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We present a new algorithm for the identification and physical characterization of current sheets and reconnection sites in 2D and 3D large-scale relativistic magnetohydrodynamic numerical simulations. This has been implemented in the pluto code and tested in the cases of a single current sheet, a 2D jet, and a 3D unstable plasma column. Its main features are (i) a computational cost that allows its use in large-scale simulations and (ii) the capability to deal with complex 2D and 3D structures of the reconnection sites. In the performed simulations, we identify the computational cells that are part of a current sheet by a measure of the gradient of the magnetic field along different directions. Lagrangian particles, which follow the fluid, are used to sample plasma parameters before entering the reconnection sites that form during the evolution of the different configurations considered. Specifically, we track the distributions of the magnetization parameter σ and the thermal to magnetic pressure ratio β that – according to particle-in-cell simulation results – control the properties of particle acceleration in magnetic reconnection regions. Despite the fact that initial conditions of the simulations were not chosen ‘ad hoc’, the 3D simulation returns results suitable for efficient particle acceleration and realistic non-thermal particle distributions.

Context: Radio-loud AGNs are thought to possess various sites of particle acceleration, which gives rise to the observed non-thermal spectra. Stochastic turbulent acceleration (STA) and diffusive shock acceleration (DSA) are commonly cited as potential sources of high-energy particles in weakly magnetized environments. Together, these acceleration processes and various radiative losses determine the emission characteristics of these extra-galactic radio sources. Aims: The purpose of this research is to investigate the dynamical interplay between the STA and DSA in the radio lobes of FR-II radio galaxies, as well as the manner in which these acceleration mechanisms, along with a variety of radiative losses, collectively shape the emission features seen in these extra-galactic sources. Methods: A phenomenologically motivated model of STA is considered and subsequently employed on a magneto-hydrodynamically simulated radio lobe through a novel hybrid Eulerian-Lagrangian framework. Results: STA gives rise to a curved particle spectrum that is morphologically different from the usual shock-accelerated spectrum. As a consequence of this structural difference in the underlying particle energy spectrum, various multi-wavelength features arise in the spectral energy distribution of the radio lobe. Additionally, we observe enhanced diffuse X-ray emission from radio lobes for cases where STA is taken into account in addition to DSA., 15 pages, 10 figures, Accepted for publication in A&A. Comments are welcome

A significative fraction of all massive stars in the Milky Way move supersonically through their local interstellar medium (ISM), producing bow shock nebulae by wind-ISM interaction. The stability of these observed astrospheres around cool massive stars challenges precedent two-dimensional (magneto-)hydrodynamical simulations of their surroundings. We present three-dimensional magneto-hydrodynamical (3D MHD) simulations of the circumstellar medium of runaway M-type red supergiant stars moving with velocity v_star= 50 km/s. We treat the stellar wind with a Parker spiral and assume a 7 microG magnetisation of the ISM. Our free parameter is the angle theta_mag between ISM flow and magnetisation, taken to 0, 45 and 90 degrees. It is found that simulation dimension, coordinate systems and grid effects can greatly affect the development of the modelled astrospheres. Nevertheless, as soon as the ISM flow and magnetisation directions differs by more than a few degrees (theta_mag>5 degree), the bow shock is stabilised, most clumpiness and ragged structures vanishing. The complex shape of the bowshocks induce important projection effects, e.g. at optical Ha line, producing complex of astrospheric morphologies. We speculate that those effects are also at work around earlier-type massive stars, which would explain their diversity of their observed arc-like nebula around runaway OB stars. Our 3D MHD models are fitting well observations of the astrospheres of several runaway red supergiant stars. The results interpret the smoothed astrosphere of IRC-10414 and Betelgeuse aOri) are stabilised by an organised, non-parallel ambient magnetic field. Our findings suggest that IRC-10414 is currently in a steady state of its evolution, and that Betelgeuse's bar is of interstellar origin., Accepted to MNRAS

peerReviewed

We have performed magneto-hydrodynamic simulations of relativistic jets from supermassive blackholes over a few tens of kpc for a range of jet parameters. One of the primary aims were to investigate the effect of different MHD instabilities on the jet dynamics and their dependence on the choice of jet parameters. We find that two dominant MHD instabilities affect the dynamics of the jet, small scale Kelvin- Helmholtz (KH) modes and large scale kink modes, whose evolution depend on internal jet parameters like the Lorentz factor, the ratio of the density and pressure to the external medium and the magnetisation and hence consequently on the jet power. Low power jets are susceptible to both instabilities, kink modes for jets with higher central magnetic field and KH modes for lower magnetisation. Moderate power jets do not show appreciable growth of kink modes, but KH modes develop for lower magnetisation. Higher power jets are generally stable to both instabilities. Such instabilities decelerate and decollimate the jet while inducing turbulence in the cocoon, with consequences on the magnetic field structure. We model the dynamics of the jets following a generalised treatment of the Begelman-Cioffi relations which we present here. We find that the dynamics of stable jets match well with simplified analytic models of expansion of non self-similar FRII jets, whereas jets with prominent MHD instabilities show a nearly self-similar evolution of the morphology as the energy is more evenly distributed between the jet head and the cocoon., Accepted for publication in MNRAS

