Mean-field and direct numerical simulations of magnetic flux concentrations from vertical field

Strongly stratified hydromagnetic turbulence has previously been found to produce magnetic flux concentrations if the domain is large enough compared with the size of turbulent eddies. Mean-field simulations (MFS) using parameterizations of the Reynolds and Maxwell stresses show a negative effective magnetic pressure instability and have been able to reproduce many aspects of direct numerical simulations (DNS) regarding the growth rate of this large-scale instability, shape of the resulting magnetic structures, and their height as a function of magnetic field strength. Unlike the case of an imposed horizontal field, for a vertical one, magnetic flux concentrations of equipartition strength with the turbulence can be reached. This results in magnetic spots that are reminiscent of sunspots. Here we want to find out under what conditions magnetic flux concentrations with vertical field occur and what their internal structure is. We use a combination of MFS, DNS, and implicit large-eddy simulations to characterize the resulting magnetic flux concentrations in forced isothermal turbulence with an imposed vertical magnetic field. We confirm earlier results that in the kinematic stage of the large-scale instability the horizontal wavelength of structures is about 10 times the density scale height. At later times, even larger structures are being produced in a fashion similar to inverse spectral transfer in helically driven turbulence. Using turbulence simulations, we find that magnetic flux concentrations occur for different values of the Mach number between 0.1 and 0.7. DNS and MFS show magnetic flux tubes with mean-field energies comparable to the turbulent kinetic energy. The resulting vertical magnetic flux tubes are being confined by downflows along the tubes and corresponding inflow from the sides, which keep the field concentrated.Comment: 16 pages, 22 figures, Astron. Astrophys., in pres

New scaling for the alpha effect in slowly rotating turbulence

Using simulations of slowly rotating stratified turbulence, we show that the alpha effect responsible for the generation of astrophysical magnetic fields is proportional to the logarithmic gradient of kinetic energy density rather than that of momentum, as was previously thought. This result is in agreement with a new analytic theory developed in this paper for large Reynolds numbers. Thus, the contribution of density stratification is less important than that of turbulent velocity. The alpha effect and other turbulent transport coefficients are determined by means of the test-field method. In addition to forced turbulence, we also investigate supernova-driven turbulence and stellar convection. In some cases (intermediate rotation rate for forced turbulence, convection with intermediate temperature stratification, and supernova-driven turbulence) we find that the contribution of density stratification might be even less important than suggested by the analytic theory.Comment: 10 pages, 9 figures, revised version, Astrophys. J., in pres

Turbulence and Steady Flows in 3D Global Stratified MHD Simulations of Accretion Disks

We present full 2 Pi global 3-D stratified MHD simulations of accretion disks. We interpret our results in the context of proto-planetary disks. We investigate the turbulence driven by the magneto-rotational instability (MRI) using the PLUTO Godunov code in spherical coordinates with the accurate and robust HLLD Riemann solver. We follow the turbulence for more than 1500 orbits at the innermost radius of the domain to measure the overall strength of turbulent motions and the detailed accretion flow pattern. We find that regions within two scale heights of the midplane have a turbulent Mach number of about 0.1 and a magnetic pressure two to three orders of magnitude less than the gas pressure, while outside three scale heights the magnetic pressure equals or exceeds the gas pressure and the turbulence is transonic, leading to large density fluctuations. The strongest large-scale density disturbances are spiral density waves, and the strongest of these waves has m=5. No clear meridional circulation appears in the calculations because fluctuating radial pressure gradients lead to changes in the orbital frequency, comparable in importance to the stress gradients that drive the meridional flows in viscous models. The net mass flow rate is well-reproduced by a viscous model using the mean stress distribution taken from the MHD calculation. The strength of the mean turbulent magnetic field is inversely proportional to the radius, so the fields are approximately force-free on the largest scales. Consequently the accretion stress falls off as the inverse square of the radius.Comment: Accepted for publication in Ap

MRI channel flows in vertically-stratified models of accretion disks

Simulations of the magnetorotational instability (MRI) in 'unstratified' shearing boxes exhibit powerful coherent flows, whereby the fluid vertically splits into countermoving planar jets or `channels'. Channel flows correspond to certain axisymmetric linear MRI modes, and their preponderance follows from the remarkable fact that they are approximate nonlinear solutions of the MHD equations in the limit of weak magnetic fields. We show in this paper, analytically and with one-dimensional numerical simulations, that this property is also shared by certain axisymmetric MRI modes in vertically-stratified shearing boxes. These channel flows rapidly capture significant amounts of magnetic and kinetic energy, and thus are vulnerable to secondary shear instabilities. We examine these parasites in the vertically stratified context, and estimate the maximum amplitudes that channels attain before they are destroyed. These estimates suggest that a dominant channel flow will usually drive the disk's magnetic field to thermal strengths. The prominence of these flows and their destruction place enormous demands on simulations, but channels in their initial stages also offer a useful check on numerical codes. These benchmarks are especially valuable given the increasing interest in the saturation of the stratified MRI. Lastly we speculate on the potential connection between 'run-away' channel flows and outburst behaviour in protostellar and dwarf nova disks.Comment: 17 pages, 12 figures. MNRAS, accepted

SELF-DESTRUCTING SPIRAL WAVES: GLOBAL SIMULATIONS OF A SPIRAL-WAVE INSTABILITY IN ACCRETION DISKS

This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575. The authors acknowledge the San Diego Supercomputer Center at University of California, San Diego and the Texas Advanced Computing Center at The University of Texas at Austin for providing HPC resources that have contributed to the research results reported within this paper. This work used the DiRAC Complexity system, operated by the University of Leicester IT Services, which forms part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). The equipment is funded by BIS National E-Infrastructure capital grant ST/K000373/1 and STFC Operations grant ST/K0003259/1. DiRAC is part of the national E-Infrastructure

