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We have observed unexpected spectral attenuation of ultraviolet light in freshly drawn hollow core optical fibres. When the fibre ends are left open to atmosphere, this loss feature dissipates over time. The loss matches the absorption spectrum of gaseous (molecular) chlorine and, given enough time, the transmission spectrum of the fibre recovers to that expected from the morphological structure of the fibre. Our measurements indicate an initial chlorine concentration of 0.45 $\mu$ mol/cm$^{3}$ in the hollow core, equivalent to 1.1 mol% Cl$_{2}$ at atmospheric pressure.

We analyse, using new analytical models and numerical general relativistic magnetohydrodynamic simulations, the three-dimensional properties of accretion flows inside the plunging region of black hole spacetimes (i.e., at radii smaller than the innermost stable circular orbit). These simulations are of thick discs, with aspect ratios of order unity $h/r \sim 1$, and with a magnetic field geometry given by the standard low-magnetization "SANE" configuration. This work represents the first step in a wider analysis of this highly relativistic region. We show that analytical expressions derived in the "thin disc" limit describe the numerical results remarkably well, despite the large aspect ratio of the flow. We further demonstrate that accretion within this region is typically mediated via spiral arms, and that the geometric properties of these spiral structures can be understood with a simple analytical model. These results highlight how accretion within the plunging region is fundamentally two dimensional in character, which may have a number of observational implications. We derive a modified theoretical description of the pressure within the plunging region which accounts for turbulent heating and may be of use to black hole image modelling., Comment: 21 pages, 16 figures. Accepted for publication in MNRAS

We present three-dimensional magnetohydrodynamic (MHD) simulations of the fueling of supermassive black holes in elliptical galaxies from a turbulent cooling medium on galactic scales, taking M87* as a typical case. We find that the mass accretion rate is increased by a factor of $\sim 10$ compared with analogous hydrodynamic simulations. The scaling of $\dot{M} \sim r^{1/2}$ roughly holds from $\sim 10\,\mathrm{pc}$ to $\sim 10^{-3}\,\mathrm{pc}$ ($\sim 10\, r_\mathrm{g}$) with the accretion rate through the event horizon being $\sim 10^{-2}\, M_\odot\,\mathrm{yr^{-1}}$. The accretion flow on scales $\sim 0.03-3\,\mathrm{kpc}$ takes the form of magnetized filaments. Within $\sim 30\,\mathrm{pc}$, the cold gas circularizes, forming a highly magnetized ($\beta\sim 10^{-3}$) thick disk supported by a primarily toroidal magnetic field. The cold disk is truncated and transitions to a turbulent hot accretion flow at $\sim0.3\,\mathrm{pc}$ ($10^3\,r_\mathrm{g}$). There are strong outflows towards the poles driven by the magnetic field. The outflow energy flux increases with smaller accretor size, reaching $\sim 3\times10^{43}\,\mathrm{erg\,s^{-1}}$ for $r_\mathrm{in}=8\,r_\mathrm{g}$; this corresponds to a nearly constant energy feedback efficiency of $\eta\sim0.05-0.1$ independent of accretor size. The feedback energy is enough to balance the total cooling of the M87/Virgo hot halo out to $\sim 50$ kpc. The accreted magnetic flux at small radii is similar to that in magnetically arrested disk models, consistent with the formation of a powerful jet on horizon scales in M87. Our results motivate a subgrid model for accretion in lower-resolution simulations in which the hot gas accretion rate is suppressed relative to the Bondi rate by $\sim (10r_\mathrm{g}/r_\mathrm{B})^{1/2}$., Comment: 23 pages, 14 figures, submitted to ApJ

Background Advancements in Large Language Models (LLMs) hold transformative potential in healthcare, however, recent work has raised concern about the tendency of these models to produce outputs that display racial or gender biases. Although training data is a likely source of such biases, exploration of disease and demographic associations in text data at scale has been limited. Methods We conducted a large-scale textual analysis using a dataset comprising diverse web sources, including Arxiv, Wikipedia, and Common Crawl. The study analyzed the context in which various diseases are discussed alongside markers of race and gender. Given that LLMs are pre-trained on similar datasets, this approach allowed us to examine the potential biases that LLMs may learn and internalize. We compared these findings with actual demographic disease prevalence as well as GPT-4 outputs in order to evaluate the extent of bias representation. Results Our findings indicate that demographic terms are disproportionately associated with specific disease concepts in online texts. gender terms are prominently associated with disease concepts, while racial terms are much less frequently associated. We find widespread disparities in the associations of specific racial and gender terms with the 18 diseases analyzed. Most prominently, we see an overall significant overrepresentation of Black race mentions in comparison to population proportions. Conclusions Our results highlight the need for critical examination and transparent reporting of biases in LLM pretraining datasets. Our study suggests the need to develop mitigation strategies to counteract the influence of biased training data in LLMs, particularly in sensitive domains such as healthcare.

The end of supernova remnant (SNR) evolution is characterized by a so-called "radiative" stage, in which efficient cooling of the hot bubble inside the forward shock slows expansion, leading to eventual shock breakup. Understanding SNR evolution at this stage is vital for predicting feedback in galaxies, since SNRs are expected to deposit their energy and momentum into the interstellar medium at the ends of their lives. A key prediction of SNR evolutionary models is the formation at the onset of the radiative stage of a cold, dense shell behind the forward shock. However, searches for these shells via their neutral hydrogen emission have had limited success. We instead introduce an independent observational signal of shell formation arising from the interaction between nonthermal particles accelerated by the SNR forward shock (cosmic rays) and the dense shell. Using a semi-analytic model of particle acceleration based on state-of-the-art simulations coupled with a high-resolution hydrodynamic model of SNR evolution, we predict the nonthermal emission that arises from this interaction. We demonstrate that the onset of the radiative stage leads to nonthermal signatures from radio to $\gamma$-rays, including radio and $\gamma$-ray brightening by nearly two orders of magnitude. Such a signature may be detectable with current instruments, and will be resolvable with the next generation of gamma-ray telescopes (namely, the Cherenkov Telescope Array)., Comment: 13 pages, 6 figures, accepted to ApJ

