Sub-structure formation in starless cores

Motivated by recent observational searches of sub-structure in starless molecular cloud cores, we investigate the evolution of density perturbations on scales smaller than the Jeans length embedded in contracting isothermal clouds, adopting the same formalism developed for the expanding Universe and the solar wind. We find that initially small amplitude, Jeans-stable perturbations (propagating as sound waves in the absence of a magnetic field), are amplified adiabatically during the contraction, approximately conserving the wave action density, until they either become nonlinear and steepen into shocks at a time $t_{\rm nl}$, or become gravitationally unstable when the Jeans length decreases below the scale of the perturbations at a time $t_{\rm gr}$. We evaluate analytically the time $t_{\rm nl}$ at which the perturbations enter the non-linear stage using a Burgers' equation approach, and we verify numerically that this time marks the beginning of the phase of rapid dissipation of the kinetic energy of the perturbations. We then show that for typical values of the rms Mach number in molecular cloud cores, $t_{\rm nl}$ is smaller than $t_{\rm gr}$, and therefore density perturbations likely dissipate before becoming gravitational unstable. Solenoidal modes grow at a faster rate than compressible modes, and may eventually promote fragmentation through the formation of vortical structures.Comment: 8 pages, 4 figure

Oceanic stochastic parametrizations in a seasonal forecast system

We study the impact of three stochastic parametrizations in the ocean component of a coupled model, on forecast reliability over seasonal timescales. The relative impacts of these schemes upon the ocean mean state and ensemble spread are analyzed. The oceanic variability induced by the atmospheric forcing of the coupled system is, in most regions, the major source of ensemble spread. The largest impact on spread and bias came from the Stochastically Perturbed Parametrization Tendency (SPPT) scheme - which has proven particularly effective in the atmosphere. The key regions affected are eddy-active regions, namely the western boundary currents and the Southern Ocean. However, unlike its impact in the atmosphere, SPPT in the ocean did not result in a significant decrease in forecast error. Whilst there are good grounds for implementing stochastic schemes in ocean models, our results suggest that they will have to be more sophisticated. Some suggestions for next-generation stochastic schemes are made.Comment: 24 pages, 3 figure

EIT and TRACE responses to flare plasma

Aims: To understand the contribution of active region and flare plasmas to the $\lambda$195 channels of SOHO/EIT (Extreme-ultraviolet Imaging Telescope) and TRACE (Transition Region and Coronal Explorer). Methods: We have analysed an M8 flare simultaneously observed by the Coronal Diagnostic Spectrometer (CDS), EIT, TRACE and RHESSI. We obtained synthetic spectra for the flaring region and an outer region using the differential emission measures (DEM) of emitting plasma based on CDS and RHESSI observations and the CHIANTI atomic database. We then predicted the EIT and TRACE count rates. Results: For the flaring region, both EIT and TRACE images taken through the $\lambda$195 filter are dominated by Fe ${\rm XXIV}$ (formed at about 20 MK). However, in the outer region, the emission was primarily due to the Fe${\rm XII}$, with substantial contributions from other lines. The average count rate for the outer region was within 25% the observed value for EIT, while for TRACE it was a factor of two higher. For the flare region, the predicted count rate was a factor of two (in case of EIT) and a factor of three (in case of TRACE) higher than the actual count rate. Conclusions: During a solar flare, both TRACE and EIT $\lambda$195 channels are found to be dominated by Fe ${\rm XXIV}$ emission. Reasonable agreement between predictions and observations is found, however some discrepancies need to be further investigated.Comment: 6 pages, 4 figure

Oceanic stochastic parametrizations in a seasonal forecast system

We study the impact of three stochastic parametrizations in the ocean component of a coupled model, on forecast reliability over seasonal timescales. The relative impacts of these schemes upon the ocean mean state and ensemble spread are analyzed. The oceanic variability induced by the atmospheric forcing of the coupled system is, in most regions, the major source of ensemble spread. The largest impact on spread and bias came from the Stochastically Perturbed Parametrization Tendency (SPPT) scheme - which has proven particularly effective in the atmosphere. The key regions affected are eddy-active regions, namely the western boundary currents and the Southern Ocean. However, unlike its impact in the atmosphere, SPPT in the ocean did not result in a significant decrease in forecast error. Whilst there are good grounds for implementing stochastic schemes in ocean models, our results suggest that they will have to be more sophisticated. Some suggestions for next-generation stochastic schemes are made.Comment: 24 pages, 3 figure

Organization of the respiratory supercomplexes in cells with defective complex III: Structural features and metabolic consequences

The mitochondrial respiratory chain encompasses four oligomeric enzymatic complexes (complex I, II, III and IV) which, together with the redox carrier ubiquinone and cytochrome c, catalyze electron transport coupled to proton extrusion from the inner membrane. The protonmotive force is utilized by complex V for ATP synthesis in the process of oxidative phosphorylation. Respiratory complexes are known to coexist in the membrane as single functional entities and as supramolecular aggregates or supercomplexes (SCs). Understanding the assembly features of SCs has relevant biomedical implications because defects in a single protein can derange the overall SC organization and compromise the energetic function, causing severe mitochondrial disorders. Here we describe in detail the main types of SCs, all characterized by the presence of complex III. We show that the genetic alterations that hinder the assembly of Complex III, not just the activity, cause a rearrangement of the architecture of the SC that can help to preserve a minimal energetic function. Finally, the major metabolic disturbances associated with severe SCs perturbation due to defective complex III are discussed along with interventions that may circumvent these deficiencies