Some of the radio galaxies show distortion in their jets, forming tailed or winged sources. X-shaped radio galaxies are a subclass of winged sources formation mechanism of which is still unclear. The focus of this work is to understand hydro-dynamical back-flows and their role in dynamics and non-thermal emission signatures (in presence of radiative losses and diffusive shock acceleration) during the initial phase of these galaxies. We have performed relativistic MHD simulations of an under-dense jet travelling in a tri-axial ambient using a hybrid Eulerian-Lagrangian framework to incorporate effects of micro-physical processes. We have demonstrated the dominant role played by pressure gradient in shaping XRGs in thermally dominated cases. We show that the prominence of the formed structure decreases as the jet deviates from the major axis of the ambient. The wing evolution is mainly governed by re-energized particles due to shocks that keep the structure active during the evolution time. The synthetic intensity maps of the radio galaxy show similarities with morphologies that are typically found in observed XRGs. This includes the cases with wider wings than the active lobes. The characteristic emission signatures in terms of its synchrotron spectra and implication of equipartition condition in age estimation are also discussed here. Additionally, we show that discrepancy of age can be attributed to mixing of different aged particle populations. Further, the effect of viewing angle on the difference of spectral index of the active lobes and the wings $(\Delta \alpha)$ shows a large variation and degenerate behaviour. We have demonstrated the role of diffusive shocks in the obtained variation and have concluded that the spread of $(\Delta \alpha)$ is not a dependable characteristic in determining the formation model of XRGs., Comment: 15 pages, 17 figures, 3 tables; Accepted for publication in Astronomy & Astrophysics journal

We compare a particular selection of approximate solutions of the Riemann problem in the context of ideal relativistic magnetohydrodynamics. In particular, we focus on Riemann solvers not requiring a full eigenvector structure. Such solvers recover the solution of the Riemann problem by solving a simplified or reduced set of jump conditions, whose level of complexity depends on the intermediate modes that are included. Five different approaches - namely the HLL, HLLC, HLLD, HLLEM and GFORCE schemes - are compared in terms of accuracy and robustness against one- and multi-dimensional standard numerical benchmarks. Our results demonstrate that - for weak or moderate magnetizations - the HLLD Riemann solver yields the most accurate results, followed by HLLC solver(s). The GFORCE approach provides a valid alternative to the HLL solver being less dissipative and equally robust for strongly magnetized environments. Finally, our tests show that the HLLEM Riemann solver is not cost-effective in improving the accuracy of the solution and reducing the numerical dissipation., 20 pages, 14 figures, accepted for publication in MNRAS

In the recent years, sub/mm observations of protoplanetary disks have discovered an incredible diversity of substructures in the dust emission. An important result was the finding that dust grains of mm size are embedded in very thin dusty disks. This implies that the dust mass fraction in the midplane becomes comparable to the gas, increasing the importance of the interaction between the two components there. We address this problem by means of numerical 2.5D simulations in order to study the gas and dust interaction in fully global stratified disks. To this purpose, we employ the recently developed dust grain module in the PLUTO code. Our model focuses on a typical T Tauri disk model, simulating a short patch of the disk at 10 au which includes grains of constant Stokes number of $St=0.01$ and $St=0.1$, corresponding to grains with sizes of 0.9 cm and 0.9 mm, respectively, for the given disk model. By injecting a constant pebble flux at the outer domain, the system reaches a quasi steady state of turbulence and dust concentrations driven by the streaming instability. For our given setup and using resolutions up to 2500 cells per scale height we resolve the streaming instability, leading to local dust clumping and concentrations. Our results show dust density values of around 10-100 times the gas density with a steady state pebble flux between $3.5 \times 10^{-4}$ and $2.5 \times 10^{-3} M_{\rm Earth}/\mathit{year}$ for the models with $\mathit{St}=0.01$ and $\mathit{St}=0.1$. The grain size and pebble flux for model $\mathit{St}=0.01$ compares well with dust evolution models of the first million years of disk evolution. For those grains the scatter opacity dominates the extinction coefficient at mm wavelengths. These types of global dust and gas simulations are a promising tool for studies of the gas and dust evolution at pressure bumps in protoplanetary disks., accepted at A&A