Accreting supermassive black holes (SMBHs) frequently power jets that interact with the interstellar/circumgalactic medium (ISM/CGM), regulating star-formation in the galaxy. Highly supersonic jets launched by active galactic nuclei (AGN) power a cocoon that confines them and shocks the ambient medium. We build upon the models of narrow conical jets interacting with a smooth ambient medium, to include the effect of dense clouds that are an essential ingredient of a multiphase ISM. The key physical ingredient of this model is that the clouds along the supersonic jet-beam strongly decelerate the jet-head, but the subsonic cocoon easily moves around the clouds without much resistance. We propose scalings for important physical quantities -- cocoon pressure, head & cocoon speed, and jet radius. We obtain, for the first time, the analytic condition on clumpiness of the ambient medium for the jet to dissipate within the cocoon and verify it with numerical simulations of conical jets interacting with a uniform ISM with embedded spherical clouds. A jet is defined to be dissipated when the cocoon speed exceeds the speed of the jet-head. We compare our models to more sophisticated numerical simulations, direct observations of jet-ISM interaction (e.g., quasar J1316+1753), and discuss implications for the Fermi/eROSITA bubbles. Our work also motivates effective subgrid models for AGN jet feedback in a clumpy ISM unresolved by the present generation of cosmological galaxy formation simulations., Comment: 23 pages, 12 figures, 3 tables; to be submitted; comments are welcome; accompanying video: http://youtu.be/DUpSwMMrGfk

In high-Lundquist-number plasmas, reconnection proceeds via onset of tearing, followed by a nonlinear phase during which plasmoids continuously form, merge, and are ejected from the current sheet (CS). This process is understood in fully ionized, magnetohydrodynamic plasmas. However, many plasma environments, such as star-forming molecular clouds and the solar chromosphere, are poorly ionized. We use theory and computation to study tearing-mediated reconnection in such poorly ionized systems. In this paper, we focus on the onset and linear evolution of this process. In poorly ionized plasmas, magnetic nulls on scales below $v_{\rm A,n0}/\nu_{\rm ni0}$, with $v_{\rm A,n0}$ the neutral Alfv\'{e}n speed and $\nu_{\rm ni0}$ the neutral-ion collision frequency, will self-sharpen via ambipolar diffusion. This sharpening occurs at an increasing rate, inhibiting the onset of reconnection. Once the CS becomes thin enough, however, ions decouple from neutrals and thinning of the CS slows, allowing tearing to onset in a time of order $\nu_{\rm ni0}^{-1}$. We find that the wavelength and growth rate of the mode that first disrupts the forming sheet can be predicted from a poorly ionized tearing dispersion relation; as the plasma recombination rate increases and ionization fraction decreases, the growth rate becomes an increasing multiple of $\nu_{ni0}$ and the wavelength becomes a decreasing fraction of $v_{\rm A,n0}/\nu_{\rm ni0}$., Comment: 19 pages, 13 figures

We report an anti-resonant hollow core fibre with ultraviolet transmission down to 190 nm, covering the entire UV-A, UV-B and much of the UV-C band. Guidance from 190 - 400 nm is achieved apart for a narrow high loss resonance band at 245 - 265 nm. The minimum attenuation is 0.13 dB/m at 235 nm and 0.16 dB/m at 325 nm. With an inscribed core diameter of ~ 12 $\mu$m, the fibre's bend loss at 325 nm was 0.22 dB per turn for a bend radius of 3 cm at 325 nm.

We present a 3-D ideal MHD simulation of magnetospheric accretion onto a non-rotating star. The accretion process unfolds with intricate 3-D structures driven by various mechanisms. First, the disc develops filaments at the magnetospheric truncation radius ($R_T$) due to magnetic interchange instability. These filaments penetrate deep into the magnetosphere, form multiple accretion columns, and eventually impact the star at $\sim$30$^o$ from the poles at nearly the free-fall speed. Over 50% (90%) of accretion occurs on just 5% (20%) of the stellar surface. Second, the disc region outside $R_T$ develops large-scale magnetically dominated bubbles, again due to magnetic interchange instability. These bubbles orbit at a sub-Keplerian speed, persisting for a few orbits while leading to asymmetric mass ejection. The disc outflow is overall weak because of mostly closed field lines. Third, magnetically-supported surface accretion regions appear above the disc, resembling a magnetized disc threaded by net vertical fields, a departure from traditional magnetospheric accretion models. Stellar fields are efficiently transported into the disc region due to above instabilities, contrasting with the ``X-wind'' model. The accretion rate onto the star remains relatively steady with a 23% standard deviation. The periodogram reveals variability occurring at around 0.2 times the Keplerian frequency at $R_T$, linked to the large-scale magnetic bubbles. The ratio of the spin-up torque to $\dot{M}(GM_*R_T)^{1/2}$ is around 0.8. Finally, after scaling the simulation, we investigate planet migration in the inner protoplanetary disc. The disc driven migration is slow in the MHD turbulent disc beyond $R_T$, while aerodynamic drag plays a significant role in migration within $R_T$., Comment: Accepted to MNRAS

The coupling state between ions and neutrals in the interstellar medium plays a key role in the dynamics of magnetohydrodynamic (MHD) turbulence, but is challenging to study numerically. In this work, we investigate the damping of MHD turbulence in a partially ionized medium using 3D two-fluid (ions+neutrals) simulations generated with the AthenaK code. Specifically, we examine the velocity, density, and magnetic field statistics of the two-fluid MHD turbulence in different regimes of neutral-ion coupling. Our results demonstrate that when ions and neutrals are strongly coupled, the velocity statistics resemble those of single-fluid MHD turbulence. Both the velocity structures and kinetic energy spectra of ions and neutrals are similar, while their density structures can be significantly different. With an excess of small-scale sharp density fluctuations in ions, the density spectrum in ions is shallower than that of neutrals. When ions and neutrals are weakly coupled, the turbulence in ions is more severely damped due to the ion-neutral collisional friction than that in neutrals, resulting in a steep kinetic energy spectrum and density spectrum in ions compared to the Kolmogorov spectrum. We also find that the magnetic energy spectrum basically follows the shape of the kinetic energy spectrum of ions, irrespective of the coupling regime. In addition, we find large density fluctuations in ions and neutrals and thus spatially inhomogeneous ionization fractions. As a result, the neutral-ion decoupling and damping of MHD turbulence take place over a range of length scales., Comment: 17 pages, 14 figures, accepted for publication in MNRAS

Chemistry plays a key role in many aspects of astrophysical fluids. Atoms and molecules are agents for heating and cooling, determine the ionization fraction, serve as observational tracers, and build the molecular foundation of life. We present the implementation of a chemistry module in the publicly available magneto-hydrodynamic code Athena++. We implement several chemical networks and heating and cooling processes suitable for simulating the interstellar medium (ISM). A general chemical network framework in the KIDA format is also included, allowing the user to easily implement their own chemistry. Radiation transfer and cosmic-ray ionization are coupled with chemistry and solved with the simple six-ray approximation. The chemical and thermal processes are evolved as a system of coupled ODEs with an implicit solver from the CVODE library. We perform and present a series of tests to ensure the numerical accuracy and convergence of the code. Many tests combine chemistry with gas dynamics, including comparisons with analytic solutions, 1D problems of the photo-dissociation regions and shocks, and realistic 3D simulations of the turbulent ISM. We release the code with the new public version of Athena++, aiming to provide a robust and flexible code for the astrochemical simulation community.

We introduce Mahakala, a Python-based, modular, radiative ray-tracing code for curved space-times. We employ Google's JAX framework for accelerated automatic differentiation, which can efficiently compute Christoffel symbols directly from the metric, allowing the user to easily and quickly simulate photon trajectories through non-Kerr metrics. JAX also enables Mahakala to run in parallel on both CPUs and GPUs and achieve speeds comparable to C-based codes. Mahakala natively uses the Cartesian Kerr-Schild coordinate system, which avoids numerical issues caused by the "pole" of spherical coordinates. We demonstrate Mahakala's capabilities by simulating the 1.3 mm wavelength images (the wavelength of Event Horizon Telescope observations) of general relativistic magnetohydrodynamic simulations of low-accretion rate supermassive black holes. The modular nature of Mahakala allows us to easily quantify the relative contribution of different regions of the flow to image features. We show that most of the emission seen in 1.3 mm images originates close to the black hole. We also quantify the relative contribution of the disk, forward jet, and counter jet to 1.3 mm images., Comment: 15 pages, 11 figures

We describe the implementation of multigrid solvers in the Athena++ adaptive mesh refinement (AMR) framework and their application to the solution of the Poisson equation for self-gravity. The new solvers are built on top of the AMR hierarchy and TaskList framework of Athena++ for efficient parallelization. We adopt a conservative formulation for the Laplacian operator that avoids artificial accelerations at level boundaries. Periodic, fixed, and zero-gradient boundary conditions are implemented, as well as open boundary conditions based on a multipole expansion. Hybrid parallelization using both MPI and OpenMP is adopted, and we present results of tests demonstrating the accuracy and scaling of the methods. On a uniform grid we show multigrid significantly outperforms methods based on FFTs, and requires only a small fraction of the compute time required by the (highly optimized) magnetohydrodynamic solver in Athena++. As a demonstration of the capabilities of the methods, we present the results of a test calculation of magnetized protostellar collapse on an adaptive mesh., Comment: 28 pages, 13 figures, submitted to AAS Journals

We extend the general-relativistic magnetohydrodynamics (GRMHD) capabilities of Athena++ to incorporate radiation. The intensity field in each finite-volume cell is discretized in angle, with explicit transport in both space and angle properly accounting for the effects of gravity on null geodesics, and with matter and radiation coupled in a locally implicit fashion. Here we describe the numerical procedure in detail, verifying its correctness with a suite of tests. Motivated in particular by black hole accretion in the high-accretion-rate, thin-disk regime, we demonstrate the application of the method to this problem. With excellent scaling on flagship computing clusters, the port of the algorithm to the GPU-enabled AthenaK code now allows the simulation of many previously intractable radiation-GRMHD systems., Comment: To be published in ApJS

We present global 3D radiation magnetohydrodynamical simulations of accretion onto a 6.62 solar mass black hole with quasi-steady state accretion rates reaching 0.016 to 0.9 times the critical accretion rate, which is defined as the accretion rate to power the Eddington luminosity assuming a 10% radiative efficiency, in different runs. The simulations show no sign of thermal instability over hundreds of thermal timescales at 10 $r_{\rm g}$. The energy dissipation happens close to the mid-plane in the near-critical runs and near the disk surface in the low accretion rate run. The total radiative luminosity inside $\sim$20 $r_{\rm g}$ is about 1% to 30% the Eddington limit, with a radiative efficiency of about 6% and 3%, respectively, in the sub- and near-critical accretion regimes. In both cases, self-consistent turbulence generated by the magnetorotational instability (MRI) leads to angular momentum transfer, and the disk is supported by magnetic pressure. Outflows from the central low-density funnel with a terminal velocity of $\sim$0.1$c$ are seen only in the near-critical runs. We conclude that these magnetic pressure dominated disks are thermally stable and thicker than the $\alpha$ disk, and the effective temperature profiles are much flatter than that in the $\alpha$ disks. The magnetic pressure of these disks are comparable within an order of magnitude with the previous analytical magnetic pressure dominated disk model., Comment: 17 pages, 13 figures, 3 tables, accepted for publication in ApJ

We present hydrodynamic simulations of the inner few parsecs of the Milky Way's Galactic Center that, for the first time, combine a realistic treatment of stellar winds and the circumnuclear disk as they interact with the gravitational potential of the nuclear star cluster and Sagittarius~A*. We observe a complex interaction of the stellar winds with the inner edge of the circumnuclear disk, which leads to the growth of instabilities, induced accretion of cool gas from the inner edge of the disk, and the eventual formation of a small accretion disk of $\sim 10^4-10^5$ K within $r \sim 0.1$ pc., Comment: 26 pages, 16 figures, (Submitted to ApJ)

