Bubble Statistics and Dynamics in Double-Stranded DNA
arXiv:cond-mat/0601555 · doi:10.1103/PhysRevE.74.050901
Abstract
The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two probability functions describing coherently localized separations ("bubbles") of the double strand. We find that the resulting bubble distributions are more sharply peaked at the active sites than found in thermodynamically obtained distributions. Our analysis ascribes this to the fact that the bubble life-times significantly afects the distribution function. We find that certain base-pair sequences promote long-lived bubbles and we argue that this is due to a length scale competition between the nonlinearity and disorder present in the system.
References in corpus (6)
- Theory of Bubble Nucleation and Cooperativity in DNA Melting
- Structurally specific thermal fluctuations identify functional sites for DNA transcription
- Can one predict DNA Transcription Start Sites by studying bubbles?
- Probing the mechanical unzipping of DNA
- Lengthscales and Cooperativity in DNA Bubble Formation
- Comment on "Can one predict DNA Transcription Start Sites by Studying Bubbles?"
Cited by in corpus (13)
- Physics of base-pairing dynamics in DNA
- Probability distribution of bubble lengths in DNA
- Dependence on temperature and GC content of bubble length distributions in DNA
- 1/f fluctuations of DNA temperature at thermal denaturation
- Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA
- Distributions of Bubble Lifetimes and Bubble Lengths in DNA
- Theoretical and Experimental Investigations of DNA Open States
- Simple Combined Model for Nonlinear Excitations in DNA
- Bubble lifetimes in DNA gene promoters and their mutations affecting transcription
- Modeling the interaction of DNA with alternating fields
- Thermally Induced Local Failures in Quasi-One-Dimensional Systems: Collapse in Carbon Nanotubes, Necking in Nanowires and Opening of Bubbles in DNA
- Bubble merging in breathing DNA as a vicious walker problem in opposite potentials
- On the thermodynamics of DNA in the Peyrard-Bishop-Dauxois model