bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring dynamical masses from gas kinematics in simulated high-redshift galaxies
Authors: Wellons Sarah , Faucher-Giguère Claude-André , Anglés-Alcázar Daniel , Hayward Christopher C , Feldmann Robert , Hopkins Philip F , Kereš Dušan 
Published: August 2020

ABSTRACT
Advances in instrumentation have recently extended detailed measurements of gas kinematics to large samples of high-redshift galaxies. Relative to most nearby, thin disc galaxies, in which gas rotation accurately traces the gravitational potential, the interstellar medium (ISM) of $z$ ≳ 1 galaxies is typically more dynamic and exhibits elevated turbulence. If not properly modelled, these effects can strongly bias dynamical mass measurements. We use high-resolution FIRE-2 cosmological zoom-in simulations to analyse the physical effects that must be considered to correctly infer dynamical masses from gas kinematics. Our analysis covers a range of galaxy properties from low-redshift Milky-Way-mass galaxies to massive high-redshift galaxies (M⋆ &gt; 1011 M⊙ at $z$ = 1). Selecting only snapshots where a disc is present, we calculate the rotational profile $\bar{v}_\phi (r)$ of the cool ($10^{3.5}\,\lt {\it T}\lt 10^{4.5}~\rm {K}$) gas and compare it to the circular velocity $v_{\rm c}=\sqrt{GM_{\rm enc}/r}$. In the simulated galaxies, the gas rotation traces the circular velocity at intermediate radii, but the two quantities diverge significantly in the centre and in the outer disc. Our simulations appear to over-predict observed rotational velocities in the centres of massive galaxies (likely from a lack of black hole feedback), so we focus on larger radii. Gradients in the turbulent pressure at these radii can provide additional radial support and bias dynamical mass measurements low by up to 40 per cent. In both the interior and exterior, the gas’ motion can be significantly non-circular due to e.g. bars, satellites, and inflows/outflows. We discuss the accuracy of commonly used analytic models for pressure gradients (or ‘asymmetric drift’) in the ISM of high-redshift galaxies.
From parallel to perpendicular – On the orientation of magnetic fields in molecular clouds
Authors: Seifried D , Walch S , Weis M , Reissl S , Soler J D , Klessen R S , Joshi P R 
Published: August 2020

ABSTRACT
We present synthetic dust polarization maps of simulated molecular clouds with the goal to systematically explore the origin of the relative orientation of the magnetic field ($\mathbf {B}$) with respect to the cloud sub-structure identified in density (n; 3D) and column density (N; 2D). The polarization maps are generated with the radiative transfer code polaris, which includes self-consistently calculated efficiencies for radiative torque alignment. The molecular clouds are formed in two sets of 3D magnetohydrodynamical simulations: (i) in colliding flows (CF), and (ii) in the SILCC-Zoom simulations. In 3D, for the CF simulations with an initial field strength below ∼5 μG, $\mathbf {B}$ is oriented either parallel or randomly with respect to the n-structures. For CF runs with stronger initial fields as well as all SILCC-Zoom simulations, which have an initial field strength of 3 μG, a flip from parallel to perpendicular orientation occurs at high densities of $n_\rm {trans}\, \simeq$ 102–103 cm−3. We suggest that this flip happens if the cloud’s mass-to-flux ratio, μ, is close to or below the critical value of 1. This corresponds to a field strength around 3–5 μG, close to the Galactic average. In 2D, we use the method of Projected Rayleigh Statistics (PRS) to study the relative orientation of $\mathbf {B}$. If present, the flip in orientation occurs in the projected maps at $N_\rm {trans}\, \simeq$ 1021 − 21.5 cm−2. This value is similar to the observed transition value from sub- to supercritical magnetic fields in the interstellar medium. However, projection effects can strongly reduce the predictive power of the PRS method: Depending on the considered cloud or line-of-sight, the projected maps of the SILCC-Zoom simulations do not always show the flip, although it is expected given the 3D morphology. Such projection effects can explain the variety of recently observed field configurations, in particular within a single cloud. Finally, we do not find a correlation between the observed orientation of $\mathbf {B}$ and the N-PDF.
Modelling the asymmetry of the halo cross-correlation function with relativistic effects at quasi-linear scales
Authors: Saga Shohei , Taruya Atsushi , Breton Michel-Andrès , Rasera Yann 
Published: August 2020

