Application of an Energy-Vorticity Turbulence Model to Fully rough Pipe flow

Based on a more direct analogy between turbulent and molecular transport, a foundation was recently presented for an energy-vorticity turbulence model. The new turbulent-energytransport equation contains two closure coefficients; a viscous-dissipation coefficient and a turbulent-transport coefficient. To help evaluate the closure coefficients and provide insight into the energy-vorticity turbulence variables, fully rough pipe flow is considered. For this fully developed flow, excellent agreement with experimental data for velocity profiles and friction factors is attained over a wide range of closure coefficients, provided that a given relation between the coefficients is maintained

The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome

We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3′ end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 90° kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold

Velocity Statistics in the Two-Dimensional Granular Turbulence

We studied the macroscopic statistical properties on the freely evolving quasi-elastic hard disk (granular) system by performing a large-scale (up to a few million particles) event-driven molecular dynamics systematically and found that remarkably analogous to an enstrophy cascade process in the decaying two-dimensional fluid turbulence. There are four typical stages in the freely evolving inelastic hard disk system, which are homogeneous, shearing (vortex), clustering and final state. In the shearing stage, the self-organized macroscopic coherent vortices become dominant. In the clustering stage, the energy spectra are close to the expectation of Kraichnan-Batchelor theory and the squared two-particle separation strictly obeys Richardson law.Comment: 4 pages, 4 figures, to be published in PR

The floor in the interplanetary magnetic field: Estimation on the basis of relative duration of ICME observations in solar wind during 1976-2000

To measure the floor in interplanetary magnetic field and estimate the time- invariant open magnetic flux of Sun, it is necessary to know a part of magnetic field of Sun carried away by CMEs. In contrast with previous papers, we did not use global solar parameters: we identified different large-scale types of solar wind for 1976-2000 interval, obtained a fraction of interplanetary CMEs (ICMEs) and calculated magnitude of interplanetary magnetic field B averaged over 2 Carrington rotations. The floor of magnetic field is estimated as B value at solar cycle minimum when the ICMEs were not observed and it was calculated to be 4,65 \pm 6,0 nT. Obtained value is in a good agreement with previous results.Comment: 10 pages, 2 figures, submitted in GR

Clustering dynamics of Lagrangian tracers in free-surface flows

We study the formation of clusters of passive Lagrangian tracers in a non-smooth turbulent flow in a flat free-slip surface as a model for particle dynamics on free surfaces. Single particle and pair dispersion show different behavior for short and large times: on short times particles cluster exponentially rapidly until patches of the size of the divergence correlation length are depleted; on larger times the pair dispersion is dominated by almost ballistic hopping between clusters. We also find that the distribution of particle density is close to algebraic and can trace this back to the exponential distribution of the divergence field of the surface flow.Comment: 5 pages, 5 Postscript figure

Anomalous Scaling of Structure Functions and Dynamic Constraints on Turbulence Simulations

The connection between anomalous scaling of structure functions (intermittency) and numerical methods for turbulence simulations is discussed. It is argued that the computational work for direct numerical simulations (DNS) of fully developed turbulence increases as $Re^{4}$, and not as $Re^{3}$ expected from Kolmogorov's theory, where $Re$ is a large-scale Reynolds number. Various relations for the moments of acceleration and velocity derivatives are derived. An infinite set of exact constraints on dynamically consistent subgrid models for Large Eddy Simulations (LES) is derived from the Navier-Stokes equations, and some problems of principle associated with existing LES models are highlighted.Comment: 18 page

Path lengths in turbulence

By tracking tracer particles at high speeds and for long times, we study the geometric statistics of Lagrangian trajectories in an intensely turbulent laboratory flow. In particular, we consider the distinction between the displacement of particles from their initial positions and the total distance they travel. The difference of these two quantities shows power-law scaling in the inertial range. By comparing them with simulations of a chaotic but non-turbulent flow and a Lagrangian Stochastic model, we suggest that our results are a signature of turbulence.Comment: accepted for publication in Journal of Statistical Physic

Generalized harmonic formulation in spherical symmetry

In this pedagogically structured article, we describe a generalized harmonic formulation of the Einstein equations in spherical symmetry which is regular at the origin. The generalized harmonic approach has attracted significant attention in numerical relativity over the past few years, especially as applied to the problem of binary inspiral and merger. A key issue when using the technique is the choice of the gauge source functions, and recent work has provided several prescriptions for gauge drivers designed to evolve these functions in a controlled way. We numerically investigate the parameter spaces of some of these drivers in the context of fully non-linear collapse of a real, massless scalar field, and determine nearly optimal parameter settings for specific situations. Surprisingly, we find that many of the drivers that perform well in 3+1 calculations that use Cartesian coordinates, are considerably less effective in spherical symmetry, where some of them are, in fact, unstable.Comment: 47 pages, 15 figures. v2: Minor corrections, including 2 added references; journal version

MET currents and otoacoustic emissions from mice with a detached tectorial membrane indicate the extracellular matrix regulates Ca2+ near stereocilia

The tectorial membrane (TM) is an acellular structure of the cochlea that is attached to the stereociliary bundles of the outer hair cells (OHCs), electromotile cells that amplify motion of the cochlear partition and sharpen its frequency selectivity. Although the TM is essential for hearing, its role is still not fully understood. In Tecta/Tectb−/− double knockout mice, in which the TM is not coupled to the OHC stereocilia, hearing sensitivity is considerably reduced compared with that of wild‐type animals. In vivo, the OHC receptor potentials, assessed using cochlear microphonics, are symmetrical in both wild‐type and Tecta/Tectb−/− mice, indicating that the TM does not bias the hair bundle resting position. The functional maturation of hair cells is also unaffected in Tecta/Tectb−/− mice, and the resting open probability of the mechanoelectrical transducer (MET) channel reaches values of ∼50% when the hair bundles of mature OHCs are bathed in an endolymphatic‐like Ca2+ concentration (40 μM) in vitro. The resultant large MET current depolarizes OHCs to near –40 mV, a value that would allow optimal activation of the motor protein prestin and normal cochlear amplification. Although the set point of the OHC receptor potential transfer function in vivo may therefore be determined primarily by endolymphatic Ca2+ concentration, repetitive acoustic stimulation fails to produce adaptation of MET‐dependent otoacoustic emissions in vivo in the Tecta/Tectb−/− mice. Therefore, the TM is likely to contribute to the regulation of Ca2+ levels around the stereocilia, and thus adaptation of the OHC MET channel during prolonged sound stimulation

A Biased Review of Sociophysics

Various aspects of recent sociophysics research are shortly reviewed: Schelling model as an example for lack of interdisciplinary cooperation, opinion dynamics, combat, and citation statistics as an example for strong interdisciplinarity.Comment: 16 pages for J. Stat. Phys. including 2 figures and numerous reference