Accretion-ejection instability in magnetized disks: Feeding the corona with Alfven waves

We present a detailed calculation of the mechanism by which the Accretion-Ejection Instability can extract accretion energy and angular momentum from a magnetized disk, and redirect them to its corona. In a disk threaded by a poloidal magnetic field of the order of equipartition with the gas pressure, the instability is composed of a spiral wave (analogous to galactic ones) and a Rossby vortex. The mechanism detailed here describes how the vortex, twisting the footpoints of field lines threading the disk, generates Alfven waves propagating to the corona. We find that this is a very efficient mechanism, providing to the corona (where it could feed a jet or a wind) a substantial fraction of the accretion energy.Comment: accepted by A&

Local models of stellar convection II: Rotation dependence of the mixing length relations

We study the mixing length concept in comparison to three-dimensional numerical calculations of convection with rotation. In a limited range, the velocity and temperature fluctuations are linearly proportional to the superadiabaticity, as predicted by the mixing length concept and in accordance with published results. The effects of rotation are investigated by varying the Coriolis number, Co = 2 Omega tau, from zero to roughly ten, and by calculating models at different latitudes. We find that \alpha decreases monotonically as a function of the Coriolis number. This can be explained by the decreased spatial scale of convection and the diminished efficiency of the convective energy transport, the latter of which leads to a large increase of the superadibaticity, \delta = \nabla - \nabla_ad as function of Co. Applying a decreased mixing length parameter in a solar model yields very small differences in comparison to the standard model within the convection zone. The main difference is the reduction of the overshooting depth, and thus the depth of the convection zone, when a non-local version of the mixing length concept is used. Reduction of \alpha by a factor of roughly 2.5 is sufficient to reconcile the difference between the model and helioseismic results. The numerical results indicate reduction of \alpha by this order of magnitude.Comment: Final published version, 8 pages, 9 figure

A local prescription for the softening length in self-gravitating gaseous discs

In 2D-simulations of self-gravitating gaseous discs, the potential is often computed in the framework of "softened gravity" initially designed for N-body codes. In this special context, the role of the softening length LAMBDA is twofold: i) to avoid numerical singularities in the integral representation of the potential (i.e., arising when the relative separation vanishes), and ii) to acount for stratification of matter in the direction perpendicular to the disc mid-plane. So far, most studies have considered LAMBDA as a free parameter and various values or formulae have been proposed without much mathematical justification. In this paper, we demonstrate by means of a rigorous calculus that it is possible to define LAMBDA such that the gravitational potential of a flat disc coincides at order zero with that of a geometically thin disc of the same surface density. Our prescription for LAMBDA, valid in the local, axisymmetric limit, has the required properties i) and ii). It is mainly an analytical function of the radius and disc thickness, and is sensitive to the vertical stratification. For mass density profiles considered (namely, profiles expandable over even powers of the altitude), we find that LAMBDA : i) is independant of the numerical mesh, ii) is always a fraction of the local thickness H, iii) goes through a minimum at the singularity (i.e., at null separation), and iv) is such that 0.13 < LAMBDA/H < 0.29 typically (depending on the separation and on density profile). These results should help us to improve the quality of 2D- and 3D-simulations of gaseous discs in several respects (physical realism, accuracy, and computing time).Comment: accepted in A&A, 7 pages, 7 figures, web link for the F90 code and on-line calculations : http://www.obs.u-bordeaux1.fr/radio/JMHure/intro2single.ph

Information Transfer in Gonadotropin-releasing Hormone (GnRH) Signaling: extracellular signal-regulated kinase (ERK)-mediated feedback loops control hormone sensing

