Influence of media disorder on DNA melting

Abstract

Motivated by the fractal form of the compact chromatin in vivo, we study the melting of a lattice DNA on the infinite cluster backbone near the three-dimensional site percolation critical point $(p_c=0.3116)$, which exhibits fractal-like properties, using Monte Carlo simulations. Further, we extend our study to other values of atmospheric disorder $(p_c\leq p \leq 1)$ and show how the melting temperature varies with a decrease in the availability of lattice sites mimicking the crowded environment inside the cell nucleus. Importantly, we found that the melting transition sharpens with a linear increase in the denaturation temperature as we increase the degree of disorder. Two separate disorder regimes showing weak and strong effects on melting can be 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.