The reconstruction of plasma parameters in the interplanetary medium is very important to understand the interplanetary propagation of solar eruptions and for Space Weather application purposes. Because only a few spacecraft are measuring in situ these parameters, reconstructions are currently performed by running complex numerical Magneto-hydrodynamic (MHD) simulations starting from remote sensing observations of the Sun. Current models apply full 3D MHD simulations of the corona or extrapolations of photospheric magnetic fields combined with semi-empirical relationships to derive the plasma parameters on a sphere centered on the Sun (inner boundary). The plasma is then propagated in the interplanetary medium up to the Earth’s orbit and beyond. Nevertheless, this approach requires significant theoretical and computational efforts, and the results are only in partial agreement with the in situ observations. In this paper we describe a new approach to this problem called RIMAP – Reverse In situ data and MHD APproach. The plasma parameters in the inner boundary at 0.1 AU are derived directly from the in situ measurements acquired at 1 AU, by applying a back reconstruction technique to remap them into the inner heliosphere. This remapping is done by using the Weber and Davies solar wind theoretical model to reconstruct the wind flowlines. The plasma is then re-propagated outward from 0.1 AU by running a MHD numerical simulation based on the PLUTO code. The interplanetary spiral reconstructions obtained with RIMAP are not only in a much better agreement with the in situ observations, but are also including many more small-scale longitudinal features in the plasma parameters that are not reproduced with the approaches developed so far.

Cosmic rays (CRs) are frequently modeled as an additional fluid in hydrodynamic (HD) and magnetohydrodynamic (MHD) simulations of astrophysical flows. The standard CR two-fluid model is described in terms of three conservation laws (expressing conservation of mass, momentum and total energy) and one additional equation (for the CR pressure) that cannot be cast in a satisfactory conservative form. The presence of non-conservative terms with spatial derivatives in the model equations prevents a unique weak solution behind a shock. We investigate a number of methods for the numerical solution of the two-fluid equations and find that, in the presence of shock waves, the results generally depend on the numerical details (spatial reconstruction, time stepping, the CFL number, and the adopted discretization). All methods converge to a unique result if the energy partition between the thermal and non-thermal fluids at the shock is prescribed using a subgrid prescription. This highlights the non-uniqueness problem of the two-fluid equations at shocks. From our numerical investigations, we report a robust method for which the solutions are insensitive to the numerical details even in absence of a subgrid prescription, although we recommend a subgrid closure at shocks using results from kinetic theory. The subgrid closure is crucial for a reliable post-shock solution and also its impact on large scale flows because the shock microphysics that determines CR acceleration is not accurately captured in a fluid approximation. Critical test problems, limitations of fluid modeling, and future directions are discussed., Comment: 18 pages, 12 figures, 2 tables; MNRAS accepted version

We present 2D MHD numerical simulations of tearing-unstable current sheets coupled to a population of non-thermal test-particles, in order to address the problem of numerical convergence with respect to grid resolution, numerical method and physical resistivity. Numerical simulations are performed with the PLUTO code for astrophysical fluid dynamics through different combinations of Riemann solvers, reconstruction methods, grid resolutions at various Lundquist numbers. The constrained transport method is employed to control the divergence-free condition of magnetic field. Our results indicate that the reconnection rate of the background tearing-unstable plasma converges only for finite values of the Lundquist number and for sufficiently large grid resolutions. In general, it is found that (for a 2nd-order scheme) the minimum threshold for numerical convergence during the linear phases requires the number of computational zones covering the initial current sheet width to scale roughly as $\sim \sqrt{\bar{S}}$, where $\bar{S}$ is the Lundquist number defined on the current sheet width. On the other hand, the process of particle acceleration is found to be nearly independent of the underlying numerical details inasmuch as the system becomes tearing-unstable and enters in its nonlinear stages. In the limit of large $\bar{S}$, the ensuing power-law index quickly converge to $p \approx 1.7$, consistently with the fast reconnection regime., 14 pages, 11 figures

We present a numerical code for radiation hydrodynamics designed as a module for the freely available PLUTO code. We adopt a gray approximation and include radiative transfer following a two-moment approach by imposing the M1 closure to the radiation fields. This closure allows for a description of radiative transport in both the diffusion and free-streaming limits, and is able to describe highly anisotropic radiation transport as can be expected in the vicinity of an accreting planet in a protoplanetary disk. To reduce the computational cost caused by the timescale disparity between radiation and matter fields, we integrate their evolution equations separately in an operator-split way, using substepping to evolve the radiation equations. We further increase the code's efficiency by adopting the reduced speed of light approximation (RSLA). Our integration scheme for the evolution equations of radiation fields relies on implicit-explicit schemes, in which radiation-matter interaction terms are integrated implicitly while fluxes are integrated via Godunov-type solvers. The module is suitable for general astrophysical computations in 1, 2, and 3 dimensions in Cartesian, spherical and cylindrical coordinates, and can be implemented on rotating frames. We demonstrate the algorithm performance on different numerical benchmarks, paying particular attention to the applicability of the RSLA for computations of physical processes in protoplanetary disks. We show 2D simulations of vertical convection in disks and 3D simulations of gas accretion by planetary cores, which are the first of their kind to be solved with a two-moment approach., Comment: 27 pages, 16 figures