Estimating the Shannon information associated with individual neurons is a non-trivial problem. Three key methods used to estimate the mutual information between neuron inputs and outputs are described, and a list of further readings is provided., Comment: 7 pages, 2 figures

We present high-resolution, three-dimensional hydrodynamic simulations of the fueling of supermassive black holes in elliptical galaxies from a turbulent medium on galactic scales, taking M87* as a typical case. The simulations use a new GPU-accelerated version of the Athena++ AMR code, and span more than 6 orders of magnitude in radius, reaching scales similar to the black hole horizon. The key physical ingredients are radiative cooling and a phenomenological heating model. We find that the accretion flow takes the form of multiphase gas at radii less than about a kpc. The cold gas accretion includes two dynamically distinct stages: the typical disk stage in which the cold gas resides in a rotationally supported disk and relatively rare chaotic stages ($\lesssim 10\%$ of the time) in which the cold gas inflows via chaotic streams. Though cold gas accretion dominates the time-averaged accretion rate at intermediate radii, accretion at the smallest radii is dominated by hot virialized gas at most times. The accretion rate scales with radius as $\dot{M}\propto r^{1/2}$ when hot gas dominates and we obtain $\dot{M}\simeq10^\mathrm{-4}-10^\mathrm{-3}\,M_\odot\,\mathrm{yr^{-1}}$ near the event horizon, similar to what is inferred from EHT observations. The orientation of the cold gas disk can differ significantly on different spatial scales. We propose a subgrid model for accretion in lower-resolution simulations in which the hot gas accretion rate is suppressed relative to the Bondi rate by $\sim (r_\mathrm{g}/r_{\rm Bondi})^{1/2}$. Our results can also provide more realistic initial conditions for simulations of black hole accretion at the event horizon scale., Comment: 28 pages, 25 figures, 2 tables, accepted for publication in ApJ

We apply 3D hydrodynamical simulations to study the rotational aspect of gas flow patterns around eccentric companions embedded in an accretion disk around its primary host. We sample a wide range of companion mass ratio q and disk aspect ratio h, and confirm a generic transition from prograde (steady tidal interaction dominated) to retrograde (background Keplerian shear dominated) circum-companion flow when orbital eccentricity exceeds a critical value et. We find et \sim h for sub-thermal companions while et \sim (q/h)^1/3 for super-thermal companions, and propose an empirical formula to unify the two scenarios. Our results also suggest that et is insensitive to modest levels of turbulence, modeled in the form of a kinematic viscosity term. In the context of stellar-mass Black Holes (sBHs) embedded in AGN accretion disks, the bifurcation of their circum-stellar disk (CSD) rotation suggest the formation of a population of nearly anti-aligned sBHs, whose relevance to low spin gravitational waves (GW) events can be probed in more details with future population models of sBH evolution in AGN disks, making use of our quantitative scaling for et; In the context of circum-planetary disks (CPDs), our results suggest the possibility of forming retrograde satellites in-situ in retrograde CPDs around eccentric planets., Comment: Accepted to ApJL, 10 pages, 5 figures

Magnetic fields on the order of 100 $\mu$G observed in young supernova remnants cannot be amplified by shock compression alone. To investigate the amplification caused by turbulent dynamo, we perform three-dimensional MHD simulations of the interaction between shock wave and inhomogeneous density distribution with a shallow spectrum in the preshock medium. The postshock turbulence is mainly driven by the strongest preshock density contrast and follows the Kolmogorov scaling. The resulting turbulence amplifies the postshock magnetic field. The time evolution of the magnetic fields agrees with the prediction of the nonlinear turbulent dynamo theory in Xu & Lazarian (2016). When the initial weak magnetic field is perpendicular to the shock normal, the maximum amplification of the field's strength achieves a factor of $\approx200$, which is twice larger than that for a parallel shock. We find that the perpendicular shock exhibits a smaller turbulent Alfv\'en Mach number in the vicinity of the shock front than the parallel shock. However, the strongest magnetic field has a low volume filling factor and is limited by the turbulent energy due to the reconnection diffusion taking place in a turbulent and magnetized fluid. The magnetic field strength averaged along the $z$-axis is reduced by a factor $\gtrsim10$. We decompose the turbulent velocity and magnetic field into solenoidal and compressive modes. The solenoidal mode is dominant and evolves to follow the Kolmogorov scaling, even though the preshock density distribution has a shallow spectrum. When the preshock density distribution has a Kolmogorov spectrum, the turbulent velocity's compressive component increases., Comment: 19 pages, 15 figures, accepted for publication in ApJ

On the path to exascale the landscape of computer device architectures and corresponding programming models has become much more diverse. While various low-level performance portable programming models are available, support at the application level lacks behind. To address this issue, we present the performance portable block-structured adaptive mesh refinement (AMR) framework Parthenon, derived from the well-tested and widely used Athena++ astrophysical magnetohydrodynamics code, but generalized to serve as the foundation for a variety of downstream multi-physics codes. Parthenon adopts the Kokkos programming model, and provides various levels of abstractions from multi-dimensional variables, to packages defining and separating components, to launching of parallel compute kernels. Parthenon allocates all data in device memory to reduce data movement, supports the logical packing of variables and mesh blocks to reduce kernel launch overhead, and employs one-sided, asynchronous MPI calls to reduce communication overhead in multi-node simulations. Using a hydrodynamics miniapp, we demonstrate weak and strong scaling on various architectures including AMD and NVIDIA GPUs, Intel and AMD x86 CPUs, IBM Power9 CPUs, as well as Fujitsu A64FX CPUs. At the largest scale on Frontier (the first TOP500 exascale machine), the miniapp reaches a total of $1.7\times10^{13}$ zone-cycles/s on 9,216 nodes (73,728 logical GPUs) at ~92% weak scaling parallel efficiency (starting from a single node). In combination with being an open, collaborative project, this makes Parthenon an ideal framework to target exascale simulations in which the downstream developers can focus on their specific application rather than on the complexity of handling massively-parallel, device-accelerated AMR., Comment: 17 pages, 11 figures, accepted for publication in IJHPCA, Codes available at https://github.com/parthenon-hpc-lab

Evolutionary theory predicts that children fare better if they resemble their father. However, if a man is promiscuous then his children tend to be (unwittingly) raised within other families; such children should fare better if they do not resemble their father. This suggests that father-son facial similarity should decrease as a function of male promiscuity. To test this hypothesis, the degree of similarity between each of 37 pairs of father-son photographs was rated by 83 participants. The promiscuity score of a father was defined as the number of sexual relationships he had been involved in. A linear regression of father-son similarity ratings against fathers' promiscuity scores indicated that the slope of the fitted line was significantly less than zero (slope=-0.176, p < 0.001), and that fathers' promiscuity scores account for 75% of the variance father-son facial similarity ratings. Additionally, a significant negative non-parametric correlation (Spearman's rho rho=-0.886, p=0.019) between father-son similarity ratings and fathers' promiscuity scores was found.

Most psychophysical experiments discard half the data collected. Specifically, experiments discard reaction time data, and use binary responses (e.g. yes/no) to measure performance. Here, Shannon's information theory is used to define Shannon competence $s'$, which depends on the mutual information between stimulus strength (e.g. luminance) and a combination of reaction times and binary responses. Mutual information is the entropy of the joint distribution of responses minus the residual entropy after a model has been fitted to these responses. Here, this model is instantiated as a proportional rate diffusion model, with the additional innovation that the full covariance structure of responses is taken into account. Results suggest information associated with reaction times is independent of (i.e. additional to) information associated with binary responses, and that reaction time and binary responses together provide substantially more than the sum of their individual contributions (i.e. they act synergistically). Consequently, the additional information supplied by reaction times suggests that using combined reaction time and binary responses requires fewer stimulus presentations, without loss of precision in psychophysical parameters. Finally, because s' takes account of both reaction time and binary responses, (and in contrast to d') $s'$ is immune to speed-accuracy trade-offs, which vary between observers and experimental designs.

Using the shifted-excitation Raman difference spectroscopy technique and an optical fibre featuring a negative curvature excitation core and a coaxial ring of high numerical aperture collection cores, we have developed a portable, background and fluorescence free, endoscopic Raman probe. The probe consists of a single fibre with a diameter of less than 0.25 mm packaged in a sub-millimetre tubing, making it compatible with standard bronchoscopes. The Raman excitation light in the fibre is guided in air and therefore interacts little with silica, enabling an almost background free transmission of the excitation light. In addition, we used the shifted-excitation Raman difference spectroscopy technique and a tunable 785 nm laser to separate the fluorescence and the Raman spectrum from highly fluorescent samples, demonstrating the suitability of the probe for biomedical applications. Using this probe we also acquired fluorescence free human lung tissue data.

The dynamical evolution of protoplanetary disks is of key interest for building a comprehensive theory of planet formation and to explain the observational properties of these objects. Using the magnetohydrodynamics code Athena++, with an isothermal shearing box setup, we study the boundary between the active and dead zone, where the accretion rate changes and mass can accumulate. We quantify how the turbulence level is affected by the presence of a non uniform ohmic resistivity in the radial-x direction that leads to a region of inhibited turbulence (or dead zone). Comparing the turbulent activity to that of ideal simulations, the turbulence inhibited area shows density fluctuations and magnetic activity at its boundaries, driven by energy injection from the active (ideal) zone boundaries. We find magnetic dissipation to be significantly stronger in the ideal regions, and the turbulence penetration through the boundary of the dead zone is determined by the value of the resistivity itself, through the ohmic dissipation process, though the thickness of the transition does not play a significant role in changing the dissipation. We investigate the 1D spectra along the shearing direction: magnetic spectra appear flat at large scales both in ideal as well as resistive simulations, though a Kolmogorov scaling over more than one decade persists in the dead zone, suggesting the turbulent cascade is determined by the hydrodynamics of the system: MRI dynamo action is inhibited where sufficiently high resistivity is present., Comment: 11 pages 12 figures

We present results of the first global magnetohydrodynamic (MHD) simulations of accretion disks fed by Roche lobe overflow, including vertical stratification, in order to investigate the roles of spiral shocks, magnetorotational instability (MRI), and the accretion stream on disk structure and evolution. Our models include a simple treatment of gas thermodynamics, with orbital Mach numbers at the inner edge of the disk $M_{\rm in}$ of 5 and 10. We find mass accretion rates to vary considerably on all time scales, with only the Mach 5 model reaching a clear quasi-stationary state. For Mach 10, the model undergoes an outside-in magnetically-driven accretion event occurring on a time scale of $\sim10$ orbital periods of the binary. Both models exhibit spiral shocks inclined with respect to the binary plane, with their position and inclination changing rapidly. However, the time-averaged location of these shocks in the equatorial plane is well-fit by simple linear models. MRI turbulence in the disk generates toroidal magnetic field patterns (butterfly diagrams) that are in some cases irregular, perhaps due to interaction with spiral structure. While many of our results are in good agreement with local studies, we find some features (most notably those related to spiral shocks) can only be captured in global models such as studied here. Thus, while global studies remain computationally expensive -- even as idealized models -- they are essential (along with more sophisticated treatment of radiation transport and disk thermodynamics) for furthering our understanding of accretion in binary systems., Comment: 30 pages, 13 figures; Accepted for publication in ApJ

We present cosmological hydrodynamic simulations of a quasar-mass halo ($M_{\rm halo} \approx 10^{12.5}\,{\rm M}_{\odot}$ at z=2) that for the first time resolve gas transport down to the inner 0.1 pc surrounding the central massive black hole. We model a multi-phase interstellar medium including stellar feedback by supernovae, stellar winds, and radiation, and a hyper-Lagrangian refinement technique increasing the resolution dynamically approaching the black hole. We do not include black hole feedback. We show that the sub-pc inflow rate (1) can reach ~6 M$_{\odot}$yr$^{-1}$ roughly in steady state during the epoch of peak nuclear gas density (z~2), sufficient to power a luminous quasar, (2) is highly time variable in the pre-quasar phase, spanning 0.001-10 M$_{\odot}$yr$^{-1}$ on Myr timescales, and (3) is limited to short (~2 Myr) active phases (0.01-0.1 M$_{\odot}$yr$^{-1}$) followed by longer periods of inactivity at lower nuclear gas density and late times (z~1), owing to the formation of a hot central cavity. Inflowing gas is primarily cool, rotational support dominates over turbulence and thermal pressure, and star formation can consume as much gas as provided by inflows across 1 pc - 10 kpc. Gravitational torques from multi-scale stellar non-axisymmetries dominate angular momentum transport over gas self-torquing and pressure gradients, with accretion weakly dependent on black hole mass. Sub-pc inflow rates correlate with nuclear (but decouple from global) star formation and can exceed the Eddington rate by x10. The black hole can move ~10 pc from the galaxy center on ~0.1 Myr. Accreting gas forms pc-scale, rotationally supported, obscuring structures often misaligned with the galaxy-scale disk. These simulations open a new avenue to investigate black hole-galaxy co-evolution., Comment: 34 pages, 23 figures, ApJ accepted

In the cold neutral medium, high out-of-equilibrium temperatures are created by intermittent dissipation processes, including shocks, viscous heating, and ambipolar diffusion. The high-temperature excursions are thought to explain the enhanced abundance of CH$^{+}$ observed along diffuse molecular sight-lines. Intermittent high temperatures should also have an impact on H$_2$ line luminosities. We carry out simulations of MHD turbulence in molecular clouds including heating and cooling, and post-process them to study H$_2$ line emission and hot-gas chemistry, particularly the formation of CH$^+$. We explore multiple magnetic field strengths and equations of state. We use a new H$_2$ cooling function for $n_{\rm H} \leq 10^5\,{\rm cm}^{-3}$, $T\leq 5000\,{\rm K}$, and variable H$_2$ fraction. We make two important simplifying assumptions: (i) the ${\rm H}_2/{\rm H}$ fraction is fixed everywhere, and (ii) we exclude from our analysis regions where the ion-neutral drift velocity is calculated to be greater than 5 km/s. Our models produce H$_2$ emission lines in accord with many observations, although extra excitation mechanisms are required in some clouds. For realistic r.m.s. magnetic field strengths ($\approx 10$ $\mu$G) and velocity dispersions, we reproduce observed CH$^+$ abundances. These findings contrast with those of Valdivia et al. (2017). Comparison of predicted dust polarization with observations by {\it Planck} suggests that the mean field $\gtrsim 5 \mu$G, so that the turbulence is sub-Alfv\'enic. We recommend future work treating ions and neutrals as separate fluids to more accurately capture the effects of ambipolar diffusion on CH$^+$ abundance., Comment: 20 pages, 18 figures, accepted for publication to MNRAS

Similarity-driven multi-view linear reconstruction (SiMLR) is an algorithm that exploits inter-modality relationships to transform large scientific datasets into smaller, more well-powered and interpretable low-dimensional spaces. SiMLR contributes a novel objective function for identifying joint signal, regularization based on sparse matrices representing prior within-modality relationships and an implementation that permits application to joint reduction of large data matrices, each of which may have millions of entries. We demonstrate that SiMLR outperforms closely related methods on supervised learning problems in simulation data, a multi-omics cancer survival prediction dataset and multiple modality neuroimaging datasets. Taken together, this collection of results shows that SiMLR may be applied with default parameters to joint signal estimation from disparate modalities and may yield practically useful results in a variety of application domains., Comment: accepted to Nature Computational Science

We present 3D general relativistic magnetohydrodynamic (GRMHD) simulations of the accretion flow surrounding Sagittarius A* that are initialized using larger-scale MHD simulations of the $\sim$ 30 Wolf--Rayet (WR) stellar winds in the Galactic center. The properties of the resulting accretion flow on horizon scales are set not by ad hoc initial conditions but by the observationally constrained properties of the WR winds with limited free parameters. For this initial study we assume a non-spinning black hole. Our simulations naturally produce a $\sim 10^{-8} M_\odot$ yr$^{-1}$ accretion rate, consistent with previous phenomenological estimates. We find that a magnetically arrested flow is formed by the continuous accretion of coherent magnetic field being fed from large radii. Near the event horizon, the magnetic field is so strong that it tilts the gas with respect to the initial angular momentum and concentrates the originally quasi-spherical flow to a narrow disk-like structure. We also present 230 GHz images calculated from our simulations where the inclination angle and physical accretion rate are not free parameters but are determined by the properties of the WR stellar winds. The image morphology is highly time variable. Linear polarization on horizon scales is coherent with weak internal Faraday rotation., Comment: Accepted by ApJL. 14 pages, 8 figures. Animations available at https://smressle.bitbucket.io/animations.html

The design and implementation of a new framework for adaptive mesh refinement (AMR) calculations is described. It is intended primarily for applications in astrophysical fluid dynamics, but its flexible and modular design enables its use for a wide variety of physics. The framework works with both uniform and nonuniform grids in Cartesian and curvilinear coordinate systems. It adopts a dynamic execution model based on a simple design called a "task list" that improves parallel performance by overlapping communication and computation, simplifies the inclusion of a diverse range of physics, and even enables multiphysics models involving different physics in different regions of the calculation. We describe physics modules implemented in this framework for both non-relativistic and relativistic magnetohydrodynamics (MHD). These modules adopt mature and robust algorithms originally developed for the Athena MHD code and incorporate new extensions: support for curvilinear coordinates, higher-order time integrators, more realistic physics such as a general equation of state, and diffusion terms that can be integrated with super-time-stepping algorithms. The modules show excellent performance and scaling, with well over 80% parallel efficiency on over half a million threads. The source code has been made publicly available., Comment: 50 pages, 41 figures, accepted for publication in American Astronomical Society journals

