Influence of Media Disorder on DNA Melting: A Monte Carlo Study

TL;DR

This study uses Monte Carlo simulations to investigate how atmospheric disorder influences DNA melting temperatures and bubble statistics, revealing two distinct regimes of disorder effects and their impact on DNA stability.

Contribution

It introduces a novel Monte Carlo approach to model lattice DNA melting in disordered environments, identifying two regimes of disorder influence and their effects on melting behavior.

Findings

Melting temperature increases nearly linearly with disorder up to p≈0.6.

Significant change in bubble size exponents at melting points for p≤0.5.

Two regimes of disorder effects on DNA melting are identified.

Abstract

We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with probability $p$ while diluting the rest, rendering them unavailable to the DNA. By varying the disorder over a wide range from $p=1$ (zero disorder) up to the percolation critical point $p_c=0.3116$, we show the melting temperature $(T_m)$ to increase nearly linearly with disorder up to $p\approx 0.6$, while strong non-linearity enters for $p\lesssim 0.6$. Associated changes in the bubble statistics have been investigated, showing a substantial change in the bubble size exponents at corresponding melting points for $p\leq 0.5$. Based on these findings two distinct disorder regimes showing weak and strong effects on melting are identified. For simulations, we use the pruned and enriched Rosenbluth method in conjunction with a depth-first implementation of the Leath algorithm to generate the underlying disorder.