ABSTRACT
The observed galaxy distribution via galaxy redshift surveys appears distorted due to redshift-space distortions (RSD). While one dominant contribution to RSD comes from the Doppler effect induced by the peculiar velocity of galaxies, the relativistic effects, including the gravitational redshift effect, are recently recognized to give small but important contributions. Such contributions lead to an asymmetric galaxy clustering along the line of sight, and produce non-vanishing odd multipoles when cross-correlating between different biased objects. However, non-zero odd multipoles are also generated by the Doppler effect beyond the distant-observer approximation, known as the wide-angle effect, and at quasi-linear scales, the interplay between wide-angle and relativistic effects becomes significant. In this paper, based on the formalism developed by Taruya et al., we present a quasi-linear model of the cross-correlation function taking a proper account of both the wide-angle and gravitational redshift effects, as one of the major relativistic effects. Our quasi-linear predictions of the dipole agree well with simulations even at the scales below $20\, h^{-1}\,$Mpc, where non-perturbative contributions from the halo potential play an important role, flipping the sign of the dipole amplitude. When increasing the bias difference and redshift, the scale where the sign flip happens is shifted to a larger scale. We derive a simple approximate formula to quantitatively account for the behaviours of the sign flip.
Rapid filamentary accretion as the origin of extended thin discs
Authors: Kretschmer Michael , Agertz Oscar , Teyssier Romain 
Published: August 2020

ABSTRACT
Galactic outflows driven by stellar feedback are crucial for explaining the inefficiency of star formation in galaxies. Although strong feedback can promote the formation of galactic discs by limiting star formation at early times and removing low angular momentum (AM) gas, it is not understood how the same feedback can result in diverse objects such as elliptical galaxies or razor thin spiral galaxies. We investigate this problem using cosmological zoom-in simulations of two galaxies forming within 1012 M⊙ haloes with almost identical mass accretion histories and halo spin parameters. However, the two resulting galaxies end up with very different bulge-to-disc ratios at z = 0. At z &gt; 1.5, the two galaxies feature a surface density of star formation ΣSFR ≃ 10 M⊙ yr−1 kpc−2, leading to strong outflows. After the last starburst episode, both galaxies feature a dramatic gaseous disc growth from 1 to 5 kpc during 1 Gyr, a decisive event we dub ‘the Grand Twirl’. After this event, the evolutionary tracks diverge strongly, with one galaxy ending up as a bulge-dominated galaxy, whereas the other ends up as a disc-dominated galaxy. The origins of this dichotomy are the AM of the accreted gas, and whether it adds constructively to the initial disc angular momentum. The build-up of this extended disc leads to a rapid lowering of ΣSFR by over two orders of magnitude with ΣSFR ≲ 0.1 M⊙ yr−1 kpc−2, in remarkable agreement with what is derived from Milky Way stellar populations. As a consequence, supernovae explosions are spread out and cannot launch galactic outflows anymore, allowing for the persistence of a thin, gently star-forming, extended disc.
Methanol and glycolaldehyde production from formaldehyde in massive star-forming regions
Authors: Silva Silvia G S , Vichietti Rafael M , Haiduke Roberto L A , Machado Francisco B C , Spada Rene F K 
Published: August 2020

