Bubble Statistics and Dynamics in Double-Stranded DNA

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes are consistent with the model potential for the hydrogen bonds between complementary strands. The portion of configuration space contributing to the partition function is determined, at any temperature, by selecting the ensemble of paths wh...

In this letter, we point out the inaccurate figures in a letter by Peyrard and Bishop, who investigated the statistical mechanics of a nonlinear model for DNA denaturation. We give the correct figures.

We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the Principal Component Analysis of the trajectorie...

We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of ``bubbles'', localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in $P(R)$ and unusual force-extension curves. An analyt...

We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of ...

We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA molecules (shortly BCC-DNA). To study bubble coalescence thermodynamics of BCI-DNA and BCC-DNA models we use methods of statistical physics. Namely, we define Hamiltonian of each model and give their translation-invariant Gibbs measures (TIGMs)...

Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting time and meeting position probability distributions are derived from the solutions. Probability distribution functions reflect the value of the loop exponent of the entropic interaction. Our results extend previous results which concentrate...

We present detailed molecular dynamics results for the displacement autocorrelation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is smaller than, or exceeds the correlation length. In the first case, the spectra are dominated by a single peak, whose frequency approaches the bare acoustic frequency of the harmonic chain, and whose linewidth approaches zero as $T_c-T$. In the...

The nonlinear excitations induced in DNA by external force are considered on the basis of Peyrard-Bishop-Dauxois model. It is shown that such impact can lead to creation of bubbles which can propogate through the molecule. The interaction of such bubbles with an excess electron or hole is considered. The numerical experiments demonstrate the possibility of charge transfer induced by bubbles. The possible applications of the obtained results in nanobioelectronics are discussed...

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity, in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used, with energies corresponding to physiological temperature. The bubble lifetime profiles along the DNA sequences demonstrate a significant reduction of the ave...