The shaping of astrophysical outflows into bright, dense, and collimated jets due to magnetic pressure is here investigated using laboratory experiments. Here we look at the impact on jet collimation of a misalignment between the outflow, as it stems from the source, and the magnetic field. For small misalignments, a magnetic nozzle forms and redirects the outflow in a collimated jet. For growing misalignments, this nozzle becomes increasingly asymmetric, disrupting jet formation. Our results thus suggest outflow/magnetic field misalignment to be a plausible key process regulating jet collimation in a variety of objects from our Sun’s outflows to extragalatic jets. Furthermore, they provide a possible interpretation for the observed structuring of astrophysical jets. Jet modulation could be interpreted as the signature of changes over time in the outflow/ambient field angle, and the change in the direction of the jet could be the signature of changes in the direction of the ambient field., Mass outflow is a common process in astrophysical objects. Here the authors investigate in which conditions an astrophysically-scaled laser-produced plasma flow can be collimated and evolves in the presence of a misaligned external magnetic field.

Radio relics are diffuse radio sources in galaxy clusters that are associated with merger shock waves. Detailed observations of radio relics in total intensity and in polarisation show complex structures on kiloparsec scales. The relation between the observed features and the underlying morphology of the magnetic field is not clear. Using three-dimensional magneto-hydrodynamical simulations, we study the polarised emission produced by a shock wave that propagates through a turbulent medium that resembles the intracluster medium. We model the polarised synchrotron emission on the basis of diffusive shock acceleration of cosmic-ray electrons. We find that the synchrotron emission produced in a shocked turbulent medium can reproduce some of the observed features in radio relics. Shock compression can give rise to a high polarisation fraction at the shock front and a partial alignment of the polarisation $E$-vectors with the shock normal. Our work confirms that radio relics can also be formed in an environment with a tangled magnetic field. We also discuss the effect of Faraday Rotation intrinsic to the source, and how our results depend on the angular resolution of observations., Accepted for publication in MNRAS, 22 pages, 23 figures

We have simulated the evolution of non-thermal cosmic ray electrons (CREs) in 3D relativistic magneto hydrodynamic (MHD) jets evolved up to a height of 9 kpc. The CREs have been evolved in space and in energy concurrently with the relativistic jet fluid, duly accounting for radiative losses and acceleration at shocks. We show that jets stable to MHD instabilities show expected trends of regular flow of CREs in the jet spine and acceleration at a hotspot followed by a settling backflow. However, unstable jets create complex shock structures at the jet-head (kink instability), the jet spine-cocoon interface and the cocoon itself (Kelvin-Helmholtz modes). CREs after exiting jet-head undergo further shock crossings in such scenarios and are re-accelerated in the cocoon. CREs with different trajectories in turbulent cocoons have different evolutionary history with different spectral parameters. Thus at the same spatial location, there is mixing of different CRE populations, resulting in a complex total CRE spectrum when averaged over a given area. Cocoons of unstable jets can have an excess build up of energetic electrons due to re-acceleration at turbulence driven shocks and slowed expansion of the decelerated jet. This will add to the non-thermal energy budget of the cocoon., Published in MNRAS. arxiv V1 has 2 updated references

The multimessenger event GW170817/GRB 170817A confirmed that binary neutron star (BNS) mergers can produce short gamma-ray burst (SGRB) jets. This evidence promoted new investigations on the mechanisms through which a BNS merger remnant can launch such a powerful relativistic outflow and on the propagation of the latter across the surrounding post-merger environment. In particular, great strides have been made in jet propagation models, establishing connections between the initial jet launching conditions, including the incipient jet launching time (with respect to merger) and the injection parameters, and the observable SGRB prompt and afterglow emission. However, present semi-analytical models and numerical simulations (with one notable exception) adopt simple hand-made prescriptions to account for the post-merger environment, lacking a direct association with any specific merging BNS system. Here, we present the first three-dimensional relativistic hydrodynamics simulations of incipient SGRB jets propagating through a post-merger environment that is directly imported from the outcome of a previous general relativistic BNS merger simulation. Our results show that the evolution and final properties of the jet can be largely affected by the anisotropies and the deviations from axisymmetry and homologous expansion characterizing more realistic BNS merger environments. In addition, we find that the inclusion of the gravitational pull from the central compact object, often overlooked, can have a major impact. Finally, we consider different jet launching times referred to the same BNS merger model and discuss the consequences for the ultimate jet properties., 16 pages, 20 figures

