We present the Flagship galaxy mock, a simulated catalogue of billions of galaxies designed to support the scientific exploitation of the Euclid mission. Euclid is a medium-class mission of the European Space Agency optimised to determine the properties of dark matter and dark energy on the largest scales of the Universe. It probes structure formation over more than 10 billion years primarily from the combination of weak gravitational lensing and galaxy clustering data. The breath of Euclid's data will also foster a wide variety of scientific analyses. The Flagship simulation was developed to provide a realistic approximation to the galaxies that will be observed by Euclid and used in its scientific analyses. We ran a state-of-the-art N-body simulation with four trillion particles, producing a lightcone on the fly. From the dark matter particles, we produced a catalogue of 16 billion haloes in one octant of the sky in the lightcone up to redshift z=3. We then populated these haloes with mock galaxies using a halo occupation distribution and abundance matching approach, calibrating the free parameters of the galaxy mock against observed correlations and other basic galaxy properties. Modelled galaxy properties include luminosity and flux in several bands, redshifts, positions and velocities, spectral energy distributions, shapes and sizes, stellar masses, star formation rates, metallicities, emission line fluxes, and lensing properties. We selected a final sample of 3.4 billion galaxies with a magnitude cut of H_E<26, where we are complete. We have performed a comprehensive set of validation tests to check the similarity to observational data and theoretical models. In particular, our catalogue is able to closely reproduce the main characteristics of the weak lensing and galaxy clustering samples to be used in the mission's main cosmological analysis. (abridged)

Cosmic shear is a powerful probe of cosmology, but it is affected by the intrinsic alignment (IA) of galaxy shapes with the large-scale structure. Upcoming surveys such as Euclid and Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) require an accurate understanding of IA, particularly for higher-order cosmic shear statistics that are vital for extracting the most cosmological information. In this paper, we report the first detection of third-order IA correlations using the LOWZ galaxy sample from the Sloan Digital Sky Survey (SDSS) Baryon Oscillation Spectroscopic Survey (BOSS). We compare our measurements with predictions from the MICE cosmological simulation and an analytical model inspired by the Non-linear Linear Alignment (NLA) model and informed by second-order correlations. We also explore the dependence of the third-order correlation on the galaxies' luminosity. We find that the amplitude A(IA) of the IA signal is non-zero at the 4.7 sigma (7.6 sigma) level for scales between 6 h(-1) Mpc (1 h(-1) Mpc) and 20 h(-1) Mpc. For scales above 6 h(-1) Mpc the inferred A(IA) agrees both with the prediction from the simulation and estimates from second-order statistics within 1 sigma but deviations arise at smaller scales. Our results demonstrate the feasibility of measuring third-order IA correlations and using them for constraining IA models. The agreement between second- and third-order IA constraints also opens the opportunity for a consistent joint analysis and IA self-calibration, promising tighter parameter constraints for upcoming cosmological surveys.

Site-specific recombinases have been used in higher eukaryotes, especially in animals, for a broad range of applications, including chromosomal translocations, large deletions, site-specific integration, and tissue-specific as well as conditional knock-outs. The application of site-specific recombination has also been demonstrated in simple eukaryotes like fungi and protozoa. However, its use in fungal research, especially in phytopathogenic fungi, has often been limited to "recycle" the marker genes used in transformation experiments. We show that Cre recombinase can be used for conditional gene deletions in the phytopathogenic fungus Ustilago maydis. Conditional gene knock-outs can be generated via the transcriptional control of the recombinase by U. maydis promoters specifically activated during the biotrophic phase of fungal growth, enabling gene deletions at defined developmental stages inside the plant tissue. Also, we show that a tamoxifen-activated Cre-recombinase allows the tight control necessary for the induced deletion of essential genes by the addition of tamoxifen. These tools will be helpful to address the function of genes under both axenic and in planta conditions for the U. maydis-maize pathosystem and should pave the way for similar approaches in other plant pathosystems.

