Dynamics of a bubble formed in double stranded DNA

We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation.The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let

Roles of stiffness and excluded volume in DNA denaturation

The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated loops of length l, $P \sim l^{-c}$. If excluded volume effects are fully taken into account, c= 2.10(4) is consistent with a first order transition. The stiffness of the double stranded chain has the effect of sharpening the transition, if it is continuous, but not of changing its order and the value of the exponent c, which is also robust with respect to inclusion of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as publishe

Why is the DNA Denaturation Transition First Order?

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between denaturated loops and the rest of the chain by exploiting recent results on scaling properties of polymer networks of arbitrary topology. The phase transition is found to be first order in d=2 dimensions and above, in agreement with experiments and at variance with previous theoretical results, in which only excluded-volume interactions within denaturated loops were taken into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let

Phase transition in a non-conserving driven diffusive system

An asymmetric exclusion process comprising positive particles, negative particles and vacancies is introduced. The model is defined on a ring and the dynamics does not conserve the number of particles. We solve the steady state exactly and show that it can exhibit a continuous phase transition in which the density of vacancies decreases to zero. The model has no absorbing state and furnishes an example of a one-dimensional phase transition in a homogeneous non-conserving system which does not belong to the absorbing state universality classes

Continuous gravity measurementsr evealal ow-density lava lake at Kılauea Volcano, Hawai‘i

On 5 March 2011, the lava lake within the summit eruptive vent at Kīlauea Volcano, Hawai‘i, began to drain as magma withdrew to feed a dike intrusion and fissure eruption on the volcano’s east rift zone. The draining was monitored by a variety of continuous geological and geophysical measurements, including deformation, thermal and visual imagery, and gravity. Over the first ~14 hours of the draining, the ground near the eruptive vent subsided by about 0.15 m, gravity dropped by more than 100 μGal, and the lava lake retreated by over 120 m. We used GPS data to correct the gravity signal for the effects of subsurface mass loss and vertical deformation in order to isolate the change in gravity due to draining of the lava lake alone. Using a model of the eruptive vent geometry based on visual observations and the lava level over time determined from thermal camera data, we calculated the best fit lava density to the observed gravity decrease—to our knowledge, the first geophysical determination of the density of a lava lake anywhere in the world. Our result, 950 ± 300 kg m-3, suggests a lava density less than that of water and indicates that Kīlauea’s lava lake is gas-rich, which can explain why rockfalls that impact the lake trigger small explosions. Knowledge of such a fundamental material property as density is also critical to investigations of lava-lake convection and degassing and can inform calculations of pressure change in the subsurface magma plumbing system

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.Comment: 4 pages of Latex, including 4 Postscript figures. To be published in Phys. Rev. Let

Denaturation of Heterogeneous DNA

The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second order melting transition in the simplest (Peyrard-Bishop) model. However, sequence heterogeneity is dramatically amplified upon adopting a more realistic treatment of the backbone stiffness. The model yields features of ``multi-step melting'' similar to those observed in experiments.Comment: 4 pages, LaTeX, text and figures also available at http://matisse.ucsd.edu/~hw

Influence of the structural modulations and the Chain-ladder interaction in the Sr_14−xCa_xCu_24O_41Sr\_{14-x}Ca\_{x}Cu\_{24}O\_{41} compounds

We studied the effects of the incommensurate structural modulations on the ladder subsystem of the $Sr\_{14-x}Ca\_{x}Cu\_{24}O\_{41}$ family of compounds using ab-initio explicitly-correlated calculations. From these calculations we derived $t-J$ model as a function of the fourth crystallographic coordinate $\tau$ describing the incommensurate modulations. It was found that in the highly calcium-doped system, the on-site orbital energies are strongly modulated along the ladder legs. On the contrary the two sites of the ladder rungs are iso-energetic and the holes are thus expected to be delocalized on the rungs. Chain-ladder interactions were also evaluated and found to be very negligible. The ladder superconductivity model for these systems is discussed in the light of the present results.Comment: 8 octobre 200

Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.Comment: 7 pages, 4 figure

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta