Régime non-linéaire de formation des structures cosmiques: Empreintes sur la covariance du spectre de puissance et dynamique des inhomogénéités d’énergie noire

In the near future numerous galaxy surveys are going to provide a cartography of the distribution of matter in the universe, with which it will be possible to constrain the cosmological parameters with an unprecedented precision. This means that theoretical predictions of the observables at issue need to attain a high level of precision, so that we can extract the maximum cosmological information when comparing them to observations. Upcoming surveys have been conceived to understand the nature of dark energy, a component of which we have postulated the existence to explain the acceleration of the expansion of the universe observed at low redshift. In the standard cosmological model this component is represented as a cosmological constant Λ that dominate the energy budget of the universe today. Even if the ΛCDM model remains in good agreement with observations, a number of theoretical problems regarding the nature of the cosmological constant justify the study of a great number of alternative models, that now have to be put to the test with observations. To do so, it is necessary to take into account the effects of the non-linear dynamics of the gravitational collapse process. This thesis is placed in this context, using N-body simulations as a tool to link observations to the theory of cosmic structure formation in non-linear regime. On one side we are going to explore the impact of non-linear effects on the estimation of cosmological parameters in a statistical framework. This requires the computation of the covariance matrix of the matter power spectrum. The estimation of this matrix using simulations allows the quantification of the importance of non-linear effects that, if neglected, can bias the results or lead to an under-estimation of the statistical errors on the cosmological parameters. On the other side, we are going to present the numerical methods to solve the evolution of a dark energy fluid with perturbations that have a very low speed of propagation with respect to the speed of light. Collapsing dark energy perturbations leave a distinctive imprint on the distribution of matter in the universe. In this case, dark energy cannot be treated as a homogeneous fluid and its evolution has to be followed in the non-linear regime together with the dark matter component. These numerical methods, once coupled to an N-body code, will allow the production of the first simulations of the evolution of an inhomogeneous dark energy model.Dans le futur proche, de nombreux sondages de galaxies fourniront une cartographie de la distribution de la matière dans l’univers, avec laquelle il sera possible de contraindre les paramètres cosmologiques avec une precision inégalée. Cela implique que les predictions théoriques des observables en question doivent atteindre une precision suffisante pour pouvoir être comparées aux observations et extraire le maximum d’information cosmologique. Ces sondages ont été conçus pour comprendre la nature de l’énergie noire, une composante dont on a supposé l’existence pour expliquer l’accélération de l’expansion de l’univers observée à bas décalage vers le rouge. Dans le modèle standard de la cosmologie, cette composante est représentée par une constante cosmologique Λ qui domine le budget énergétique de l’univers aujourd’hui. Même si le modèle ΛCDM reste en bon accord avec les observations, de nombreux problèmes théoriques concernant la nature de la constante cosmologique motivent l’étude d’un très grand nombre de modèles alternatifs, qui doivent maintenant être mis à l’épreuve des observations. Pour ce faire, il est nécessaire de tenir compte des effets de la dynamique non-linéaire du processus d’effondrement gravitationnel. Cette thèse se place dans ce contexte, en utilisant les simulations N-corps comme outil pour relier aux observations la théorie de la formation des structures cosmiques dans le régime non-linéaire. D’un coté je vais explorer l’impact des effets non-linéaires sur l’estimation des paramètres cosmologiques dans le cadre d’une interprétation statistique des données. Celle ci nécessite le calcul de la matrice de covariance du spectre de puissance de la matière. L’estimation de cette matrice au moyen des simulations permet de quantifier l’importance des ces effets qui, si négligés, peuvent biaiser les résultats ou amener à une sous-estimation des erreurs statistiques sur les paramètres cosmologiques. De l’autre, je vais présenter les méthodes numériques pour résoudre l’evolution d’un fluide d’énergie noire dans le cas où les perturbations ont une vitesse de propagation très faible devant celle de la lumière. En s’effondrant l’énergie noire laisse des empreintes distinctes sur la distribution de matière dans l’univers. Dans ce cas, l’énergie noire ne peut être traitée comme un fluide homogène et son evolution doit être suivie dans le régime non-linéaire en meme temps que celle de la matière noire. Ces méthodes numériques, une fois couplées avec un code N-corps, permettront de produire les premières simulations de l’evolution cosmique d’un modèle d’énergie noire in-homogène

Non-linear Eulerian Hydrodynamics of Dark Energy: Riemann problem and Finite Volume Schemes

Upcoming large-scale-structure surveys can shed new light on the properties of dark energy. In particular, if dark energy is a dynamical component, it must have spatial perturbations. Their behaviour is regulated by the speed of sound parameter, which is currently unconstrained. In this work we present the numerical methods that will allow to perform cosmological simulations of inhomogeneous dark energy scenarios where the speed of sound is small and non-vanishing. We treat the dark energy component as an effective fluid and build upon established numerical methods for hydrodynamics to construct a numerical solution of the effective continuity and Euler equations. In particular, we develop conservative finite volume schemes that rely on the solution of the Riemann problem, which we provide here in both exact and approximate forms for the case of a dark energy fluid.Comment: 35 pages, 18 figures, submitted to JCA

Matter Power Spectrum Covariance Matrix from the DEUS-PUR {\Lambda}CDM simulations: Mass Resolution and non-Gaussian Errors