GLOBAL SIMULATIONS OF PROTOPLANETARY DISKS WITH OHMIC RESISTIVITY AND AMBIPOLAR DIFFUSION

Protoplanetary disks are believed to accrete onto their central T Tauri star because of magnetic stresses. Recently published shearing box simulations indicate that Ohmic resistivity, ambipolar diffusion and the Hall effect all play important roles in disk evolution. In the presence of a vertical magnetic field, the disk remains laminar between 1-5au, and a magnetocentrifugal disk wind forms that provides an important mechanism for removing angular momentum. Questions remain, however, about the establishment of a true physical wind solution in the shearing box simulations because of the symmetries inherent in the local approximation. We present global MHD simulations of protoplanetary disks that include Ohmic resistivity and ambipolar diffusion, where the time-dependent gas-phase electron and ion fractions are computed under FUV and X-ray ionization with a simplified recombination chemistry. Our results show that the disk remains laminar, and that a physical wind solution arises naturally in global disk models. The wind is sufficiently efficient to explain the observed accretion rates. Furthermore, the ionization fraction at intermediate disk heights is large enough for magneto-rotational channel modes to grow and subsequently develop into belts of horizontal field. Depending on the ionization fraction, these can remain quasi-global, or break-up into discrete islands of coherent field polarity. The disk models we present here show a dramatic departure from our earlier models including Ohmic resistivity only. It will be important to examine how the Hall effect modifies the evolution, and to explore the influence this has on the observational appearance of such systems, and on planet formation and migration.Comment: 18 pages, 12 figures, accepted for publication in Ap

Genetic load and transgenic mitigating genes in transgenic Brassica rapa (field mustard) × Brassica napus (oilseed rape) hybrid populations

<p>Abstract</p> <p>Background</p> <p>One theoretical explanation for the relatively poor performance of <it>Brassica rapa </it>(weed) × <it>Brassica napus </it>(crop) transgenic hybrids suggests that hybridization imparts a negative genetic load. Consequently, in hybrids genetic load could overshadow any benefits of fitness enhancing transgenes and become the limiting factor in transgenic hybrid persistence. Two types of genetic load were analyzed in this study: random/linkage-derived genetic load, and directly incorporated genetic load using a transgenic mitigation (TM) strategy. In order to measure the effects of random genetic load, hybrid productivity (seed yield and biomass) was correlated with crop- and weed-specific AFLP genomic markers. This portion of the study was designed to answer whether or not weed × transgenic crop hybrids possessing more crop genes were less competitive than hybrids containing fewer crop genes. The effects of directly incorporated genetic load (TM) were analyzed through transgene persistence data. TM strategies are proposed to decrease transgene persistence if gene flow and subsequent transgene introgression to a wild host were to occur.</p> <p>Results</p> <p>In the absence of interspecific competition, transgenic weed × crop hybrids benefited from having more crop-specific alleles. There was a positive correlation between performance and number of <it>B. napus </it>crop-specific AFLP markers [seed yield vs. marker number (r = 0.54, P = 0.0003) and vegetative dry biomass vs. marker number (r = 0.44, P = 0.005)]. However under interspecific competition with wheat or more weed-like conditions (i.e. representing a situation where hybrid plants emerge as volunteer weeds in subsequent cropping systems), there was a positive correlation between the number of <it>B. rapa </it>weed-specific AFLP markers and seed yield (r = 0.70, P = 0.0001), although no such correlation was detected for vegetative biomass. When genetic load was directly incorporated into the hybrid genome, by inserting a fitness-mitigating dwarfing gene that that is beneficial for crops but deleterious for weeds (a transgene mitigation measure), there was a dramatic decrease in the number of transgenic hybrid progeny persisting in the population.</p> <p>Conclusion</p> <p>The effects of genetic load of crop and in some situations, weed alleles might be beneficial under certain environmental conditions. However, when genetic load was directly incorporated into transgenic events, e.g., using a TM construct, the number of transgenic hybrids and persistence in weedy genomic backgrounds was significantly decreased.</p

Current status of turbulent dynamo theory: From large-scale to small-scale dynamos

Several recent advances in turbulent dynamo theory are reviewed. High resolution simulations of small-scale and large-scale dynamo action in periodic domains are compared with each other and contrasted with similar results at low magnetic Prandtl numbers. It is argued that all the different cases show similarities at intermediate length scales. On the other hand, in the presence of helicity of the turbulence, power develops on large scales, which is not present in non-helical small-scale turbulent dynamos. At small length scales, differences occur in connection with the dissipation cutoff scales associated with the respective value of the magnetic Prandtl number. These differences are found to be independent of whether or not there is large-scale dynamo action. However, large-scale dynamos in homogeneous systems are shown to suffer from resistive slow-down even at intermediate length scales. The results from simulations are connected to mean field theory and its applications. Recent work on helicity fluxes to alleviate large-scale dynamo quenching, shear dynamos, nonlocal effects and magnetic structures from strong density stratification are highlighted. Several insights which arise from analytic considerations of small-scale dynamos are discussed.Comment: 36 pages, 11 figures, Spa. Sci. Rev., submitted to the special issue "Magnetism in the Universe" (ed. A. Balogh