Extragalactic radio sources appear under different morphologies, the most frequent ones are classified as Fanaroff-Riley type I (FR I), typically with lower luminosities, and Fanaroff-Riley type II, (FR II), typically more luminous. This simple classification, however, has many exceptions that we intend to investigate. Following previous analyses in the three-dimensional Hydrodynamic and Magneto-Hydrodynamic limits, we extend the numerical investigation to the Relativistic Magneto-Hydrodynamic regime, to include sources whose jet kinetic power sets in the range that separates FR Is from FR IIs. We consider weakly and mildly relativistic, underdense, supersonic jets that propagate in a stratified medium. In the model, the ambient temperature increases with distance from the jet origin maintaining constant pressure. We present three cases with low, high and intermediate kinetic luminosity that evolve into different morphologies. We find that the resulting morphology can be highly time dependent and that, apart from the jet power, the jet-to-ambient density ratio and the magnetization parameter play a crucial role in the jet evolution as well., Comment: Accepted for publication on Astronomy & Astrophysics

Interplanetary Coronal Mass Ejection (ICME) shocks are known to accelerate particles and contribute significantly to Solar Energetic Particle (SEP) events. We have performed Magnetohydrodynamic-Particle in Cell (MHD-PIC) simulations of ICME shocks to understand the acceleration mechanism. These shocks vary in Alfv��nic Mach numbers as well as in magnetic field orientations (parallel \& quasi-perpendicular). We find that Diffusive Shock Acceleration (DSA) plays a significant role in accelerating particles in a parallel ICME shock. In contrast, Shock Drift Acceleration (SDA) plays a pivotal role in a quasi-perpendicular shock. High-Mach shocks are seen to accelerate particles more efficiently. Our simulations suggest that background turbulence and local particle velocity distribution around the shock can indirectly hint at the acceleration mechanism. Our results also point towards a few possible \textit{in situ} observations that could validate our understanding of the topic., Accepted for publication in the Astrophysical Journal, 16 pages, 20 figures

Non-thermal emission from Active Galactic Nuclei (AGN) jets extends up-to large scales in-spite of them being prone to a slew of magneto-hydrodynamic instabilities. The main focus of this study is to understand the impact of MHD instabilities on the non-thermal emission from large-scale AGN jets. We perform high-resolution three-dimensional numerical magneto-hydrodynamic simulations of a plasma column to investigate the dynamical and emission properties of jet configurations at kilo-parsec scales with different magnetic field profiles, jet speeds, and density contrast. We also obtain synthetic non-thermal emission signatures for different viewing angles using an approach that assumes static particle spectra and that obtained by evolving the particle spectra using Lagrangian macro-particles incorporating the effects of shock acceleration and radiative losses. We find that the shocks due to Kelvin-Helmholtz (KH) instability in the axial magnetic field configurations can strongly affect the jet dynamics. Additionally, we also find the presence of weak biconical shocks in the under-dense jet columns. The inclusion of a helical magnetic field hinders the vortex growth at the shear surface thereby stabilizing the jet column. With the evolving particle spectra approach, the synthetic SEDs obtained for cases with strong KH instability show the presence of multiple humps ranging from radio to TeV gamma-ray band. We conclude that the high-energy electrons accelerated in the vicinity of freshly formed shocks due to KH instability, result in high X-ray emission., 18 pages, 12 figures, Accepted for publication in A&A

Astrophysical fluid flow studies often encompass a wide range of physical processes to account for the complexity of the system under consideration. In addition to gravity, a proper treatment of thermodynamic processes via continuum radiation transport and/or photoionization is becoming the state of the art. We present a major update of our continuum radiation transport module, MAKEMAKE, and a newly developed module for photoionization, SEDNA, coupled to the magnetohydrodynamics code PLUTO. These extensions are currently not publicly available; access can be granted on a case-by-case basis. We explain the theoretical background of the equations solved, elaborate on the numerical layout, and present a comprehensive test suite for radiation-ionization hydrodynamics. The grid-based radiation and ionization modules support static one-dimensional, two-dimensional, and three-dimensional grids in Cartesian, cylindrical, and spherical coordinates. Each module splits the radiation field into two components, one originating directly from a point source - solved using a ray-tracing scheme - and a diffuse component - solved with a three-dimensional flux-limited diffusion (FLD) solver. The FLD solver for the continuum radiation transport makes use of either the equilibrium one-temperature approach or the linearization two-temperature approach. The FLD solver for the photoionization module enables accounting for the temporal evolution of the radiation field from direct recombination of free electrons into hydrogen's ground state as an alternative to the on-the-spot approximation. A brief overview of completed and ongoing scientific studies is given to explicitly illustrate the multipurpose nature of the numerical framework presented.

Particle acceleration is an ubiquitous phenomenon in astrophysical and space plasma. Diffusive shock acceleration (DSA) and stochastic turbulent acceleration are known to be the possible mechanisms for producing very high energetic particles, particularly in weakly magnetized regions. An interplay of different acceleration processes along with various radiation losses is typically observed in astrophysical sources. While DSA is a systematic acceleration process that energizes particles in the vicinity of shocks, stochastic turbulent acceleration (STA) is a random energizing process, where the interaction between cosmic ray particles and electromagnetic fluctuations results in particle acceleration. This process is usually interpreted as a biased random walk in energy space, modelled through a Fokker-Planck equation. In the present work, we describe a novel Eulerian algorithm, adopted to incorporate turbulent acceleration in the presence of DSA and radiative processes like synchrotron and Inverse-Compton emission. The developed framework extends the hybrid Eulerian-Lagrangian module in a full-fledged relativistic Magneto-hydrodynamic (RMHD) code PLUTO. From our validation tests and case studies, we showcase the competing and complementary nature of both acceleration processes. Axisymmetric simulations of an RMHD jet with this extended hybrid framework clearly demonstrate that emission due to shocks is localized while that due to turbulent acceleration originates in the backflow and is more diffuse, particularly in the high energy X-ray band., Comment: 16 Pages, 15 Figures, Accepted for publication in The Astrophysical Journal

Recent studies showed that observations of line emission from shocks in YSO jets require a substantial amount of ionization of the pre-shock matter. Photoionization from X-ray emitted close to the central source may be responsible for the initial ionization fraction. The aim of our work is to study the effect of X-ray photoionization, coming from the vicinity of the central star, on the ionization fraction inside the jet that can be advected at large distances. For this purpose we have performed axisymmetric MHD jet launching simulations including photoionization and optically thin losses using PLUTO. For typical X-ray luminosities in classical T-Tauri stars, we see that the photoionization is responsible for ionizing to 10%-20% the jet close to the star.

High-resolution radio observations of cluster radio relics often show complex spatial and spectral features. However, it is not clear what these features reveal about the underlying magnetic field properties. We performed three-dimensional magneto-hydrodynamical simulations of merger shock waves propagating through a magnetised, turbulent intracluster medium. Our model includes the diffusive shock acceleration of cosmic-ray electrons, their spatial advection and energy losses at run-time. With this set-up we can investigate the relation between radio substructure and pre-shock plasma conditions in the host cluster. We find that upstream turbulence plays a major role in shaping the properties of radio relics produced downstream. Within the assumption of diffusive shock acceleration, we can reproduce the observed discrepancy between the X-ray derived Mach number of shocks, and the Mach number inferred from radio spectra. Our simulated spectral index maps and profiles across the radio relic also suggest that the standard deviation of the upstream magnetic field must be relatively small ($\sigma_B\leq 1 \, \mu$G) in order to reproduce observations and therefore, radio relics can potentially constrain the distribution of magnetic fields in galaxy clusters outskirts., Comment: Accepted for publication in MNRAS, 22 pages, 25 figures

In recent years, cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) have substantially improved the clinical outcome of pseudomyxoma peritonei (PMP) originating from mucinous appendiceal cancer. However, current histopathological grading of appendiceal PMP frequently fails in predicting disease outcome. We recently observed that the integration of cancer cell transcriptional traits with those of cancer-associated fibroblasts (CAFs) improves prognostic prediction for tumors of the large intestine. We therefore generated global expression profiles on a consecutive series of 24 PMP patients treated with CRS plus HIPEC. Multiple lesions were profiled for nine patients. We then used expression data to stratify the samples by a previously published “high-risk appendiceal cancer” (HRAC) signature and by a CAF signature that we previously developed for colorectal cancer, or by a combination of both. The prognostic value of the HRAC signature was confirmed in our cohort and further improved by integration of the CAF signature. Classification of cases profiled for multiple lesions revealed the existence of outlier samples and highlighted the need of profiling multiple PMP lesions to select representative samples for optimal performances. The integrated predictor was subsequently validated in an independent PMP cohort. These results provide new insights into PMP biology, revealing a previously unrecognized prognostic role of the stromal component and supporting integration of standard pathological grade with the HRAC and CAF transcriptional signatures to better predict disease outcome.

We describe a novel Godunov-type numerical method for solving the equations of resistive relativistic magnetohydrodynamics. In the proposed approach, the spatial components of both magnetic and electric fields are located at zone interfaces and are evolved using the constrained transport formalism. Direct application of Stokes' theorem to Faraday's and Ampere's laws ensures that the resulting discretization is divergence-free for the magnetic field and charge-conserving for the electric field. Hydrodynamic variables retain, instead, the usual zone-centred representation commonly adopted in finite-volume schemes. Temporal discretization is based on Runge-Kutta implicit-explicit (IMEX) schemes in order to resolve the temporal scale disparity introduced by the stiff source term in Ampere's law. The implicit step is accomplished by means of an improved and more efficient Newton-Broyden multidimensional root-finding algorithm. The explicit step relies on a multidimensional Riemann solver to compute the line-averaged electric and magnetic fields at zone edges and it employs a one-dimensional Riemann solver at zone interfaces to update zone-centred hydrodynamic quantities. For the latter, we introduce a five-wave solver based on the frozen limit of the relaxation system whereby the solution to the Riemann problem can be decomposed into an outer Maxwell solver and an inner hydrodynamic solver. A number of numerical benchmarks demonstrate that our method is superior in stability and robustness to the more popular charge-conserving divergence cleaning approach where both primary electric and magnetic fields are zone-centered. In addition, the employment of a less diffusive Riemann solver noticeably improves the accuracy of the computations., 25 pages, 14 figures