ABSTRACT Shape estimates that quantifying the halo anisotropic mass distribution are valuable parameters that provide information on their assembly process and evolution. Measurements of the mean shape estimates for a sample of cluster-sized haloes can be used to test halo formation scenarios, as well as improving the modelling of potential biases in constraining cosmological parameters using these systems. In this work, we test the recovery of halo cluster shapes and masses applying weak-lensing stacking techniques. To this end, we use lensing shear and a new dark-matter halo catalogue, derived from the light-cone output of the cosmological simulation MICE-GC. We perform this study by combining the lensing signals obtained for several samples of haloes, selected according to their mass and redshift, taking into account the main directions of the dark-matter distributions. In the analysis, we test the impact of several potential introduced systematics, such as the adopted modelling, the contribution of the neighbouring mass distribution, miscentring, and misalignment effects. Our results show that when some considerations regarding the halo relaxation state are taken into account, the lensing semi-axial ratio estimates are in agreement within a 5 per cent with the mean shapes of the projected dark-matter particle distribution of the stacked haloes. The presented methodology provides a useful tool to derive reliable shapes of galaxy clusters and to contrast them with those expected from numerical simulations. Furthermore, our proposed modelling, that takes into account the contribution of neighbouring haloes, allows to constraint the elongation of the surrounding mass distribution.

The intrinsic alignment (IA) of galaxies is potentially a major limitation in deriving cosmological constraints from weak lensing surveys. In order to investigate this effect, we assign intrinsic shapes and orientations to galaxies in the light-cone output of the MICE simulation, spanning similar to 5000 deg2 and reaching redshift z 1/4 1.4. This assignment is based on a semianalytic IA model that uses photometric properties of galaxies as well as the spin and shape of their host halos. Advancing on previous work, we include more realistic distributions of galaxy shapes and a luminosity-dependent galaxy-halo alignment. The IA model parameters are calibrated against COSMOS and BOSS LOWZ observations. The null detection of IA in observations of blue galaxies is accounted for by setting random orientations for these objects. We compare the two-point alignment statistics measured in the simulation against predictions from the analytical IA models NLA and TATT over a wide range of scales, redshifts, and luminosities for red and blue galaxies separately. We find that both models fit the measurements well at scales above 8 h-1 Mpc, while TATT outperforms NLA at smaller scales. The IA parameters derived from our fits are in broad agreement with various observational constraints from red galaxies. Lastly, we build a realistic source sample, mimicking DES Year 3 observations and use it to predict the IA contamination to the observed shear statistics. We find this prediction to be within the measurement uncertainty, which might be a consequence of the random alignment of blue galaxies in the simulation.

We use the small scales of the Dark Energy Survey (DES) Year-3 cosmic shear measurements, which are excluded from the DES Year-3 cosmological analysis, to constrain the baryonic feedback. To model the baryonic feedback, we adopt a baryonic correction model and use the numerical package \texttt{Baccoemu} to accelerate the evaluation of the baryonic nonlinear matter power spectrum. We design our analysis pipeline to focus on the constraints of the baryonic suppression effects, utilizing the implication given by a principal component analysis on the Fisher forecasts. Our constraint on the baryonic effects can then be used to better model and ameliorate the effects of baryons in producing cosmological constraints from the next generation large-scale structure surveys. We detect the baryonic suppression on the cosmic shear measurements with a $\sim 2 \sigma$ significance. The characteristic halo mass for which half of the gas is ejected by baryonic feedback is constrained to be $M_c > 10^{13.2} h^{-1} M_{\odot}$ (95\% C.L.). The best-fit baryonic suppression is $\sim 5\%$ at $k=1.0 {\rm Mpc}\ h^{-1}$ and $\sim 15\%$ at $k=5.0 {\rm Mpc} \ h^{-1}$. Our findings are robust with respect to the assumptions about the cosmological parameters, specifics of the baryonic model, and intrinsic alignments.

