Bell's Theorem and Nonlinear Systems

For all Einstein-Podolsky-Rosen-type experiments on deterministic systems the Bell inequality holds, unless non-local interactions exist between certain parts of the setup. Here we show that in nonlinear systems the Bell inequality can be violated by non-local effects that are arbitrarily weak. Then we show that the quantum result of the existing Einstein-Podolsky-Rosen-type experiments can be reproduced within deterministic models that include arbitrarily weak non-local effects.Comment: Accepted for publication in Europhysics Letters. 14 pages, no figures. In the Appendix (not included in the EPL version) the author says what he really thinks about the subjec

Wave-number Selection by Target Patterns and Side Walls in Rayleigh-Benard Convection

We present experimental results for Rayleigh-Benard convection patterns in a cylindrical container with static side-wall forcing induced by a heater. This forcing stabilized a pattern of concentric rolls (a target pattern) with the central roll (the umbilicus) at the center of the cell after a jump from the conduction to the convection state. A quasi-static increase of the control parameter (epsilon) beyond 0.8 caused the umbilicus of the pattern to move off center. As observed by others, a further quasi-static increase of epsilon up to 15.6 caused a sequence of transitions. Each transition began with the displacement of the umbilicus and then proceeded with the loss of one convection roll at the umbilicus and the return of the umbilicus to a location near the center of the cell. Alternatively, with decreasing epsilon new rolls formed at the umbilicus but large umbilicus displacements did not occur. In addition to quantitative measurements of the umbilicus displacement, we determined and analyzed the entire wave-director field of each image. The wave numbers varied in the axial direction, with minima at the umbilicus and at the cell wall and a maximum at a radial position close to 2/3 Gamma. The wave numbers at the maximum showed hysteretic jumps at the transitions, but on average agreed well with the theoretical predictions for the wave numbers selected in the far field of an infinitely extended target pattern.Comment: ReVTeX, 11 pages, 16 eps figures include

Direct observation of stalled fork restart via fork regression in the T4 replication system

The restart of a stalled replication fork is a major challenge for DNA replication. Depending on the nature of the damage, different repair processes might be triggered; one is template switching, which is a bypass of a leading-strand lesion via fork regression. Using magnetic tweezers to study the T4 bacteriophage enzymes, we have reproduced in vitro the complete process of template switching. We show that the UvsW DNA helicase in cooperation with the T4 holoenzyme can overcome leading-strand lesion damage by a pseudostochastic process, periodically forming and migrating a four-way Holliday junction. The initiation of the repair process requires partial replisome disassembly via the departure of the replicative helicase. The results support the role of fork regression pathways in DNA repair

Wavy stripes and squares in zero P number convection

A simple model to explain numerically observed behaviour of chaotically varying stripes and square patterns in zero Prandtl number convection in Boussinesq fluid is presented. The nonlinear interaction of mutually perpendicular sets of wavy rolls, via higher mode, may lead to a competition between the two sets of wavy rolls. The appearance of square patterns is due to the secondary forward Hopf bifurcation of a set of wavy rolls.Comment: 8 pages and 3 figures, late

Collaborative coupling between polymerase and helicase for leading-strand synthesis

Rapid and processive leading-strand DNA synthesis in the bacteriophage T4 system requires functional coupling between the helicase and the holoenzyme, consisting of the polymerase and trimeric clamp loaded by the clamp loader. We investigated the mechanism of this coupling on a DNA hairpin substrate manipulated by a magnetic trap. In stark contrast to the isolated enzymes, the coupled system synthesized DNA at the maximum rate without exhibiting fork regression or pauses. DNA synthesis and unwinding activities were coupled at low forces, but became uncoupled displaying separate activities at high forces or low dNTP concentration. We propose a collaborative model in which the helicase releases the fork regression pressure on the holoenzyme allowing it to adopt a processive polymerization conformation and the holoenzyme destabilizes the first few base pairs of the fork thereby increasing the efficiency of helicase unwinding. The model implies that both enzymes are localized at the fork, but does not require a specific interaction between them. The model quantitatively reproduces homologous and heterologous coupling results under various experimental conditions