Simulated synchrotron and Inverse Compton emission from Pulsar Wind Nebulae

We present a complete set of diagnostic tools aimed at reproducing synthetic non-thermal (synchrotron and/or Inverse Compton, IC) emissivity, integrated flux energy, polarization and spectral index simulated maps in comparison to observations. The time dependent relativistic magnetohydrodynamic (RMHD) equations are solved with a shock capturing code together with the evolution of the maximum particles energy. Applications to Pulsar Wind Nebulae (PWNe) are shown.Comment: 3 pages, 7 figures, proceeding of the conference "40 Years of Pulsars ", 12-17 August 2007, Montreal, Canada, submitted to AI

A solar active region loop compared with a 2D MHD model

We analyzed a coronal loop observed with the Normal Incidence Spectrometer (NIS), which is part of the Coronal Diagnostic Spectrometer (CDS) on board the Solar and Heliospheric Observatory (SOHO). The measured Doppler shifts and proper motions along the selected loop strongly indicate unidirectional flows. Analysing the Emission Measure Curves of the observed spectral lines, we estimated that the temperature along the loop was about 380000 K. We adapted a solution of the ideal MHD steady equations to our set of measurements. The derived energy balance along the loop, as well as the advantages/disadvantages of this MHD model for understanding the characteristics of solar coronal loops are discussed.Comment: A&A in press, 10 pages, 6 figure

High Order Upwind Schemes for Multidimensional Magnetohydrodynamics

A general method for constructing high order upwind schemes for multidimensional magnetohydrodynamics (MHD), having as a main built-in condition the divergence-free constraint \divb=0 for the magnetic field vector \bb, is proposed. The suggested procedure is based on {\em consistency} arguments, by taking into account the specific operator structure of MHD equations with respect to the reference Euler equations of gas-dynamics. This approach leads in a natural way to a staggered representation of the \bb field numerical data where the divergence-free condition in the cell-averaged form, corresponding to second order accurate numerical derivatives, is exactly fulfilled. To extend this property to higher order schemes, we then give general prescriptions to satisfy a $(r+1)^{th}$ order accurate \divb=0 relation for any numerical \bb field having a $r^{th}$ order interpolation accuracy. Consistency arguments lead also to a proper formulation of the upwind procedures needed to integrate the induction equations, assuring the exact conservation in time of the divergence-free condition and the related continuity properties for the \bb vector components. As an application, a third order code to simulate multidimensional MHD flows of astrophysical interest is developed using ENO-based reconstruction algorithms. Several test problems to illustrate and validate the proposed approach are finally presented.Comment: 34 pages, including 14 figure

Primitive Variable Solvers for Conservative General Relativistic Magnetohydrodynamics

Conservative numerical schemes for general relativistic magnetohydrodynamics (GRMHD) require a method for transforming between ``conserved'' variables such as momentum and energy density and ``primitive'' variables such as rest-mass density, internal energy, and components of the four-velocity. The forward transformation (primitive to conserved) has a closed-form solution, but the inverse transformation (conserved to primitive) requires the solution of a set of five nonlinear equations. Here we discuss the mathematical properties of the inverse transformation and present six numerical methods for performing the inversion. The first method solves the full set of five nonlinear equations directly using a Newton-Raphson scheme and a guess from the previous timestep. The other methods reduce the five nonlinear equations to either one or two nonlinear equations that are solved numerically. Comparisons between the methods are made using a survey over phase space, a two-dimensional explosion problem, and a general relativistic MHD accretion disk simulation. The run-time of the methods is also examined. Code implementing the schemes is available for download on the web.Comment: Accepted to ApJ, 33 pages, 8 figures (color and greyscale), 1 machine-readable table (tab2.txt), code available at http://rainman.astro.uiuc.edu/codelib, a high-resolution and full-color PDF version is located at http://rainman.astro.uiuc.edu/codelib/codes/pvs_grmhd/ms.pd

Incorporating Uncertainties in Atomic Data Into the Analysis of Solar and Stellar Observations: A Case Study in Fe XIII

Information about the physical properties of astrophysical objects cannot be measured directly but is inferred by interpreting spectroscopic observations in the context of atomic physics calculations. Ratios of emission lines, for example, can be used to infer the electron density of the emitting plasma. Similarly, the relative intensities of emission lines formed over a wide range of temperatures yield information on the temperature structure. A critical component of this analysis is understanding how uncertainties in the underlying atomic physics propagates to the uncertainties in the inferred plasma parameters. At present, however, atomic physics databases do not include uncertainties on the atomic parameters and there is no established methodology for using them even if they did. In this paper we develop simple models for the uncertainties in the collision strengths and decay rates for Fe XIII and apply them to the interpretation of density sensitive lines observed with the EUV Imagining spectrometer (EIS) on Hinode. We incorporate these uncertainties in a Bayesian framework. We consider both a pragmatic Bayesian method where the atomic physics information is unaffected by the observed data, and a fully Bayesian method where the data can be used to probe the physics. The former generally increases the uncertainty in the inferred density by about a factor of 5 compared with models that incorporate only statistical uncertainties. The latter reduces the uncertainties on the inferred densities, but identifies areas of possible systematic problems with either the atomic physics or the observed intensities.Comment: in press at Ap