The computation model used in the study of GnRH signalling which was used to generate the data appearing in this paper is in ORE at http://hdl.handle.net/10871/27844Cell signaling pathways are noisy communication channels, and statistical measures derived from information theory can be used to quantify the information they transfer. Here we use single cell signaling measures to calculate mutual information as a measure of information transfer via gonadotropin-releasing hormone (GnRH) receptors (GnRHR) to extracellular signal-regulated kinase (ERK) or nuclear factor of activated T-cells (NFAT). This revealed mutual information values <1 bit, implying that individual GnRH-responsive cells cannot unambiguously differentiate even two equally probable input concentrations. Addressing possible mechanisms for mitigation of information loss, we focused on the ERK pathway and developed a stochastic activation model incorporating negative feedback and constitutive activity. Model simulations revealed interplay between fast (min) and slow (min-h) negative feedback loops with maximal information transfer at intermediate feedback levels. Consistent with this, experiments revealed that reducing negative feedback (by expressing catalytically inactive ERK2) and increasing negative feedback (by Egr1-driven expression of dual-specificity phosphatase 5 (DUSP5)) both reduced information transfer from GnRHR to ERK. It was also reduced by blocking protein synthesis (to prevent GnRH from increasing DUSP expression) but did not differ for different GnRHRs that do or do not undergo rapid homologous desensitization. Thus, the first statistical measures of information transfer via these receptors reveals that individual cells are unreliable sensors of GnRH concentration and that this reliability is maximal at intermediate levels of ERK-mediated negative feedback but is not influenced by receptor desensitization.This work was supported by a Biochemical and Biophysical Science Research Council award (BBSRC BB/J014699/1; to C. A. M. and K. T.-A.)

Numerical simulations of the Accretion-Ejection Instability in magnetised accretion disks

The Accretion-Ejection Instability (AEI) described by Tagger & Pellat (1999) is explored numerically using a global 2d model of the inner region of a magnetised accretion disk. The disk is initially currentless but threaded by a vertical magnetic field created by external currents, and frozen in the flow. In agreement with the theory a spiral instability, similar in many ways to those observed in self-gravitating disks, develops when the magnetic field is, within a factor of a few, at equipartition with the disk thermal pressure. Perturbations in the flow build up currents and create a perturbed magnetic field within the disk. The present non-linear simulations give good evidence that such an instability can occur in the inner region of accretion disks, and generate accretion of gas and vertical magnetic flux toward the central object, if the equilibrium radial profiles of density and magnetic flux exceed a critical threshold.Comment: single tar file with GIF figure

Orbital Advection by Interpolation: A Fast and Accurate Numerical Scheme for Super-Fast MHD Flows

In numerical models of thin astrophysical disks that use an Eulerian scheme, gas orbits supersonically through a fixed grid. As a result the time step is sharply limited by the Courant condition. Also, because the mean flow speed with respect to the grid varies with position, the truncation error varies systematically with position. For hydrodynamic (unmagnetized) disks an algorithm called FARGO has been developed that advects the gas along its mean orbit using a separate interpolation substep. This relaxes the constraint imposed by the Courant condition, which now depends only on the peculiar velocity of the gas, and results in a truncation error that is more nearly independent of position. This paper describes a FARGO-like algorithm suitable for evolving magnetized disks. Our method is second order accurate on a smooth flow and preserves the divergence-free constraint to machine precision. The main restriction is that the magnetic field must be discretized on a staggered mesh. We give a detailed description of an implementation of the code and demonstrate that it produces the expected results on linear and nonlinear problems. We also point out how the scheme might be generalized to make the integration of other supersonic/super-fast flows more efficient. Although our scheme reduces the variation of truncation error with position, it does not eliminate it. We show that the residual position dependence leads to characteristic radial variations in the density over long integrations.Comment: 32 pages, 18 figures, accepted for publication in The Astrophysical Journal. Contains an additional appendix providing more details for some of the test problems (to be published as an addendum in the ApJS December 2008, v179n2 issue

Acoustic wave propagation in the solar sub-photosphere with localised magnetic field concentration: effect of magnetic tension

Aims: We analyse numerically the propagation and dispersion of acoustic waves in the solar-like sub-photosphere with localised non-uniform magnetic field concentrations, mimicking sunspots with various representative magnetic field configurations. Methods: Numerical simulations of wave propagation through the solar sub-photosphere with a localised magnetic field concentration are carried out using SAC, which solves the MHD equations for gravitationally stratified plasma. The initial equilibrium density and pressure stratifications are derived from a standard solar model. Acoustic waves are generated by a source located at the height corresponding approximately to the visible surface of the Sun. By means of local helioseismology we analyse the response of vertical velocity at the level corresponding to the visible solar surface to changes induced by magnetic field in the interior. Results: The results of numerical simulations of acoustic wave propagation and dispersion in the solar sub-photosphere with localised magnetic field concentrations of various types are presented. Time-distance diagrams of the vertical velocity perturbation at the level corresponding to the visible solar surface show that the magnetic field perturbs and scatters acoustic waves and absorbs the acoustic power of the wave packet. For the weakly magnetised case, the effect of magnetic field is mainly thermodynamic, since the magnetic field changes the temperature stratification. However, we observe the signature of slow magnetoacoustic mode, propagating downwards, for the strong magnetic field cases