Hybrid codes treating composite systems made up of fluid and particle components are becoming increasing more popular in order to address multiple scale in complex astrophysical environments. Here we review some recent additions to the PLUTO code consisting of three flexible particle physics implementations targeting i) cosmic ray particles, ii) sub-grid electron acceleration and emission from high-energy astrophysical environments and iii) dust grains in protoplanetary disks. While the fluid equations are generally solved using standard finite-volume techniques, integration of particles as well as their feedback onto the gas is treated using standard techniques borrowed from Particle-In-Cell (PIC) frameworks. Some novel numerical benchmarks, not discussed in the original method papers, are also presented.

Radio sources of low power are the most common in the universe. Their jets typically move at nonrelativistic velocity and show plume-like morphologies that in many instances appear distorted and bent. We investigate the role of magnetic field on the propagation and evolution of low-power jets and the connection between the field intensity and the resulting morphology. The problem is addressed by means of three-dimensional magnetohydrodynamic (MHD) simulations. We consider supersonic jets that propagate in a stratified medium. The ambient temperature increases with distance from the jet origin maintaining constant pressure. Jets with low magnetization show an enhanced collimation at small distances with respect to hydrodynamic (HD) cases studied in a previous paper. These jets eventually evolve in a way similar to the HD cases. Jets with higher magnetization are affected by strong nonaxisymmetric modes that lead to the sudden jet energy release. From there on, distorted plumes of jet material move at subsonic velocities. This transition is associated with the formation of structures reminiscent of the `warm spots' observed in wide-angle-tail (WAT) sources., Comment: In press on Astronomy & Astrophysics

We present a numerical implementation for the solution of the relativistic radiation hydrodynamics and magnetohydrodynamics equations, designed as an independent module within the freely available code PLUTO. The radiation transfer equations are solved under the grey approximation and imposing the M1 closure, which allows the radiation transport to be handled in both the free-streaming and diffusion limits. Equations are integrated following an implicit-explicit scheme, where radiation-matter interaction terms are integrated implicitly, whereas transport and all of the remaining source terms are solved explicitly by means of the same Godunov-type solvers included in PLUTO. Among these, we introduce a new Harten-van Leer-contact (HLLC) solver for optically thin radiation transport. The code is suitable for multidimensional computations in Cartesian, spherical and cylindrical coordinates, using either a single processor or parallel architectures. Adaptive grid computations are also made possible, by means of the CHOMBO library. The algorithm performance is demonstrated through a series of numerical benchmarks by investigating various different configurations with a particular emphasis on the behavior of the solutions in the free-streaming and diffusion limits., 25 pages, 17 figures

The implementation of a new particle module describing the physics of dust grains coupled to the gas via drag forces is the subject of this work. The proposed particle-gas hybrid scheme has been designed to work in Cartesian as well as in cylindrical and spherical geometries. The numerical method relies on a Godunov-type second-order scheme for the fluid and an exponential midpoint rule for dust particles which overcomes the stiffness introduced by the linear coupling term. Besides being time-reversible and globally second-order accurate in time, the exponential integrator provides energy errors which are always bounded and it remains stable in the limit of arbitrarily small particle stopping times yielding the correct asymptotic solution. Such properties make this method preferable to the more widely used semi-implicit or fully implicit schemes at a very modest increase in computational cost. Coupling between particles and grid quantities is achieved through particle deposition and field-weighting techniques borrowed from Particle-In-Cell simulation methods. In this respect, we derive new weight factors in curvilinear coordinates that are more accurate than traditional volume- or area-weighting. A comprehensive suite of numerical benchmarks is presented to assess the accuracy and robustness of the algorithm in Cartesian, cylindrical and spherical coordinates. Particular attention is devoted to the streaming instability which is analyzed in both local and global disk models. The module is part of the PLUTO code for astrophysical gas-dynamics and it is mainly intended for the numerical modeling of protoplanetary disks in which solid and gas interact via aerodynamic drag., Comment: 22 pages, 13 figures

We carry out a linear stability analysis of a magnetized relativistic rotating cylindrical jet flow using the approximation of zero thermal pressure. We identify several modes of instability in the jet: Kelvin-Helmholtz, current driven and two kinds of centrifugal-buoyancy modes -- toroidal and poloidal. The Kelvin-Helmholtz mode is found at low magnetization and its growth rate depends very weakly on the pitch parameter of the background magnetic field and on rotation. The current driven mode is found at high magnetization, the values of its growth rate and the wavenumber, corresponding to the maximum growth, increase as we decrease the pitch parameter of the background magnetic field. This mode is stabilized by rotation, especially, at high magnetization. The centrifugal-buoyancy modes, arising due to rotation, tend also to be more stable when magnetization is increased. Overall, relativistic jet flows appear to be more stable with respect to their non-relativistic counterpart., Comment: 15 pages, 15 figures, accepted for pubblication in MNRAS