The upcoming generation of galaxy surveys will probe the distribution of matter in the universe with unprecedented accuracy. Measurements of the matter power spectrum at different scales and redshifts will provide stringent constraints on the cosmological parameters. However, on non-linear scales this will require an accurate evaluation of the covariance matrix. Here, we compute the covariance matrix of the 3D matter density power spectrum for the concordance $\Lambda$CDM cosmology from an ensemble of N-body simulations of the Dark Energy Universe Simulation - Parallel Universe Runs (DEUS-PUR). This consists of 12288 realisations of a $(656\,h^{-1}\,\textrm{Mpc})^3$ simulation box with $256^3$ particles. We combine this set with an auxiliary sample of 96 simulations of the same volume with $1024^3$ particles. We find N-body mass resolution effect to be an important source of systematic errors on the covariance at high redshift and small intermediate scales. We correct for this effect by introducing an empirical statistical method which provide an accurate determination of the covariance matrix over a wide range of scales including the Baryon Oscillations interval. Contrary to previous studies that used smaller N-body ensembles, we find the power spectrum distribution to significantly deviate from expectations of a Gaussian random density field at $k\gtrsim 0.25\,h\,\textrm{Mpc}^{-1}$ and $z<0.5$. This suggests that in the case of finite volume surveys an unbiased estimate of the ensemble averaged band power at these scales and redshifts may require a careful assessment of non-Gaussian errors more than previously considered.Comment: 9 pages, 8 figures, accepted for publication in MNRAS, covariance matrices available upon request to the author

Euclid preparation : II. The EUCLIDEMULATOR - a tool to compute the cosmology dependence of the nonlinear matter power spectrum

We present a new power spectrum emulator named EuclidEmulator that estimates the nonlinear correction to the linear dark matter power spectrum depending on the six cosmological parameters ωb, ωm, ns, h, w0, and σ8. It is constructed using the uncertainty quantification software UQLab using a spectral decomposition method called polynomial chaos expansion. All steps in its construction have been tested and optimized: the large highresolution N-body simulations carried out with PKDGRAV3 were validated using a simulation from the Euclid Flagship campaign and demonstrated to have converged up to wavenumbers k ≈ 5 h Mpc−1 for redshifts z ≤ 5. The emulator is based on 100 input cosmologies simulated in boxes of (1250 Mpc/h)3 using 20483 particles. We show that by creating mock emulators it is possible to successfully predict and optimize the performance of the final emulator prior to performing any N-body simulations. The absolute accuracy of the final nonlinear power spectrum is as good as one obtained with N-body simulations, conservatively, ∼1 per cent for k 1 h Mpc−1 and z 1. This enables efficient forward modelling in the nonlinear regime, allowing for estimation of cosmological parameters using Markov ChainMonteCarlo methods. EuclidEmulator has been compared to HALOFIT, CosmicEmu, and NGenHalofit, and shown to be more accurate than these other approaches. This work paves a new way for optimal construction of future emulators that also consider other cosmological observables, use higher resolution input simulations, and investigate higher dimensional cosmological parameter spaces.Peer reviewe

Female Chromosome X Mosaicism is Age-Related and Preferentially Affects the Inactivated X Chromosome

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events 4 2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases

Comparing approximate methods for mock catalogues and covariance matrices \u2013 III: bispectrum

We compare the measurements of the bispectrum and the estimate of its covariance obtained from a set of different methods for the efficient generation of approximate dark matter halo catalogues to the same quantities obtained from full N-body simulations. To this purpose we employ a large set of 300 realizations of the same cosmology for each method, run with matching initial conditions in order to reduce the contribution of cosmic variance to the comparison. In addition, we compare how the error on cosmological parameters such as linear and non-linear bias parameters depends on the approximate method used for the determination of the bispectrum variance. As general result, most methods provide errors within 10 per cent of the errors estimated from N-body simulations. Exceptions are those methods requiring calibration of the clustering amplitude but restrict this to 2-point statistics. Finally we test how our results are affected by being limited to a few hundreds measurements from N-body simulation by comparing with a larger set of several thousands of realizations performed with one approximate method

Functional Mechanisms Underlying Pleiotropic Risk Alleles at the 19p13.1 Breast–Ovarian Cancer Susceptibility Locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P = 9.2 X 10-20), ER-negative BC (P = 1.1 X 10-13), BRCA1 -associated BC (P = 7.7 X 10-16) and triple negative BC (P-diff = 2 X 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P = 2 X 10-3) and ABHD8 (P \u3c 2 X 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8 , and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3\u27-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms

Type 2 diabetes (T2D) affects Latinos at twice the rate seen in populations of European descent. We recently identified a risk haplotype spanning SLC16A11 that explains ∼20% of the increased T2D prevalence in Mexico. Here, through genetic fine-mapping, we define a set of tightly linked variants likely to contain the causal allele(s). We show that variants on the T2D-associated haplotype have two distinct effects: (1) decreasing SLC16A11 expression in liver and (2) disrupting a key interaction with basigin, thereby reducing cell-surface localization. Both independent mechanisms reduce SLC16A11 function and suggest SLC16A11 is the causal gene at this locus. To gain insight into how SLC16A11 disruption impacts T2D risk, we demonstrate that SLC16A11 is a proton-coupled monocarboxylate transporter and that genetic perturbation of SLC16A11 induces changes in fatty acid and lipid metabolism that are associated with increased T2D risk. Our findings suggest that increasing SLC16A11 function could be therapeutically beneficial for T2D. Video Abstract [Figure presented] Keywords: type 2 diabetes (T2D); genetics; disease mechanism; SLC16A11; MCT11; solute carrier (SLC); monocarboxylates; fatty acid metabolism; lipid metabolism; precision medicin

Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction.

Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk