DNA denaturation bubbles at criticality
arXiv:0802.2194 · doi:10.1103/PhysRevE.77.031919
Abstract
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-stacking interactions. Small bubbles extending over less than 10 base pairs are associated with much larger free energies of formation per site than larger bubbles. As the critical temperature is approached, the free energy associated with further bubble growth becomes vanishingly small. An analysis of average displacement profiles of bubbles of varying sizes at different temperatures reveals almost identical scaled shapes in the absence of nonlinear stacking; nonlinear stacking leads to distinct scaled shapes of large and small bubbles.
8 pages, 8 figures
References in corpus (9)
- Denaturation of Heterogeneous DNA
- Order of the phase transition in models of DNA thermal denaturation
- Structurally specific thermal fluctuations identify functional sites for DNA transcription
- Can one predict DNA Transcription Start Sites by studying bubbles?
- Probability distribution of bubble lengths in DNA
- Thermodynamic instabilities in one dimension: correlations, scaling and solitons
- Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?"
- Thermodynamic instabilities in one dimensional particle lattices: a finite-size scaling approach
- Phase transitions in one dimension: are they all driven by domain walls?
Cited by in corpus (8)
- The thermal denaturation of DNA studied with neutron scattering
- Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics
- Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model
- Dependence on temperature and GC content of bubble length distributions in DNA
- Distributions of Bubble Lifetimes and Bubble Lengths in DNA
- Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
- Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Polya Counting to a Physical System
- Large bubble drives melting in circular DNA