We present a numerical study of turbulence and dynamo action in stratified shearing boxes with zero mean magnetic flux. We assume that the fluid obeys the perfect gas law and has finite (constant) thermal diffusivity. We identify two regimes. The first is a conductive regime in which the heat is transported mostly by conduction and the density decreases with height. In the limit of large thermal diffusivity this regime resembles the more familiar isothermal case. The second is the convective regime, observed at smaller values of the thermal diffusivity, in which the layer becomes unstable to overturning motions, the heat is carried mostly by advection, and the density becomes nearly constant throughout the layer. In this latter constant-density regime we observe evidence for large-scale dynamo action leading to a substantial increase in transport efficiency relative to the conductive case. We then present an approach to deriving global properties of accretion disks from the knowledge of local solutions derived from numerical simulations based on the shearing box approximation. In this way we can discuss the consistency of the convective solutions.

Pulsar wind nebulae inside young supernova remnants, and in particular the Crab nebula, are probably the best laboratories for high-energy astrophysics and relativistic plasma physics. They have been modeled numerically for more than a decade through multi-dimensional relativistic MHD simulations, relying on axial symmetry until a few years ago while currently using full three-dimensional simulations employing adaptive meshes. Here, we discuss the most recent findings, especially those obtained by our Arcetri group, focusing on the problem of magnetic field dissipation inside the nebula.

In the last years, Laboratory Information Management Systems (LIMS) have been growing from mere inventory systems into increasingly comprehensive software platforms, spanning functionalities as diverse as data search, annotation and analysis. Our institution started in 2011 a LIMS project named the Laboratory Assistant Suite with the purpose of assisting researchers throughout all of their laboratory activities, providing graphical tools to support decision-making tasks and building complex analyses on integrated data. The modular architecture of the system exploits multiple databases with different technologies. To provide an efficient and easy tool for retrieving information of interest, we developed the Multi-Dimensional Data Manager (MDDM). By means of intuitive interfaces, scientists can execute complex queries without any knowledge of query languages or database structures, and easily integrate heterogeneous data stored in multiple databases. Together with the other software modules making up the platform, the MDDM has helped improve the overall quality of the data, substantially reduced the time spent with manual data entry and retrieval and ultimately broadened the spectrum of interconnections among the data, offering novel perspectives to the biomedical analysts.

Rapid technological evolution is providing biomedical research laboratories with huge amounts of complex and heterogeneous data. The LIMS project Laboratory Assistant Suite (LAS), started by our Institution, aims to assist researchers throughout all of their laboratory activities, providing graphical tools to support decision-making tasks and building complex analyses on integrated data. Thanks to a clinical data management module, linking biological samples analysed by translational research with the originating patients and their clinical history, it can effectively provide insight into tumor development. Furthermore, the LAS tracks molecular experiments and allows automatic annotation of biological samples with their molecular results. A genomic annotation module makes use of semantic web technologies to represent relevant concepts from the genomic domain. The LAS system has helped improve the overall quality of the data and broadened the spectrum of interconnections among the data, offering novel perspectives to the biomedical analyst.

We describe a new hybrid framework to model non-thermal spectral signatures from highly energetic particles embedded in a large-scale classical or relativistic MHD flow. Our method makes use of \textit{Lagrangian} particles moving through an Eulerian grid where the (relativistic) MHD equations are solved concurrently. Lagrangian particles follow fluid streamlines and represent ensembles of (real) relativistic particles with a finite energy distribution. The spectral distribution of each particle is updated in time by solving the relativistic cosmic ray transport equation based on local fluid conditions. This enables us to account for a number of physical processes, such as adiabatic expansion, synchrotron and inverse Compton emission. An accurate semi-analytically numerical scheme that combines the method of characteristics with a Lagrangian discretization in the energy coordinate is described. In presence of (relativistic) magnetized shocks, a novel approach to consistently model particle energization due to diffusive shock acceleration has been presented. Our approach relies on a refined shock-detection algorithm and updates the particle energy distribution based on the shock compression ratio, magnetic field orientation and amount of (parameterized) turbulence. The evolved distribution from each \textit{Lagrangian} particle is further used to produce observational signatures like emission maps and polarization signals accounting for proper relativistic corrections. We further demonstrate the validity of this hybrid framework using standard numerical benchmarks and evaluate the applicability of such a tool to study high energy emission from extra-galactic jets., Comment: 23 pages, 14 figures, Accepted for publication in The Astrophysical Journal