ABSTRACT
Based on typical physical and chemical conditions expected in massive and dense hot cores during the protostar collapse, the formation of glycolaldehyde (CH2OHCHO) and methanol (CH3OH) was investigated from H2 and CO and formaldehyde (H2CO) as an intermediate. Thermochemical properties and rate constants were obtained for gas-phase reactions using high-level electronic structure methods and chemical kinetic calculations, and the concentrations of the molecules were evolved along time. The chemical equilibrium was reached in minutes at 1500 K, a time interval much shorter than that required time for a protostar formation process. The results indicate that the formaldehyde and methanol abundances are always larger than those for glycolaldehyde, for example, at 2000 K and [H2]0 equals to 1023 molecule cm−3, the abundances of H2CO, CH3OH, and CH2OHCHO relative to H2 are equal to 3 × 10−6, 5 × 10−6, and 1 × 10−12, while for [H2]0 equals to 1020 molecule cm−3 these abundances are 3 × 10−9, 5 × 10−12, and 2 × 10−21, respectively. Considering that our results can be applied to explain the proximity of methanol and formaldehyde maser emissions, from the whole set of results, the CH3OH abundance relative to H2CO ranges from 10−3 to 102.
Soft X-ray emission lines in the X-ray binary Swift J1858.6–0814 observed with XMM–Newton Reflection Grating Spectrometer: disc atmosphere or wind?
Authors: Buisson D J K , Altamirano D , Díaz Trigo M , Mendez M , Armas Padilla M , Castro Segura N , Degenaar N D , van den Eijnden J , Fogantini F A , Gandhi P , Knigge C , Muñoz-Darias T , Özbey Arabacı M , Vincentelli F M 
Published: August 2020

ABSTRACT
We find soft X-ray emission lines from the X-ray binary Swift J1858.6–0814 in data from XMM–NewtonReflection Grating Spectrometer (RGS): N vii, O vii, and O viii, as well as notable residuals short of a detection at Ne ix and other higher ionization transitions. These could be associated with the disc atmosphere, as in accretion disc corona sources, or with a wind, as has been detected in Swift J1858.6–0814 in emission lines at optical wavelengths. Indeed, the N vii line is redshifted, consistent with being the emitting component of a P-Cygni profile. We find that the emitting plasma has an ionization parameter log (ξ) = 1.35 ± 0.2 and a density n &gt; 1.5 × 1011 cm−3. From this, we infer that the emitting plasma must be within 1013 cm of the ionizing source, ∼5 × 107 rg for a 1.4 M⊙ neutron star, and from the line width that it is at least 104 rg away [2 × 109(M/1.4 M⊙) cm]. We compare this with known classes of emission-line regions in other X-ray binaries and active galactic nuclei.
Electron–positron pair plasma in TXS 0506+056 and the ‘neutrino flare’ in 2014–2015
Authors: Fraija N , Aguilar-Ruiz E , Galván-Gámez A 
Published: August 2020

ABSTRACT
The detection of a prolonged flaring activity from blazar TXS 0506+056 in temporal and spatial coincidence with the energetic neutrino IceCube-170922A provided evidence about the photohadronic interactions in this source. However, analysis of the archival neutrino and multiwavelength data from the direction of this blazar between 2014 September and 2015 March revealed a ‘neutrino flare’ without observing quasi-simultaneous activity in the gamma-ray bands, posing challenges to established models. Electron–positron (e±) pairs generated from the accretion discs have been amply proposed as a mechanism of bulk acceleration of sub-relativistic and relativistic jets. These pairs annihilate inside the source producing a line around the electron mass, which is blueshifted in the observed frame (on Earth) and redshifted in the frame of the dissipation region of the jet. The redshifted photons in the dissipation region interact with accelerated protons, producing high-energy neutrinos that contribute significantly to the diffuse neutrino flux in the ∼10–20 TeV energy range in connection with gamma-rays from the photopion process, which can be detected by future MeV orbiting satellites. Based on this phenomenological model, we can explain the ‘neutrino flare’ reported in 2014–1015.
Completeness of the Gaia verse II: what are the odds that a star is missing from Gaia DR2?
Authors: Boubert Douglas , Everall Andrew 
Published: August 2020

