SImulator of GAlaxy Millimetre/submillimetre Emission (SIGAME): CO emission from massive z=2 main-sequence galaxies

We present SIGAME (SImulator of GAlaxy Millimetre/submillimetre Emission), a new numerical code designed to simulate the 12CO rotational line emission spectrum of galaxies. Using sub-grid physics recipes to post-process the outputs of smoothed particle hydrodynamics (SPH) simulations, a molecular gas phase is condensed out of the hot and partly ionized SPH gas. The gas is subjected to far-UV radiation fields and cosmic ray ionization rates which are set to scale with the local star formation rate volume density. Level populations and radiative transport of the CO lines are solved with the 3-D radiative transfer code LIME. We have applied SIGAME to cosmological SPH simulations of three disc galaxies at z=2 with stellar masses in the range ~(0.5-2)x10^11 Msun and star formation rates ~40-140 Msun/yr. Global CO luminosities and line ratios are in agreement with observations of disc galaxies at z~2 up to and including J=3-2 but falling short of the few existing J=5-4 observations. The central 5 kpc regions of our galaxies have CO 3-2/1-0 and 7-6/1-0 brightness temperature ratios of ~0.55-0.65 and ~0.02-0.08, respectively, while further out in the disc the ratios drop to more quiescent values of ~0.5 and <0.01. Global CO-to-H2 conversion (alpha_CO) factors are ~=1.5 Msun*pc^2/(K km s/1), i.e. ~2-3 times below typically adopted values for disc galaxies, and alpha_CO increases with radius, in agreement with observations of nearby galaxies. Adopting a top-heavy Giant Molecular Cloud (GMC) mass spectrum does not significantly change the results. Steepening the GMC density profile leads to higher global line ratios for J_up>=3 and CO-to-H2 conversion factors [~=3.6 Msun*pc^2/(K km/s)].Comment: 28 pages, 20 figures. Accepted for Publication in MNRAS. Substantial revisions from the previous version, including tests with model galaxies similar to the Milky Way. Improved figures and added table

Investigating the [C II\,{\rm \scriptsize II}]-to-H I\,{\rm \scriptsize I} conversion factor and the H I\,{\rm \scriptsize I} gas budget of galaxies at z≈6z\approx 6 with hydrodynamical simulations

One of the most fundamental baryonic matter components of galaxies is the neutral atomic hydrogen (H$\,{\rm \scriptsize I}$). At low redshifts, this component can be traced directly through the 21-cm transition, but to infer H$\,{\rm \scriptsize I}$ gas content of the most distant galaxies, a viable tracer is needed. We here investigate the fidelity of the fine structure transition of the ($^2P_{3/2} - ^2P_{1/3}$) transition of singly-ionized carbon [C$\,{\rm \scriptsize II}$] at $158\,\mu$m as a proxy for H$\,{\rm \scriptsize I}$ in a set simulated galaxies at $z\approx 6$, following the work by Heintz et al. (2021). We select 11,125 star-forming galaxies from the SIMBA simulations, with far-infrared line emissions post-processed and modeled within the SIGAME framework. We find a strong connection between [C$\,{\rm \scriptsize II}$] and H$\,{\rm \scriptsize I}$, with the relation between this [C$\,{\rm \scriptsize II}$]-to-H$\,{\rm \scriptsize I}$ relation ($\beta_{\rm [C\,{\rm \scriptsize II}]}$) being anti-correlated with the gas-phase metallicity of the simulated galaxies. We further use these simulations to make predictions for the total baryonic matter content of galaxies at $z\approx 6$, and specifically the HI gas mass fraction. We find mean values of $M_{\rm HI}/M_\star = 1.4$, and $M_{\rm HI}/M_{\rm bar,tot} = 0.45$. These results provide strong evidence for H$\,{\rm \scriptsize I}$ being the dominant baryonic matter component by mass in galaxies at $z\approx 6$.Comment: 7 pages, 3 figures. Accepted for publication by ApJ

Predictions of the L[CII]_{\rm[CII]}-SFR and [CII_{\rm II}] Luminosity Function at the Epoch of Reionization

We present the first predictions for the $L_{\rm [CII]}$ - SFR relation and [CII] luminosity function (LF) in the Epoch of Reionization (EoR) based on cosmological hydrodynamics simulations using the SIMBA suite plus radiative transfer calculations via S\'IGAME. The sample consists of 11,137 galaxies covering halo mass $\log M_{\rm halo}\in$[9, 12.4] $M_\odot$, star formation rate SFR$\in$[0.01, 330] $M_\odot$ yr$^{-1}$, and metallicity $<Z_{\rm gas}>_{\rm SFR}\in$[0.1, 0.9] $Z_\odot$. The simulated $L_{\rm [CII]}$-SFR relation is consistent with the range observed, but with a spread of $\simeq$0.3 dex at the high end of SFR ($>$100 $M_\odot$ yr$^{-1}$) and $\simeq$0.6 dex at the lower end, and there is tension between our predictions and the values of $L_{\rm [CII]}$ above 10$^{8.5}$ $L_\odot$ observed in some galaxies reported in the literature. The scatter in the $L_{\rm [CII]}$-SFR relation is mostly driven by galaxy properties, such that at a given SFR, galaxies with higher molecular gas mass and metallicity have higher $L_{\rm [CII]}$. The [CII] LF predicted by SIMBA is consistent with the upper limits placed by the only existing untargeted flux-limited [CII] survey at the EoR (ASPECS) and those predicted by semi-analytic models. We compare our results with existing models and discuss differences responsible for the discrepant slopes in the $L_{\rm [CII]}$-SFR relatiion.Comment: 19 pages, 14 figures, Accepted by Ap

sígame v3: Gas Fragmentation in Postprocessing of Cosmological Simulations for More Accurate Infrared Line Emission Modeling

