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

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 $p\le 0.5$. 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.

arXiv comment10 pages; 7 figures

References in corpus (17)

• Roles of stiffness and excluded volume in DNA denaturation
• A Simple Model for the DNA Denaturation Transition
• Anomalous diffusion in fractal globules
• Thermodynamics of Lattice Heteropolymers
• Simulations of lattice animals and trees
• Can one predict DNA Transcription Start Sites by studying bubbles?
• Shape anisotropy of polymers in disordered environment
• Statistics of self-avoiding walks on randomly diluted lattice
• Effects of Molecular Crowding on stretching of polymers in poor solvent
• 2-d Self-Avoiding Walks on a Cylinder
• Numerical study on a disordered model for DNA denaturation transition
• Ring polymers in crowded environment: conformational properties
• Equivalence of quenched and annealed averaging in models of disordered polymers
• Softening of DNA near Melting as Disappearance of an Emergent Property
• Elasticity of a DNA chain dotted with bubbles under force
• Loop formation in polymers in crowded environment
• Adsorption of melting deoxyribonucleic acid