Theory of Bubble Nucleation and Cooperativity in DNA Melting
arXiv:cond-mat/0412591 · doi:10.1103/PhysRevLett.94.035504
Abstract
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles and the possibility of a two states transition are studied.
arXiv comment4 figures. Accepted for publication in Physical Review Letters
References in corpus (3)
Cited by in corpus (42)
- Bubbles and denaturation in DNA
- Physics of base-pairing dynamics in DNA
- Bubble Statistics and Dynamics in Double-Stranded DNA
- Effect of salt concentration on the stability of heterogeneous DNA
- Thermodynamics of Twisted DNA with Solvent Interaction
- Probing the mechanical unzipping of DNA
- Probability distribution of bubble lengths in DNA
- Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics
- Dynamics of DNA breathing in the Peyrard-Bishop model with damping and external force
- The probability analysis of opening of DNA
- Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model
- Lengthscales and Cooperativity in DNA Bubble Formation
- Thermal and mechanical properties of a DNA model with solvation barrier
- Denaturation Patterns in Heterogeneous DNA
- Stacking Interactions in Denaturation of DNA Fragments
- Dependence on temperature and GC content of bubble length distributions in DNA
- Twist versus Nonlinear Stacking in Short DNA Molecules
- J-factors of short DNA molecules
- End-to-end distance and contour length distribution functions of DNA helices
- Twisting and Bending Stress in DNA Minicircles
- Flexibility of short DNA helices under mechanical stretching
- DNA size in confined environments
- Numerical study on a disordered model for DNA denaturation transition
- Distributions of Bubble Lifetimes and Bubble Lengths in DNA
- Theoretical and Experimental Investigations of DNA Open States
- Entropic Penalties in Circular DNA Assembly
- Phase diagram of mechanically stretched DNA: The salt effect
- Theoretical investigation of finite size effects at DNA melting
- Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
- Pulling short DNA molecules having defects on different locations
- Bubble lifetimes in DNA gene promoters and their mutations affecting transcription
- Base pair fluctuations in helical models for nucleic acids
- Effect of external stress on the thermal melting of DNA
- Twisting short dsDNA with applied tension
- Modelling Disorder: the Cases of Wetting and DNA Denaturation
- Anharmonic stacking in supercoiled DNA
- First-passage probability: a test for DNA Hamiltonian parameters
- On the discrete Peyrard-Bishop model of DNA: stationary solutions and stability
- Comment on "Bubble nucleation and cooperativity in DNA melting" [Phys. Rev. Letters 94, 035504 (2005), arXiv:cond-mat/0412591]
- 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
- Nanomechanical resonance captures pre-melting transition in DNA unravelling