We study the flow structure in 3D magnetohydrodynamic (MHD) simulations of accretion onto Sagittarius A* via the magnetized winds of the orbiting Wolf-Rayet stars. These simulations cover over 3 orders of magnitude in radius to reach $\approx$ 300 gravitational radii, with only one poorly constrained parameter (the magnetic field in the stellar winds). Even for winds with relatively weak magnetic fields (e.g., plasma $\beta$ $\sim$ $10^6$), flux freezing/compression in the inflowing gas amplifies the field to $\beta$ $\sim$ few well before it reaches the event horizon. Overall, the dynamics, accretion rate, and spherically averaged flow profiles (e.g., density, velocity) in our MHD simulations are remarkably similar to analogous hydrodynamic simulations. We attribute this to the broad distribution of angular momentum provided by the stellar winds, which sources accretion even absent much angular momentum transport. We find that the magneto-rotational instability is not important because of i) strong magnetic fields that are amplified by flux freezing/compression, and ii) the rapid inflow/outflow times of the gas and inefficient radiative cooling preclude circularization. The primary effect of magnetic fields is that they drive a polar outflow that is absent in hydrodynamics. The dynamical state of the accretion flow found in our simulations is unlike the rotationally supported tori used as initial conditions in horizon scale simulations, which could have implications for models being used to interpret Event Horizon Telescope and GRAVITY observations of Sgr A*., Comment: Accepted by MNRAS; 22 pages; 24 figures, comments welcome

FU Ori is the prototype of FU Orionis systems which are outbursting protoplanetary disks. Magnetic fields in FU Ori's accretion disks have previously been detected using spectropolarimetry observations for Zeeman effects. We carry out global radiation ideal MHD simulations to study FU Ori's inner accretion disk. We find that (1) when the disk is threaded by vertical magnetic fields, most accretion occurs in the magnetically dominated atmosphere at z$\sim$R, similar to the "surface accretion" mechanism in previous locally-isothermal MHD simulations. (2) A moderate disk wind is launched in the vertical field simulations with a terminal speed of $\sim$300-500 km/s and a mass loss rate of 1-10\% the disk accretion rate, which is consistent with observations. Disk wind fails to be launched in simulations with net toroidal magnetic fields. (3) The disk photosphere at the unit optical depth can be either in the wind launching region or the accreting surface region. Magnetic fields have drastically different directions and magnitudes between these two regions. Our fiducial model agrees with previous optical Zeeman observations regarding both the field directions and magnitudes. On the other hand, simulations indicate that future Zeeman observations at near-IR wavelengths or towards other FU Orionis systems may reveal very different magnetic field structures. (4) Due to energy loss by the disk wind, the disk photosphere temperature is lower than that predicted by the thin disk theory, and the previously inferred disk accretion rate may be lower than the real accretion rate by a factor of $\sim$2-3., Comment: 22 pages, 20 figures, accepted by MNRAS

We use 2D (axisymmetric) and 3D hydrodynamic simulations to study Bondi-Hoyle-Lyttleton (BHL) accretion with and without transverse upstream gradients. We mainly focus on the regime of high (upstream) Mach number, weak upstream gradients and small accretor size, which is relevant to neutron star (NS) accretion in wind-fed Supergiant X-ray binaries (SgXBs). We present a systematic exploration of the flow in this regime. When there are no upstream gradients, the flow is always stable regardless of accretor size or Mach number. For finite upstream gradients, there are three main types of behavior: stable flow (small upstream gradient), turbulent unstable flow without a disk (intermediate upstream gradient), and turbulent flow with a disk-like structure (relatively large upstream gradient). When the accretion flow is turbulent, the accretion rate decreases non-convergently as the accretor size decreases. The flow is more prone to instability and the disk is less likely to form than previously expected; the parameters of most observed SgXBs place them in the regime of a turbulent, disk-less accretion flow. Among the SgXBs with relatively well-determined parameters, we find OAO 1657-415 to be the only one that is likely to host a persistent disk (or disk-like structure); this finding is consistent with observations., Comment: 25 pages, 28 figures, 2 tables. Accepted by MNRAS

Recent high resolution observations unveil ring structures in circumstellar disks. The origin of these rings has been widely investigated under various theoretical scenarios. In this work we perform global 3D non-ideal MHD simulations including effects from both Ohmic resistivity and ambipolar diffusion (AD) to model the HL Tau disk. The non-ideal MHD diffusion profiles are calculated based on the global dust evolution calculation including sintering effects. Disk ionization structure changes dramatically across the snow line due to the change of dust size distribution close to snow line of major volatiles. We find that accretion is mainly driven by disk wind. Gaps and rings can be quickly produced from different accretion rates across snow line. Furthermore, ambipolar diffusion (AD) leads to highly preferential accretion at midplane, followed by magnetic reconnection. This results a local zone of decretion that drains of mass in the field reconnection area, which leaves a gap and an adjacent ring just outside it. Overall, under the favorable condition, both snow lines and non-ideal MHD effects can lead to gaseous gaps and rings in protoplanetary disks., Comment: 13 pages, 10 figures, published on ApJ

Recent developments in compact object astrophysics, especially the discovery of merging neutron stars by LIGO, the imaging of the black hole in M87 by the Event Horizon Telescope (EHT) and high precision astrometry of the Galactic Center at close to the event horizon scale by the GRAVITY experiment motivate the development of numerical source models that solve the equations of general relativistic magnetohydrodynamics (GRMHD). Here we compare GRMHD solutions for the evolution of a magnetized accretion flow where turbulence is promoted by the magnetorotational instability from a set of nine GRMHD codes: Athena++, BHAC, Cosmos++, ECHO, H-AMR, iharm3D, HARM-Noble, IllinoisGRMHD and KORAL. Agreement between the codes improves as resolution increases, as measured by a consistently applied, specially developed set of code performance metrics. We conclude that the community of GRMHD codes is mature, capable, and consistent on these test problems., Comment: Accepted version for publication in ApJS (May 28th, 2019)