Dual-specificity phosphatase 5 controls the localized inhibition, propagation, and transforming potential of ERK signaling

Deregulated extracellular signal-regulated kinase (ERK) signaling drives cancer growth. Normally, ERK activity is self-limiting by the rapid inactivation of upstream kinases and delayed induction of dual-specificity MAP kinase phosphatases (MKPs/DUSPs). However, interactions between these feedback mechanisms are unclear. Here we show that, although the MKP DUSP5 both inactivates and anchors ERK in the nucleus, it paradoxically increases and prolongs cytoplasmic ERK activity. The latter effect is caused, at least in part, by the relief of ERK-mediated RAF inhibition. The importance of this spatiotemporal interaction between these distinct feedback mechanisms is illustrated by the fact that expression of oncogenic BRAF(V600E), a feedback-insensitive mutant RAF kinase, reprograms DUSP5 into a cell-wide ERK inhibitor that facilitates cell proliferation and transformation. In contrast, DUSP5 deletion causes BRAF(V600E)-induced ERK hyperactivation and cellular senescence. Thus, feedback interactions within the ERK pathway can regulate cell proliferation and transformation, and suggest oncogene-specific roles for DUSP5 in controlling ERK signaling and cell fate

Information Transfer in Gonadotropin-Releasing Hormone (GnRH) Signaling:Extracellular Signal-Regulated Kinase (ERK)-Mediated Feedback Loops Control Hormone Sensing

Cell signaling pathways are noisy communication channels, and statistical measures derived from information theory can be used to quantify the information they transfer. Here we use single cell signaling measures to calculate mutual information as a measure of information transfer via gonadotropin-releasing hormone (GnRH) receptors (GnRHR) to extracellular signal-regulated kinase (ERK) or nuclear factor of activated T-cells (NFAT). This revealed mutual information values <1 bit, implying that individual GnRH-responsive cells cannot unambiguously differentiate even two equally probable input concentrations. Addressing possible mechanisms for mitigation of information loss, we focused on the ERK pathway and developed a stochastic activation model incorporating negative feedback and constitutive activity. Model simulations revealed interplay between fast (min) and slow (min-h) negative feedback loops with maximal information transfer at intermediate feedback levels. Consistent with this, experiments revealed that reducing negative feedback (by expressing catalytically inactive ERK2) and increasing negative feedback (by Egr1-driven expression of dual-specificity phosphatase 5 (DUSP5)) both reduced information transfer from GnRHR to ERK. It was also reduced by blocking protein synthesis (to prevent GnRH from increasing DUSP expression) but did not differ for different GnRHRs that do or do not undergo rapid homologous desensitization. Thus, the first statistical measures of information transfer via these receptors reveals that individual cells are unreliable sensors of GnRH concentration and that this reliability is maximal at intermediate levels of ERK-mediated negative feedback but is not influenced by receptor desensitization

A microquasar classification from a disk instability perspective

The spectacular variability of microquasars has led to a long string of efforts in order to classify their observed behaviors in a few states. The progress made in the understanding of the Quasi-Periodic Oscillations observed in these objects now makes it possible to develop a new way to find order in their behavior, based on the theorized physical processes associated with these oscillations. This will also have the interest of reuniting microquasars in a single classification based on the physical processes at work and therefore independent of their specificities (mass, variation timescale, outburst history, etc.). This classification is aimed to be a tool to further our understanding of microquasars behavior and not to replace phenomenological states. We start by considering three instabilities that can cause accretion in the disk. We compare the conditions for their development, and the Quasi-Periodic Oscillations they can be expected to produce, with the spectral states in which these Quasi-Periodic Oscillations are observed and sometimes coexist. From the three instabilities that we proposed to explain the three states of GRS 1915+105 we actually found the theoretical existence of four states. We compared those four states with observations and also how those four states can be seen in a model-independent fashion. Those four state can be used to find an order in microquasar observations, based on the properties of the Quasi-Periodic Oscillations and the physics of the associated instabilities.Comment: accepted by A&