ABSTRACT The high abundance of disc galaxies without a large central bulge challenges predictions of current hydrodynamic simulations of galaxy formation. We aim to shed light on the formation of these objects by studying the redshift and mass dependence of their intrinsic 3D shape distributions in the COSMOS galaxy survey below redshift z = 1.0. This distribution is inferred from the observed distribution of 2D shapes, using a reconstruction method which we test using hydrodynamic simulations. Our tests reveal a moderate bias for the inferred average disc circularity and relative thickness, but a large bias on the dispersion of these quantities. Applying the reconstruction method on COSMOS data, we find variations of the average disc circularity and relative thickness with redshift of around ∼1 per cent and ∼10 per cent, respectively, which is comparable to the error estimates on these quantities. The average relative disc thickness shows a significant mass dependence which can be accounted for by the scaling of disc radius with galaxy mass. We conclude that our data provides no evidence for a strong dependence of the average circularity and absolute thickness of disc-dominated galaxies on redshift and mass that is significant with respect to the statistical uncertainties in our analysis. These findings are expected in the absence of disruptive merging or feedback events that would affect galaxy shapes. They hence support a scenario where present-day discs form early ( z > 1.0) and subsequently undergo a tranquil evolution in isolation. However, more data and a better understanding of systematics are needed to reaffirm our results.

Constraints on dark matter halo masses from weak gravitational lensing can be improved significantly by using additional information about the morphology of their density distribution, leading to tighter cosmological constraints derived from the halo mass function. This work is the first of two in which we investigate the accuracy of halo morphology and mass measurements in 2D and 3D. To this end, we determine several halo physical properties in the MICE-Grand Challenge dark matter only simulation. We present a public catalogue of these properties that includes density profiles and shape parameters measured in 2D and 3D, the halo centre at the peak of the 3D density distribution as well as the gravitational and kinetic energies and angular momentum vectors. The density profiles are computed using spherical and ellipsoidal radial bins, taking into account the halo shapes. We also provide halo concentrations and masses derived from fits to 2D and 3D density profiles using NFW and Einasto models for halos with more than 1000 particles (≳ 3 × 10^13 h^-1 M_⊙). We find that the Einasto model provides better fits compared to NFW, regardless of the halo relaxation state and shape. The mass and concentration parameters of the 3D density profiles derived from fits to the 2D profiles are in general biased. Similar biases are obtained when constraining mass and concentrations using a weak-lensing stacking analysis. We show that these biases depend on the radial range and density profile model adopted in the fitting procedure, but not on the halo shape.

Using 324 numerically modelled galaxy clusters we investigate the radial and galaxy-halo alignment of dark matter subhaloes and satellite galaxies orbiting within and around them. We find that radial alignment depends on distance to the centre of the galaxy cluster but appears independent of the dynamical state of the central host cluster. Furthermore, we cannot find a relation between radial alignment of the halo or galaxy shape with its own mass. We report that backsplash galaxies, i.e. objects that have already passed through the cluster radius but are now located in the outskirts, show a stronger radial alignment than infalling objects. We further find that there exists a population of well radially aligned objects passing very close to the central cluster's centre which were found to be on highly radial orbit.

The three-point correlation function (3PCF) of the 21-cm brightness temperature from the Epoch of Reionization (FOR) probes complementary information to the commonly studied two-point correlation function (2PCF) about the morphology of ionized regions. We investigate the 21-cm 2PCF and 3PCF in configuration space using seminumerical simulations and test whether they can be described by the local quadratic bias model. We find that fits of bias model predictions for the 2PCF and 3PCF deviate from our measurements by similar to 20 per cent at scales above the typical size of ionized regions (similar or equal to 30 Mpc) and at early times with global neutral fractions of < x(H I)> greater than or similar to 0.7. At later times and smaller scales, these deviations increase strongly, indicating a break-down of the bias model. The 2PCF and 3PCF fits of the linear bias parameter agree at the 10 per cent level for different EoR model configurations. This agreement holds, when adding redshift space distortions to the simulations. The relation between spatial fluctuations in the matter density and the 21-cm signal, as predicted by the bias model, is consistent with direct measurements of this relation in simulations for large smoothing scales (greater than or similar to 30 Mpc). From this latter test, we conclude that negative amplitudes of the 21-cm 3PCF result from negative bias parameters, which describe the anticorrelation between the matter over-densities and the 21-cm signal during the EoR. However, a more detailed interpretation of the bias parameters may require a description of non-local contributions to the bias model.

