzipping models: denaturated loops and end-segments as branches of a block copolymer network

TL;DR

This paper investigates DNA denaturation models by analyzing loop and end-segment distributions through enumeration and Monte Carlo simulations, revealing complex behaviors that challenge previous homogeneous network assumptions.

Contribution

It introduces a refined scaling framework distinguishing single and double stranded segments, explaining unexpected distribution features in DNA unzipping models.

Findings

Loop distributions support first order denaturation.

End-segment distributions show two coexisting power laws.

Discrepancies with homogeneous models are explained by network branch distinctions.

Abstract

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions are consistent with first order thermal denaturation in both cases. Results for end-segments show a coexistence of two distinct power laws in the relative distributions, which is not foreseen by a recent approach in which DNA is treated as a homogeneous network of linear polymer segments. This unexpected feature, and the discrepancies with such an approach, are explained in terms of a refined scaling picture in which a precise distinction is made between network branches representing single stranded and effective double stranded segments.