We use global three dimensional radiation magneto-hydrodynamic simulations to study the properties of inner regions of accretion disks around a 5\times 10^8 solar mass black hole with mass accretion rates reaching 7% and 20% of the Eddington value. This region of the disk is supported by magnetic pressure with surface density significantly smaller than the values predicted by the standard thin disk model but with a much larger disk scale height. The disks do not show any sign of thermal instability over many thermal time scales. More than half of the accretion is driven by radiation viscosity in the optically thin corona region for the lower accretion rate case, while accretion in the optically thick part of the disk is driven by the Maxwell and Reynolds stresses from MRI turbulence. Coronae with gas temperatures > 10^8 K are generated only in the inner \approx 10 gravitational radii in both simulations, being more compact in the higher accretion rate case. In contrast to the thin disk model, surface density increases with increasing mass accretion rate, which causes less dissipation in the optically thin region and a relatively weaker corona. The simulation results may explain the formation of X-ray coronae in Active Galactic Nuclei (AGNs), the compact size of such coronae, and the observed trend of optical to X-ray luminosity with Eddington ratio for many AGNs., Comment: 13 pages, 12 figures, submitted to ApJ

We investigate numerical convergence in simulations of magnetically arrested disks around spinning black holes. Using the general-relativistic magnetohydrodynamics code Athena++, we study the same system at four resolutions (up to an effective 512 by 256 by 512 cells) and with two different spatial reconstruction algorithms. The accretion rate and general large-scale structure of the flow agree across the simulations. This includes the amount of magnetic flux accumulated in the saturated state and the ensuing suppression of the magnetorotational instability from the strong field. The energy of the jet and the efficiency with which spin energy is extracted via the Blandford-Znajek process also show convergence. However the spatial structure of the jet shows variation across the set of grids employed, as do the Lorentz factors. Small-scale features of the turbulence, as measured by correlation lengths, are not fully converged. Despite convergence of a number of aspects of the flow, modeling of synchrotron emission shows that variability is not converged and decreases with increasing resolution even at our highest resolutions., Comment: 19 pages, 18 figures, to be published in ApJ

Gaseous disks have been proposed as a mechanism for facilitating mergers of binary black holes. We explore circumbinary disk systems to determine the evolution of the central binary. To do so, we perform 3D, hydrodynamic, locally isothermal simulations of circumbinary disks on a Cartesian grid. We focus on binaries of equal mass ratios on fixed circular orbits. To investigate the orbital evolution of the binary, we examine the various torques exerted on the system. For the case where the disk plane and binary orbital plane are aligned, we find that the total torque is positive so that the semi-major axis of the binary increases. For the misaligned case, we run simulations with the binary orbital plane and disk midplane misaligned by 45\degree and find the same results - the binary grows. The timescale for the circumbinary disk to realign to the plane of the binary is consistent with the global viscous timescale of the disk., Comment: Accepted to ApJ. 13 pages, 19 figures

The gyro-resonant cosmic-ray (CR) streaming instability is believed to play a crucial role in CR transport, leading to growth of Alfv\'en waves at small scales that scatter CRs, and impacts the interaction of CRs with the ISM on large scales. However, extreme scale separation ($\lambda \ll \rm pc$), low cosmic ray number density ($n_{\rm CR}/n_{\rm ISM} \sim 10^{-9}$), and weak CR anisotropy ($\sim v_A/c$) pose strong challenges for proper numerical studies of this instability on a microphysical level. Employing the recently developed magnetohydrodynamic-particle-in-cell (MHD-PIC) method, which has unique advantages to alleviate these issues, we conduct one-dimensional simulations that quantitatively demonstrate the growth and saturation of the instability in the parameter regime consistent with realistic CR streaming in the large-scale ISM. Our implementation of the $\delta f$ method dramatically reduces Poisson noise and enables us to accurately capture wave growth over a broad spectrum, equally shared between left and right handed Alfv\'en modes. We are also able to accurately follow the quasi-linear diffusion of CRs subsequent to wave growth, which is achieved by employing phase randomization across periodic boundaries. Full isotropization of the CRs in the wave frame requires pitch angles of most CRs to efficiently cross $90^\circ$, and can be captured in simulations with relatively high wave amplitude and/or high spatial resolution. We attribute this crossing to non-linear wave-particle interaction (rather than mirror reflection) by investigating individual CR trajectories. We anticipate our methodology will open up opportunities for future investigations that incorporate additional physics., Comment: 34 pages, 28 figures, submitted to ApJ

The prevalence of binary stars at close separations implies that many of these systems will interact or merge during the binary's lifetime. This paper presents hydrodynamic simulations of the scenario of binary coalescence through unstable mass transfer, which drives the pair to closer separations. When the donor star does not rotate synchronously with respect to the orbit, dynamical tidal waves are excited in its envelope. We show that resonance crossings with high azimuthal-order $(m\sim3$ to $6$) fundamental modes induce a visible "polygram" distortion to the star. As the binary orbit tightens, the system sweeps through resonance with modes of decreasing azimuthal order, which are selectively excited. We compare our hydrodynamic simulations to predictions from linear theory of resonant mode excitation. The linear theory provides an estimate of mode amplitudes to within a factor of two, even as the oscillations become quite non-linear as the stars coalesce. We estimate that a wave with 10% radial amplitude generates approximately 1% photometric variability; this may be detectible if such a binary coalescence is caught in action by future photometric all-sky surveys., Comment: Submitted to AAS Journals. Comments for revision are welcome

The observed rotation measures (RMs) towards the galactic centre magnetar and towards Sagittarius A* provide a strong constraint on MHD models of the galactic centre accretion flow, probing distances from the black hole separated by many orders of magnitude. We show, using 3D simulations of accretion via magnetized stellar winds of the Wolf-Rayet stars orbiting the black hole, that the large, time-variable RM observed for the pulsar PSR J1745-2900 can be explained by magnetized wind-wind shocks of nearby stars in the clockwise stellar disc. In the same simulation, both the total X-ray luminosity integrated over 2-10$''$, the time variability of the magnetar's dispersion measure, and the RM towards Sagittarius A* are consistent with observations. We argue that (in order for the large RM of the pulsar to not be a priori unlikely) the pulsar should be on an orbit that keeps it near the clockwise disc of stars. We present a 2D RM map of the central 1/2 parsec of the galactic centre that can be used to test our models. Our simulations predict that Sgr A* is typically accreting a significantly ordered magnetic field that ultimately could result in a strongly magnetized flow with flux threading the horizon at $\sim$ 10$\%$ of the magnetically arrested limit., Comment: Accepted into MNRAS Letters. Comments welcome