ABSTRACT
The second data release of the Gaia mission contained astrometry and photometry for an incredible 1692 919 135 sources, but how many sources did Gaiamiss and where do they lie on the sky? The answer to this question will be crucial for any astronomer attempting to map the Milky Way with Gaia DR2. We infer the completeness of Gaia DR2 by exploiting the fact that it only contains sources with at least five astrometric detections. The odds that a source achieves those five detections depends on both the number of observations and the probability that an observation of that source results in a detection. We predict the number of times that each source was observed by Gaia and assume that the probability of detection is either a function of magnitude or a distribution as a function of magnitude. We fit both these models to the 1.7 billion stars of Gaia DR2, and thus are able to robustly predict the completeness of Gaia across the sky as a function of magnitude. We extend our selection function to account for crowding in dense regions of the sky, and show that this is vitally important, particularly in the Galactic bulge and the Large and Small Magellanic Clouds. We find that the magnitude limit at which Gaiais still 99 per cent complete varies over the sky from G = 18.9 to fainter than G = 21. We have created a new python package selectionfunctions (https://github.com/gaiaverse/selectionfunctions) which provides easy access to our selection functions.
Wind–MRI interactions in local models of protoplanetary discs – I. Ohmic resistivity
Authors: Leung Philip K C , Ogilvie Gordon I 
Published: August 2020

ABSTRACT
A magnetic disc wind is an important mechanism that may be responsible for driving accretion and structure formation in protoplanetary discs. Recent numerical simulations have shown that these winds can take either the traditional ‘hourglass’ symmetry about the mid-plane, or a ‘slanted’ symmetry dominated by a mid-plane toroidal field of a single sign. The formation of this slanted symmetry state has not previously been explained. We use radially local 1D vertical shearing box simulations to assess the importance of large-scale MRI channel modes in influencing the formation and morphologies of these wind solutions. We consider only Ohmic resistivity and explore the effect of different magnetizations, with the mid-plane β parameter ranging from 105 to 102. We find that our magnetic winds go through three stages of development: cyclic, transitive, and steady, with the steady wind taking a slanted symmetry profile similar to those observed in local and global simulations. We show that the cycles are driven by periodic excitation of the n = 2 or 3 MRI channel mode coupled with advective eviction, and that the transition to the steady wind is caused by a much more slowly growing n = 1 mode altering the wind structure. Saturation is achieved through a combination of advective damping from the strong wind, and suppression of the instability due to a strong toroidal field. A higher disc magnetization leads to a greater tendency towards, and more rapid settling into the slanted symmetry steady wind, which may have important implications for mass and flux transport processes in protoplanetary discs.
The distribution of dark galaxies and spin bias
Authors: Jimenez Raul , Heavens Alan F 
Published: August 2020

ABSTRACT
In the light of the discovery of numerous (almost) dark galaxies from the ALFALFA and LITTLE THINGS surveys, we revisit the predictions of the existence of dark galaxies, based on the Toomre stability of rapidly spinning gas discs. We have updated the predictions for Λ-cold dark matter with parameters given by the Planck18 collaboration, computing the expected number densities of dark objects, and their spin parameter and mass distributions. Comparing with the data is more challenging, but where the spins are more reliably determined, the spins are close to the threshold for discs to be stable according to the Toomre criterion, where the expected number density is highest, and reinforces the concept that there is a bias in the formation of luminous galaxies based on the spin of their parent halo.
Zodiacal exoplanets in time – XI. The orbit and radiation environment of the young M dwarf-hosted planet K2-25b
Authors: Gaidos E , Hirano T , Wilson D J , France K , Rockcliffe K , Newton E , Feiden G , Krishnamurthy V , Harakawa H , Hodapp K W , Ishizuka M , Jacobson S , Konishi M , Kotani T , Kudo T , Kurokawa T , Kuzuhara M , Nishikawa J , Omiya M , Serizawa T , Tamura M , Ueda A , Vievard S 
Published: August 2020

ABSTRACT
M dwarf stars are high-priority targets for searches for Earth-size and potentially Earth-like planets, but their planetary systems may form and evolve in very different circumstellar environments than those of solar-type stars. To explore the evolution of these systems, we obtained transit spectroscopy and photometry of the Neptune-size planet orbiting the ≈650-Myr-old Hyades M dwarf K2-25. An analysis of the variation in spectral line shape induced by the Doppler ‘shadow’ of the planet indicates that the planet’s orbit is closely aligned with the stellar equator ($\lambda =-1.7_{-3.7}^{+5.8}$ deg), and that an eccentric orbit found by previous work could arise from perturbations by another planet on a coplanar orbit. We detect no significant variation in the depth of the He i line at 1083 nm during transit. A model of atmospheric escape as an isothermal Parker wind with a solar composition shows that this non-detection is not constraining compared to escape rate predictions of ∼0.1 M⊕  Gyr−1; at such rates, at least several Gyr are required for a Neptune-like planet to evolve into a rocky super-Earth.
Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine
Authors: Malik Deepshikha , Kobyłecki Kamil , Krawczyk Paweł , Poznański Jarosław , Jakielaszek Aleksandra , Napiórkowska Agnieszka , Dziembowski Andrzej , Tomecki Rafał , Nowotny Marcin 
Published: August 2020

Abstract
Template-independent terminal ribonucleotide transferases (TENTs) catalyze the addition of nucleotide monophosphates to the 3′-end of RNA molecules regulating their fate. TENTs include poly(U) polymerases (PUPs) with a subgroup of 3′ CUCU-tagging enzymes, such as CutA in Aspergillus nidulans. CutA preferentially incorporates cytosines, processively polymerizes only adenosines and does not incorporate or extend guanosines. The basis of this peculiar specificity remains to be established. Here, we describe crystal structures of the catalytic core of CutA in complex with an incoming non-hydrolyzable CTP analog and an RNA with three adenosines, along with biochemical characterization of the enzyme. The binding of GTP or a primer with terminal guanosine is predicted to induce clashes between 2-NH2 of the guanine and protein, which would explain why CutA is unable to use these ligands as substrates. Processive adenosine polymerization likely results from the preferential binding of a primer ending with at least two adenosines. Intriguingly, we found that the affinities of CutA for the CTP and UTP are very similar and the structures did not reveal any apparent elements for specific NTP binding. Thus, the properties of CutA likely result from an interplay between several factors, which may include a conformational dynamic process of NTP recognition.
A quantitative binding model for the Apl protein, the dual purpose recombination-directionality factor and lysis-lysogeny regulator of bacteriophage 186
Authors: Cutts Erin E , Barry Egan J , Dodd Ian B , Shearwin Keith E 
Published: August 2020

Abstract
The Apl protein of bacteriophage 186 functions both as an excisionase and as a transcriptional regulator; binding to the phage attachment site (att), and also between the major early phage promoters (pR-pL). Like other recombination directionality factors (RDFs), Apl binding sites are direct repeats spaced one DNA helix turn apart. Here, we use in vitro binding studies with purified Apl and pR-pL DNA to show that Apl binds to multiple sites with high cooperativity, bends the DNA and spreads from specific binding sites into adjacent non-specific DNA; features that are shared with other RDFs. By analysing Apl's repression of pR and pL, and the effect of operator mutants in vivo with a simple mathematical model, we were able to extract estimates of binding energies for single specific and non-specific sites and for Apl cooperativity, revealing that Apl monomers bind to DNA with low sequence specificity but with strong cooperativity between immediate neighbours. This model fit was then independently validated with in vitro data. The model we employed here is a simple but powerful tool that enabled better understanding of the balance between binding affinity and cooperativity required for RDF function. A modelling approach such as this is broadly applicable to other systems.
Semisynthesis of site-specifically succinylated histone reveals that succinylation regulates nucleosome unwrapping rate and DNA accessibility
Authors: Jing Yihang , Ding Dongbo , Tian Gaofei , Kwan Ka Chun Jonathan , Liu Zheng , Ishibashi Toyotaka , Li Xiang David 
Published: August 2020

Abstract
Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and function in chromatin remain poorly understood. Here, we utilized an expressed protein ligation (EPL) strategy to synthesize histone H4 with site-specific succinylation at K77 residue (H4K77succ), an evolutionarily conserved succinylation site at the nucleosomal DNA-histone interface. We then assembled mononucleosomes with the semisynthetic H4K77succ in vitro. We demonstrated that this succinylation impacts nucleosome dynamics and promotes DNA unwrapping from the histone surface, which allows proteins such as transcription factors to rapidly access buried regions of the nucleosomal DNA. In budding yeast, a lysine-to-glutamic acid mutation, which mimics Ksucc, at the H4K77 site reduced nucleosome stability and led to defects in DNA damage repair and telomere silencing in vivo. Our findings revealed this uncharacterized histone modification has important roles in nucleosome and chromatin dynamics.