Structure factor and dynamics of the helix-coil transition

Thermodynamical properties of the helix-coil transition were successfully described in the past by the model of Lifson, Poland and Sheraga. Here we compute the corresponding structure factor and show that it possesses a universal scaling behavior near the transition point, even when the transition is of first order. Moreover, we introduce a dynamical version of this model, that we solve numerically. A Langevin equation is also proposed to describe the dynamics of the density of hydrogen bonds. Analytical solution of this equation shows dynamical scaling near the critical temperature and predicts a gelation phenomenon above the critical temperature. In the case when comparison of the two dynamical approaches is possible, the predictions of our phenomenological theory agree with the results of the Monte Carlo simulations.Comment: 11 pages, 7 figure

Statistical mechanics of base stacking and pairing in DNA melting

We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.Comment: 13 pages with figure

Modelling Molecular Motors as Folding-Unfolding Cycles

We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response. The main improvement with respect to previous models is that this description suggests a connection between folding and function of allosteric proteins.Comment: 5 pages RevTeX, 2 Postscript figures, replaced due to LaTeX proble

Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments

In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We present a new technique for characterizing the kinetics of loop formation in vitro, as observed using the tethered particle method, and apply it to experimental data on looping induced by lambda repressor. Our method uses a modified (diffusive) hidden Markov analysis that directly incorporates the Brownian motion of the observed tethered bead. We compare looping lifetimes found with our method (which we find are consistent over a range of sampling frequencies) to those obtained via the traditional threshold-crossing analysis (which can vary depending on how the raw data are filtered in the time domain). Our method does not involve any time filtering and can detect sudden changes in looping behavior. For example, we show how our method can identify transitions between long-lived, kinetically distinct states that would otherwise be difficult to discern

Barrier properties of films of pea starch associated with xanthan gum and glycerol

O objetivo do trabalho foi avaliar as propriedades de barreira e a solubilidade de biofilmes obtidos a partir de amido de ervilha de alto teor de amilose em associação à goma xantana e glicerol. Soluções filmogênicas (SF) com diferentes teores de amido de ervilha (3, 4 e 5%), goma xantana (0, 0,05 e 0,1%) e glicerol (proporção glicerol-amido de 1:5 P/P) foram estudadas. As SF foram obtidas por ebulição (5 minutos), seguida de autoclavagem por 1 hora a 120 ºC e os filmes foram preparados por casting. O aumento da concentração de amido e de glicerol na composição causou aumento da espessura e da solubilidade dos filmes em água. O plastificante gerou ainda elevação dos coeficientes de permeabilidade ao vapor d'água e ao oxigênio. O aumento da concentração da goma xantana não interferiu nas propriedades estudadas. Os biofilmes obtidos a partir de amido de ervilha verde, associado ou não à goma xantana e glicerol, se comparados com filmes de amido de ervilha amarelas e outras fontes de amido, apresentaram boa barreira ao oxigênio e ao vapor d'água e baixa solubilidade em água.The aim of this work was to evaluate the barrier properties and solubility of biofilms made from wrinkled pea starch with high amylose content in association with xanthan gum and glycerol. Filmogenic solution (FS) with different levels of pea starch (3, 4 and 5%), xanthan gum (0, 0.05 and 0.1%) and glycerol (glycerol-starch 1:5 W/W) were tested. FS was obtained by boiling (5 minutes), autoclaving for 1 hour at 120 ºC and the films were prepared by casting. The increased concentration of starch and glycerol in the composition caused increases in thickness of the films and in their solubility in water. The plasticizer also generated higher coefficients of water vapor and oxygen permeabilities to water vapor and to oxygen. The increasing concentration of xanthan gum did not interfere in the properties studied. Biofilms produced with wrinkled pea starch, with or without xanthan gum and glycerol, showed better barrier to oxygen and water vapor and low solubility in water, in comparison with films of yellow pea starch and other starch sources.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Streamer Propagation as a Pattern Formation Problem: Planar Fronts

Streamers often constitute the first stage of dielectric breakdown in strong electric fields: a nonlinear ionization wave transforms a non-ionized medium into a weakly ionized nonequilibrium plasma. New understanding of this old phenomenon can be gained through modern concepts of (interfacial) pattern formation. As a first step towards an effective interface description, we determine the front width, solve the selection problem for planar fronts and calculate their properties. Our results are in good agreement with many features of recent three-dimensional numerical simulations.Comment: 4 pages, revtex, 3 ps file

The energy budget in Rayleigh-Benard convection

It is shown using three series of Rayleigh number simulations of varying aspect ratio AR and Prandtl number Pr that the normalized dissipation at the wall, while significantly greater than 1, approaches a constant dependent upon AR and Pr. It is also found that the peak velocity, not the mean square velocity, obeys the experimental scaling of Ra^{0.5}. The scaling of the mean square velocity is closer to Ra^{0.46}, which is shown to be consistent with experimental measurements and the numerical results for the scaling of Nu and the temperature if there are strong correlations between the velocity and temperature.Comment: 5 pages, 3 figures, new version 13 Mar, 200

Fluctuating "Pulled" Fronts: the Origin and the Effects of a Finite Particle Cutoff

Recently it has been shown that when an equation that allows so-called pulled fronts in the mean-field limit is modelled with a stochastic model with a finite number $N$ of particles per correlation volume, the convergence to the speed $v^*$ for $N \to \infty$ is extremely slow -- going only as $\ln^{-2}N$. In this paper, we study the front propagation in a simple stochastic lattice model. A detailed analysis of the microscopic picture of the front dynamics shows that for the description of the far tip of the front, one has to abandon the idea of a uniformly translating front solution. The lattice and finite particle effects lead to a ``stop-and-go'' type dynamics at the far tip of the front, while the average front behind it ``crosses over'' to a uniformly translating solution. In this formulation, the effect of stochasticity on the asymptotic front speed is coded in the probability distribution of the times required for the advancement of the ``foremost bin''. We derive expressions of these probability distributions by matching the solution of the far tip with the uniformly translating solution behind. This matching includes various correlation effects in a mean-field type approximation. Our results for the probability distributions compare well to the results of stochastic numerical simulations. This approach also allows us to deal with much smaller values of $N$ than it is required to have the $\ln^{-2}N$ asymptotics to be valid.Comment: 26 pages, 11 figures, to appear in Phys. rev.

Periodically kicked turbulence

Periodically kicked turbulence is theoretically analyzed within a mean field theory. For large enough kicking strength A and kicking frequency f the Reynolds number grows exponentially and then runs into some saturation. The saturation level can be calculated analytically; different regimes can be observed. For large enough Re we find the saturation level to be proportional to A*f, but intermittency can modify this scaling law. We suggest an experimental realization of periodically kicked turbulence to study the different regimes we theoretically predict and thus to better understand the effect of forcing on fully developed turbulence.Comment: 4 pages, 3 figures. Phys. Rev. E., in pres

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.Comment: 9 pages, 2 figure