Manifestations of Drag Reduction by Polymer Additives in Decaying, Homogeneous, Isotropic Turbulence

The existence of drag reduction by polymer additives, well established for wall-bounded turbulent flows, is controversial in homogeneous, isotropic turbulence. To settle this controversy we carry out a high-resolution direct numerical simulation (DNS) of decaying, homogeneous, isotropic turbulence with polymer additives. Our study reveals clear manifestations of drag-reduction-type phenomena: On the addition of polymers to the turbulent fluid we obtain a reduction in the energy dissipation rate, a significant modification of the fluid energy spectrum especially in the deep-dissipation range, a suppression of small-scale intermittency, and a decrease in small-scale vorticity filaments.Comment: 4 pages, 3 figure

Syn5 RNA polymerase synthesizes precise run-off RNA products

The enzyme predominantly used for in vitro run-off RNA synthesis is bacteriophage T7 RNA polymerase. T7 RNA polymerase synthesizes, in addition to run-off products of precise length, transcripts with an additional non-base-paired nucleotide at the 3′-terminus (N + 1 product). This contaminating product is extremely difficult to remove. We recently characterized the single-subunit RNA polymerase from marine cyanophage Syn5 and identified its promoter sequence. This marine enzyme catalyses RNA synthesis over a wider range of temperature and salinity than does T7 RNA polymerase. Its processivity is >30 000 nt without significant intermediate products. The requirement for the initiating nucleotide at the promoter is less stringent for Syn5 RNA polymerase as compared to T7 RNA polymerase. A major difference is the precise run-off transcripts with homogeneous 3′-termini synthesized by Syn5 RNA polymerase. Therefore, the enzyme is advantageous for the production of RNAs that require precise 3′-termini, such as tRNAs and RNA fragments that are used for subsequent assembly

From simple to complex networks: inherent structures, barriers and valleys in the context of spin glasses

Given discrete degrees of freedom (spins) on a graph interacting via an energy function, what can be said about the energy local minima and associated inherent structures? Using the lid algorithm in the context of a spin glass energy function, we investigate the properties of the energy landscape for a variety of graph topologies. First, we find that the multiplicity Ns of the inherent structures generically has a lognormal distribution. In addition, the large volume limit of ln/ differs from unity, except for the Sherrington-Kirkpatrick model. Second, we find simple scaling laws for the growth of the height of the energy barrier between the two degenerate ground states and the size of the associated valleys. For finite connectivity models, changing the topology of the underlying graph does not modify qualitatively the energy landscape, but at the quantitative level the models can differ substantially.Comment: 10 pages, 9 figs, slightly improved presentation, more references, accepted for publication in Phys Rev

Adiabatic quantum computation along quasienergies

The parametric deformations of quasienergies and eigenvectors of unitary operators are applied to the design of quantum adiabatic algorithms. The conventional, standard adiabatic quantum computation proceeds along eigenenergies of parameter-dependent Hamiltonians. By contrast, discrete adiabatic computation utilizes adiabatic passage along the quasienergies of parameter-dependent unitary operators. For example, such computation can be realized by a concatenation of parameterized quantum circuits, with an adiabatic though inevitably discrete change of the parameter. A design principle of adiabatic passage along quasienergy is recently proposed: Cheon's quasienergy and eigenspace anholonomies on unitary operators is available to realize anholonomic adiabatic algorithms [Tanaka and Miyamoto, Phys. Rev. Lett. 98, 160407 (2007)], which compose a nontrivial family of discrete adiabatic algorithms. It is straightforward to port a standard adiabatic algorithm to an anholonomic adiabatic one, except an introduction of a parameter |v>, which is available to adjust the gaps of the quasienergies to control the running time steps. In Grover's database search problem, the costs to prepare |v> for the qualitatively different, i.e., power or exponential, running time steps are shown to be qualitatively different. Curiously, in establishing the equivalence between the standard quantum computation based on the circuit model and the anholonomic adiabatic quantum computation model, it is shown that the cost for |v> to enlarge the gaps of the eigenvalue is qualitatively negligible.Comment: 11 pages, 2 figure

On Equivalence of Critical Collapse of Non-Abelian Fields

We continue our study of the gravitational collapse of spherically symmetric skyrmions. For certain families of initial data, we find the discretely self-similar Type II critical transition characterized by the mass scaling exponent $\gamma \approx 0.20$ and the echoing period $\Delta \approx 0.74$. We argue that the coincidence of these critical exponents with those found previously in the Einstein-Yang-Mills model is not accidental but, in fact, the two models belong to the same universality class.Comment: 7 pages, REVTex, 2 figures included, accepted for publication in Physical Review