Quasiperiodic waves at the onset of zero Prandtl number convection with rotation

We show the possibility of quasiperiodic waves at the onset of thermal convection in a thin horizontal layer of slowly rotating zero-Prandtl number Boussinesq fluid confined between stress-free conducting boundaries. Two independent frequencies emerge due to an interaction between a stationary instability and a self-tuned wavy instability in presence of coriolis force, if Taylor number is raised above a critical value. Constructing a dynamical system for the hydrodynamical problem, the competition between the interacting instabilities is analyzed. The forward bifurcation from the conductive state is self-tuned.Comment: 9 pages of text (LaTex), 5 figures (Jpeg format

Mechanism of strand displacement synthesis by DNA replicative polymerases

Replicative holoenzymes exhibit rapid and processive primer extension DNA synthesis, but inefficient strand displacement DNA synthesis. We investigated the bacteriophage T4 and T7 holoenzymes primer extension activity and strand displacement activity on a DNA hairpin substrate manipulated by a magnetic trap. Holoenzyme primer extension activity is moderately hindered by the applied force. In contrast, the strand displacement activity is strongly stimulated by the applied force; DNA polymerization is favoured at high force, while a processive exonuclease activity is triggered at low force. We propose that the DNA fork upstream of the holoenzyme generates a regression pressure which inhibits the polymerization-driven forward motion of the holoenzyme. The inhibition is generated by the distortion of the template strand within the polymerization active site thereby shifting the equilibrium to a DNA-protein exonuclease conformation. We conclude that stalling of the holoenzyme induced by the fork regression pressure is the basis for the inefficient strand displacement synthesis characteristic of replicative polymerases. The resulting processive exonuclease activity may be relevant in replisome disassembly to reset a stalled replication fork to a symmetrical situation. Our findings offer interesting applications for single-molecule DNA sequencing

Whirling Hexagons and Defect Chaos in Hexagonal Non-Boussinesq Convection

We study hexagon patterns in non-Boussinesq convection of a thin rotating layer of water. For realistic parameters and boundary conditions we identify various linear instabilities of the pattern. We focus on the dynamics arising from an oscillatory side-band instability that leads to a spatially disordered chaotic state characterized by oscillating (whirling) hexagons. Using triangulation we obtain the distribution functions for the number of pentagonal and heptagonal convection cells. In contrast to the results found for defect chaos in the complex Ginzburg-Landau equation and in inclined-layer convection, the distribution functions can show deviations from a squared Poisson distribution that suggest non-trivial correlations between the defects.Comment: 4 mpg-movies are available at http://www.esam.northwestern.edu/~riecke/lit/lit.html submitted to New J. Physic

Principle of Maximum Entropy Applied to Rayleigh-B\'enard Convection

A statistical-mechanical investigation is performed on Rayleigh-B\'enard convection of a dilute classical gas starting from the Boltzmann equation. We first present a microscopic derivation of basic hydrodynamic equations and an expression of entropy appropriate for the convection. This includes an alternative justification for the Oberbeck-Boussinesq approximation. We then calculate entropy change through the convective transition choosing mechanical quantities as independent variables. Above the critical Rayleigh number, the system is found to evolve from the heat-conducting uniform state towards the convective roll state with monotonic increase of entropy on the average. Thus, the principle of maximum entropy proposed for nonequilibrium steady states in a preceding paper is indeed obeyed in this prototype example. The principle also provides a natural explanation for the enhancement of the Nusselt number in convection.Comment: 13 pages, 4 figures; typos corrected; Eq. (66a) corrected to remove a double counting for $k_{\perp}=0$; Figs. 1-4 replace

Influence of through-flow on linear pattern formation properties in binary mixture convection

We investigate how a horizontal plane Poiseuille shear flow changes linear convection properties in binary fluid layers heated from below. The full linear field equations are solved with a shooting method for realistic top and bottom boundary conditions. Through-flow induced changes of the bifurcation thresholds (stability boundaries) for different types of convective solutions are deter- mined in the control parameter space spanned by Rayleigh number, Soret coupling (positive as well as negative), and through-flow Reynolds number. We elucidate the through-flow induced lifting of the Hopf symmetry degeneracy of left and right traveling waves in mixtures with negative Soret coupling. Finally we determine with a saddle point analysis of the complex dispersion relation of the field equations over the complex wave number plane the borders between absolute and convective instabilities for different types of perturbations in comparison with the appropriate Ginzburg-Landau amplitude equation approximation. PACS:47.20.-k,47.20.Bp, 47.15.-x,47.54.+rComment: 19 pages, 15 Postscript figure