The three-point correlation function (3PCF) of the 21cm brightness temperature from the Epoch of Reionization (EoR) probes complementary information to the commonly studied two-point correlation function (2PCF) about the morphology of ionized regions. We investigate the 21cm 2PCF and 3PCF in configuration space using semi-numerical simulations and test whether they can be described by the local quadratic bias model. We find that fits of bias model predictions for the 2PCF and 3PCF deviate from our measurements by ∼ 20% at scales above the typical size of ionized regions (≃ 30 Mpc) and at early times with global neutral fractions of ⟨ x_ HI⟩≳ 0.7. At later times and smaller scales these deviations increase strongly, indicating a break down of the bias model. The 2PCF and 3PCF fits of the linear bias parameter agree at the 10% level for different EoR model configurations. This agreement holds, when adding redshift space distortions to the simulations. The relation between spatial fluctuations in the matter density and the 21cm signal, as predicted by the bias model, is consistent with direct measurements of this relation in simulations for large smoothing scales (≳ 30 Mpc). From this latter test we conclude that negative amplitudes of the 21cm 3PCF result from negative bias parameters, which describe the anti-correlation between the matter over-densities and the 21cm signal during the EoR. However, a more detailed interpretation of the bias parameters may require a description of non-local contributions to the bias model.

We compare reduced three-point correlations Q of matter, haloes (as proxies for galaxies) and their cross-correlations, measured in a total simulated volume of similar to 100 (h(-1) Gpc)(3), to predictions from leading order perturbation theory on a large range of scales in configuration space. Predictions for haloes are based on the non-local bias model, employing linear (b(1)) and non-linear (c(2), g(2)) bias parameters, which have been constrained previously from the bispectrum in Fourier space. We also study predictions from two other bias models, one local (g(2) = 0) and one in which c(2) and g(2) are determined by b(1) via approximately universal relations. Overall, measurements and predictions agree when Q is derived for triangles with (r(1)r(2)r(3))(1/3) greater than or similar to 60 h(-1) Mpc, where r(1-3) are the sizes of the triangle legs. Predictions for Q(matter), based on the linear power spectrum, show significant deviations from the measurements at the BAO scale (given our small measurement errors), which strongly decrease when adding a damping term or using the non-linear power spectrum, as expected. Predictions for Q(halo) agree best with measurements at large scales when considering non-local contributions. The universal bias model works well for haloes and might therefore be also useful for tightening constraints on b(1) from Q in galaxy surveys. Such constraints are independent of the amplitude of matter density fluctuation (sigma(8)) and hence break the degeneracy between b(1) and sigma(8), present in galaxy two-point correlations.

Constraints on reionization models from future 21cm observations will rely on the statistical characterization of the spatial fluctuations in the observed 21cm brightness temperature. Three-point correlation functions (3PCF) of this 21cm signal probe information about the shape of ionized regions and can therefore improve constraints on reionization model from the power spectrum which is not sensitive to such shape information. We study the 21cm two-point correlation functions (2PCF) and 3PCF in configuration space, using semi-numerical simulations. These measurements are compared to leading order predictions from the local quadratic bias model, which is commonly used for modeling the galaxy 3PCF. Fits of the bias model predictions to the 2PCF and 3PCF measurements show an $simeq 20%$ accuracy for scales above the typical size of of ionizes regions ($simeq 30$ Mpc) and at early times for global neutral fractions of $langle x_{rm HI} ranglegtrsim 0.7$, while deviations between the predictions and measurements increase strongly for smaller scales and later reionization stages. In the regime in which the bias model performs well, the 2PCF and 3PCF fits of the linear bias parameter agree at the $10%$ level. The relation between fluctuations in the matter density and the 21cm signal, as predicted by the bias model, is consistent with simulations for large smoothing scales. Our results suggest that measurements of the 3PCF in upcoming radio observations can constrain astrophysical processes driving the reionization. Combining the 21cm 2PCF and 3PCF can further break the degeneracy between the linear growth function of matter fluctuations and the reionization bias parameters, and hence constrain cosmological models during the epoch of reionization.

Using a dark matter simulation we show how halo bias is determined by local density and not by halo mass. This is not totally surprising as, according to the peak-background split model, local matter density (delta(delta) over bar) is the property that constrains bias at large scales. Massive haloes have a high clustering because they reside in high density regions. Small haloes can be found in a wide range of environments which di ff erentially determine their clustering amplitudes. This contradicts the assumption made by standard halo occupation distribution (HOD) models that bias and occupation of haloes is determined solely by their mass. We show that the bias of central galaxies from semi-analytic models of galaxy formation as a function of luminosity and colour is therefore not correctly predicted by the standard HOD model. Using delta (delta) over tilde (of matter or galaxies) instead of halo mass, the HOD model correctly predicts galaxy bias. These results indicate the need to include information about local density and not only mass in order to correctly apply HOD analysis in these galaxy samples. This new model can be readily applied to observations and has the advantage that, in contrast with the dark matter halo mass, the galaxy density can be directly observed.

We study the linear and non-linear bias parameters which determine the mapping between the distributions of galaxies and the full matter density fields, comparing different measurements and predictions. Associating galaxies with dark matter haloes in the Marenostrum Institut de Ciencies de l'Espai (MICE) Grand Challenge N-body simulation, we directly measure the bias parameters by comparing the smoothed density fluctuations of haloes and matter in the same region at different positions as a function of smoothing scale. Alternatively, we measure the bias parameters by matching the probability distributions of halo and matter density fluctuations, which can be applied to observations. These direct bias measurements are compared to corresponding measurements from two-point and different third-order correlations, as well as predictions from the peak-background model, which we presented in previous papers using the same data. We find an overall variation of the linear bias measurements and predictions of similar to 5 per cent with respect to results from two-point correlations for different halo samples with masses between similar to 10(12) and 10(15) h(-1) M-circle dot at the redshifts z = 0.0 and 0.5. Variations between the second-and third-order bias parameters from the different methods show larger variations, but with consistent trends in mass and redshift. The various bias measurements reveal a tight relation between the linear and the quadratic bias parameters, which is consistent with results from the literature based on simulations with different cosmologies. Such a universal relation might improve constraints on cosmological models, derived from second-order clustering statistics at small scales or higher order clustering statistics.

We study halo clustering bias with second-and third-order statistics of halo and matter density fields in the Marenostrum Institut de Ciencies de l'Espai (MICE) Grand Challenge simulation. We verify that two-point correlations deliver reliable estimates of the linear bias parameters at large scales, while estimations from the variance can be significantly affected by non-linear and possibly non-local contributions to the bias function. Combining three-point auto- and cross-correlations we find, for the first time in configuration space, evidence for the presence of such non-local contributions. These contributions are consistent with predicted second-order non-local effects on the bias functions originating from the dark matter tidal field. Samples of massive haloes show indications of bias (local or non-local) beyond second order. Ignoring non-local bias causes 20-30 and 5-10 per cent overestimation of the linear bias from three-point auto-and cross-correlations, respectively. We study two third-order bias estimators that are not affected by second-order non-local contributions. One is a combination of three-point auto-and cross-correlations. The other is a combination of third-order one-and two-point cumulants. Both methods deliver accurate estimations of the linear bias. Ignoring non-local bias causes higher values of the second-order bias from three-point correlations. Our results demonstrate that third-order statistics can be employed for breaking the growth-bias degeneracy.

Measurements of the linear growth factor $D$ at different redshifts $z$ are key to distinguish among cosmological models. One can estimate the derivative $dD(z)/d\ln(1+z)$ from redshift space measurements of the 3D anisotropic galaxy two-point correlation $\xi(z)$, but the degeneracy of its transverse (or projected) component with galaxy bias $b$, i.e. $\xi_{\perp}(z) \propto\ D^2(z) b^2(z)$, introduces large errors in the growth measurement. Here we present a comparison between two methods which break this degeneracy by combining second- and third-order statistics. One uses the shape of the reduced three-point correlation and the other a combination of third-order one- and two-point cumulants. These methods use the fact that, for Gaussian initial conditions and scales larger than $20$ $h^{-1}$Mpc, the reduced third-order matter correlations are independent of redshift (and therefore of the growth factor) while the third-order galaxy correlations depend on $b$. We use matter and halo catalogs from the MICE-GC simulation to test how well we can recover $b(z)$ and therefore $D(z)$ with these methods in 3D real space. We also present a new approach, which enables us to measure $D$ directly from the redshift evolution of second- and third-order galaxy correlations without the need of modelling matter correlations. For haloes with masses lower than $10^{14}$ $h^{-1}$M$_\odot$, we find $10%$ deviations between the different estimates of $D$, which are comparable to current observational errors. At higher masses we find larger differences that can probably be attributed to the breakdown of the bias model and non-Poissonian shot noise.

We model the abundance of haloes in the $\sim(3 \ \text{Gpc}/h)^3$ volume of the MICE Grand Challenge simulation by fitting the universal mass function with an improved Jack-Knife error covariance estimator that matches theory predictions. We present unifying relations between different fitting models and new predictions for linear ($b_1$) and non-linear ($c_2$ and $c_3$) halo clustering bias. Different mass function fits show strong variations in their performance when including the low mass range ($M_h \lesssim 3 \ 10^{12} \ M_{\odot}/h$) in the analysis. Together with fits from the literature we find an overall variation in the amplitudes of around $10$% in the low mass and up to $50$% in the high mass (galaxy cluster) range ($M_h > 10^{14} \ M_{\odot}/h$). These variations propagate into a $10$% change in $b_1$ predictions and a $50$% change in $c_2$ or $c_3$. Despite these strong variations we find universal relations between $b_1$ and $c_2$ or $c_3$ for which we provide simple fits. Excluding low mass haloes, different models fitted with reasonable goodness in this analysis, show percent level agreement in their $b_1$ predictions, but are systematically $5-10$% lower than the bias directly measured with two-point halo-mass clustering. This result confirms previous findings derived from smaller volumes (and smaller masses). Inaccuracies in the bias predictions lead to $5-10$% errors in growth measurements. They also affect any HOD fitting or (cluster) mass calibration from clustering measurements.

We study the shapes of subhalo distributions from four dark-matter-only simulations of Milky Way-type haloes. Comparing the shapes derived from the subhalo distributions at high resolution to those of the underlying dark matter fields, we find the former to be more triaxial if the analysis is restricted to massive subhaloes. For three of the four analysed haloes, the increased triaxiality of the distributions of massive subhaloes can be explained by a systematic effect caused by the low number of objects. Subhaloes of the fourth halo show indications for anisotropic accretion via their strong triaxial distribution and orbit alignment with respect to the dark matter field. These results are independent of the employed subhalo finder. Comparing the shape of the observed Milky Way satellite distribution to those of high-resolution subhalo samples from simulations, we find agreement for samples of bright satellites, but significant deviations if faint satellites are included in the analysis. These deviations might result from observational incompleteness.