Energy landscape and rigidity

The effects of floppy modes in the thermodynamical properties of a system are studied. From thermodynamical arguments, we deduce that floppy modes are not at zero frequency and thus a modified Debye model is used to take into account this effect. The model predicts a deviation from the Debye law at low temperatures. Then, the connection between the topography of the energy landscape, the topology of the phase space and the rigidity of a glass is explored. As a result, we relate the number of constraints and floppy modes with the statistics of the landscape. We apply these ideas to a simple model for which we provide an approximate expression for the number of energy basins as a function of the rigidity. This allows to understand certains features of the glass transition, like the jump in the specific heat or the reversible window observed in chalcogenide glasses.Comment: 1 text+3 eps figure

Star Formation, Radio Sources, Cooling X-ray Gas, and Galaxy Interactions in the Brightest Cluster Galaxy in 2A0335+096

We present deep emission-line imaging taken with the SOAR Optical Imaging Camera of the brightest cluster galaxy (BCG) in the nearby (z=0.035) X-ray cluster 2A0335+096. We analyze long-slit optical spectroscopy, archival VLA, Chandra X-ray, and XMM UV data. 2A0335+096 is a bright, cool-core X-ray cluster, once known as a cooling flow. Within the highly disturbed core revealed by Chandra X-ray observations, 2A0335+096 hosts a highly structured optical emission-line system. The redshift of the companion is within 100 km/s of the BCG and has certainly interacted with the BCG, and is likely bound to it. The comparison of optical and radio images shows curved filaments in H-alpha emission surrounding the resolved radio source. The velocity structure of the emission-line bar between the BCG nucleus and the companion galaxy provides strong evidence for an interaction between the two in the last ~50 Myrs. The age of the radio source is similar to the interaction time, so this interaction may have provoked an episode of radio activity. We estimate a star formation rate of >7 solar mass/yr based on the Halpha and archival UV data, a rate similar to, but somewhat lower than, the revised X-ray cooling rate of 10-30 solar masses/year estimated from XMM spectra by Peterson & workers. The Halpha nebula is limited to a region of high X-ray surface brightness and cool X-ray temperature. The detailed structures of H-alpha and X-ray gas differ. The peak of the X-ray emission is not the peak of H-alpha emission, nor does it lie in the BCG. The estimated age of the radio lobes and their interaction with the optical emission-line gas, the estimated timescale for depletion and accumulation of cold gas, and the dynamical time in the system are all similar, suggesting a common trigger mechanism.Comment: Accepted AJ, July 2007 publication. Vol 134, p. 14-2

Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown

Gene 6 protein of bacteriophage T7 has 5′-3′-exonuclease activity specific for duplex DNA. We have found that gene 6 protein also has flap endonuclease activity. The flap endonuclease activity is considerably weaker than the exonuclease activity. Unlike the human homolog of gene 6 protein, the flap endonuclease activity of gene 6 protein is dependent on the length of the 5′-flap. This dependency of activity on the length of the 5′-flap may result from the structured helical gateway region of gene 6 protein which differs from that of human flap endonuclease 1. The flap endonuclease activity provides a mechanism by which RNA-terminated Okazaki fragments, displaced by the lagging strand DNA polymerase, are processed. 3′-extensions generated during degradation of duplex DNA by the exonuclease activity of gene 6 protein are inhibitory to further degradation of the 5′-terminus by the exonuclease activity of gene 6 protein. The single-stranded DNA binding protein of T7 overcomes this inhibition

Formation of singularities for equivariant 2+1 dimensional wave maps into the two-sphere

In this paper we report on numerical studies of the Cauchy problem for equivariant wave maps from 2+1 dimensional Minkowski spacetime into the two-sphere. Our results provide strong evidence for the conjecture that large energy initial data develop singularities in finite time and that singularity formation has the universal form of adiabatic shrinking of the degree-one harmonic map from $\mathbb{R}^2$ into $S^2$.Comment: 14 pages, 5 figures, final version to be published in Nonlinearit

Microarray evidence for off target effects in tick RNA interference experiments, and the lack of strong correlation between DSRNA and antibody phenotypes in tick In vitro treatments for vaccine candidate screening

No abstract availabl