We present an update to the framework called Simulator of Galaxy Millimeter/submillimeter Emission (SÍGAME). SÍGAME derives line emission in the far-infrared (FIR) for galaxies in particle-based cosmological hydrodynamics simulations by applying radiative transfer and physics recipes via a postprocessing step after completion of the simulation. In this version, a new technique is developed to model higher gas densities by parameterizing the probability distribution function (PDF) of the gas density in higher-resolution simulations run with the pseudoLagrangian, Voronoi mesh code AREPO. The parameterized PDFs are used as a look-up table, and reach higher densities than in previous work. SÍGAME v3 is tested on redshift z = 0 galaxies drawn from the SIMBA cosmological simulation for eight FIR emission lines tracing vastly different phases of the interstellar medium. This version of SÍGAME includes dust radiative transfer with SKIRT and high-resolution photoionization models with CLOUDY, the latter sampled according to the density PDF of the AREPO simulations to augment the densities in the cosmological simulation. The quartile distributions of the predicted line luminosities overlap with the observed range for nearby galaxies of similar star formation rate (SFR) for all but two emission lines: [O I]63 and CO(3–2), which are overestimated by median factors of 1.3 and 1.0 dex, respectively, compared to the observed line–SFR relation of mixed-type galaxies. We attribute the remaining disagreement with observations to the lack of precise attenuation of the interstellar light on sub-grid scales (200 pc) and differences in sample selection

SÍGAME Simulations of the [{\rm{C}}\,{\rm{II}}], [{\rm{O}}\,{\rm{I}}], and [{\rm{O}}\,{\rm{III}}] Line Emission from Star-forming Galaxies at z\simeq 6

Of the almost 40 star forming galaxies at z>~5 (not counting QSOs) observed in [CII] to date, nearly half are either very faint in [CII], or not detected at all, and fall well below expectations based on locally derived relations between star formation rate (SFR) and [CII] luminosity. Combining cosmological zoom simulations of galaxies with SIGAME (SImulator of GAlaxy Millimeter/submillimeter Emission) we have modeled the multi-phased interstellar medium (ISM) and its emission in [CII], [OI] and [OIII], from 30 main sequence galaxies at z~6 with star formation rates ~3-23Msun/yr, stellar masses ~(0.7-8)x10^9Msun, and metallicities ~(0.1-0.4)xZsun. The simulations are able to reproduce the aforementioned [CII]-faintness at z>5, match two of the three existing z>~5 detections of [OIII], and are furthermore roughly consistent with the [OI] and [OIII] luminosity relations with SFR observed for local starburst galaxies. We find that the [CII] emission is dominated by the diffuse ionized gas phase and molecular clouds, which on average contribute ~66% and ~27%, respectively. The molecular gas, which constitutes only ~10% of the total gas mass is thus a more efficient emitter of [CII] than the ionized gas making up ~85% of the total gas mass. A principal component analysis shows that the [CII] luminosity correlates with the star formation activity as well as average metallicity. The low metallicities of our simulations together with their low molecular gas mass fractions can account for their [CII]-faintness, and we suggest these factors may also be responsible for the [CII]-faint normal galaxies observed at these early epochs.Comment: 24 pages, 14 figures. Accepted for publication in the Astrophysical Journa

Suppression of type 1 pilus assembly in uropathogenic Escherichia coli by chemical inhibition of subunit polymerization

OBJECTIVES: To identify and to characterize small-molecule inhibitors that target the subunit polymerization of the type 1 pilus assembly in uropathogenic Escherichia coli (UPEC). METHODS: Using an SDS-PAGE-based assay, in silico pre-filtered small-molecule compounds were screened for specific inhibitory activity against the critical subunit polymerization step of the chaperone-usher pathway during pilus biogenesis. The biological activity of one of the compounds was validated in assays monitoring UPEC type 1 pilus biogenesis, type 1 pilus-dependent biofilm formation and adherence to human bladder epithelial cells. The time dependence of the in vivo inhibitory activity and the overall effect of the compound on UPEC growth were determined. RESULTS: N-(4-chloro-phenyl)-2-{5-[4-(pyrrolidine-1-sulfonyl)-phenyl]-[1,3,4]oxadiazol-2-yl sulfanyl}-acetamide (AL1) inhibited in vitro pilus subunit polymerization. In bacterial cultures, AL1 disrupted UPEC type 1 pilus biogenesis and pilus-dependent biofilm formation, and resulted in the reduction of bacterial adherence to human bladder epithelial cells, without affecting bacterial cell growth. Bacterial exposure to the inhibitor led to an almost instantaneous loss of type 1 pili. CONCLUSIONS: We have identified and characterized a small molecule that interferes with the assembly of type 1 pili. The molecule targets the polymerization step during the subunit incorporation cycle of the chaperone-usher pathway. Our discovery provides new insight into the design and development of novel anti-virulence therapies targeting key virulence factors of bacterial pathogens