Publications

The covariance matrix Σ of non-linear clustering statistics that are measured in current and upcoming surveys is of fundamental interest for comparing cosmological theory and data and a crucial ingredient for the likelihood approximations underlying widely used parameter inference and forecasting methods. The extreme number of simulations needed to estimate Σ to sufficient accuracy poses a severe challenge. Approximating Σ using inexpensive but biased surrogates introduces model error with respect to full simulations, especially in the non-linear regime of structure growth. To address this problem we develop a matrix generalization of Convergence Acceleration by Regression and Pooling (CARPool) to combine a small number of simulations with fast surrogates and obtain low-noise estimates of Σ that are unbiased by construction. Our numerical examples use CARPool to combine GADGET-III N-body simulations with fast surrogates computed using COmoving Lagrangian Acceleration (COLA). Even at the challenging redshift z=0.5, we find variance reductions of at least (101) and up to (104) for the elements of the matter power spectrum covariance matrix on scales 8.9×10−3<kmax<1.0 hMpc−1. We demonstrate comparable performance for the covariance of the matter bispectrum, the matter correlation function and probability density function of the matter density field. We compare eigenvalues, likelihoods, and Fisher matrices computed using the CARPool covariance estimate with the standard sample covariance estimators and generally find considerable improvement except in cases where Σ is severely ill-conditioned.

The angular size of the broad line region (BLR) of the nearby active galactic nucleus (AGN) NGC 3783 has been spatially resolved by recent observations with VLTI/GRAVITY. A reverberation mapping (RM) campaign has also recently obtained high quality light curves and measured the linear size of the BLR in a way that is complementary to the GRAVITY measurement. The size and kinematics of the BLR can be better constrained by a joint analysis that combines both GRAVITY and RM data. This, in turn, allows us to obtain the mass of the supermassive black hole in NGC3783 with an accuracy that is about a factor of two better than that inferred from GRAVITY data alone. We derive MBH=2.54+0.90−0.72×107M⊙. Finally, and perhaps most notably, we are able to measure a geometric distance to NGC 3783 of 39.9+14.5−11.9 Mpc. We are able to test the robustness of the BLR-based geometric distance with measurements based on the Tully-Fisher relation and other indirect methods. We find the geometric distance is consistent with other methods within their scatter. We explore the potential of BLR-based geometric distances to directly constrain the Hubble constant, H0, and identify differential phase uncertainties as the current dominant limitation to the H0 measurement precision for individual sources.

Disk accretion onto weakly magnetized objects possessing a material surface must proceed via the so-called boundary layer (BL) - a region at the inner edge of the disk, in which the velocity of accreting material abruptly decreases from its Keplerian value. Supersonic shear arising in the BL is known to be conducive to excitation of acoustic waves that propagate into both the accretor and the disk, enabling angular momentum and mass transport across the BL. We carry out a numerical exploration of different wave modes that operate near the BL, focusing on their morphological characteristics in the innermost parts of accretion disk. Using a large suite of simulations covering a broad range of Mach numbers (of the supersonic shear flow in the BL), we provide accurate characterization of the different types of modes, verifying their properties against analytical results, when available. We discover new types of modes, in particular, global spiral density waves launched by vortices forming in the disk near the BL as a result of the Rossby wave instability; this instability is triggered by the vortensity production in that region caused by the nonlinear damping of acoustic waves. Azimuthal wavenumbers of the dominant modes that we observe appear to increase monotonically with the Mach number of the runs, but a particular mix of modes found in a simulation is mildly stochastic. Our results provide a basis for better understanding of the angular momentum and mass transport across the BL as well as the emission variability in accreting objects.

Many sensory-driven behaviors rely on predictions about future states of the environment. Visual input typically evolves along complex temporal trajectories that are difficult to extrapolate. We test the hypothesis that spatial processing mechanisms in the early visual system facilitate prediction by constructing neural representations that follow straighter temporal trajectories. We recorded V1 population activity in anesthetized macaques while presenting static frames taken from brief video clips, and developed a procedure to measure the curvature of the associated neural population trajectory. We found that V1 populations straighten naturally occurring image sequences, but entangle artificial sequences that contain unnatural temporal transformations. We show that these effects arise in part from computational mechanisms that underlie the stimulus selectivity of V1 cells. Together, our findings reveal that the early visual system uses a set of specialized computations to build representations that can support prediction in the natural environment.

In this paper we analyze the dynamics of single-excitation states, which model the scattering of a single photon from multiple two level atoms. For short times and weak atom-field couplings we show that the atomic amplitudes are given by a sum of decaying exponentials, where the decay rates and Lamb shifts are given by the poles of a certain analytic function. This result is a refinement of the "pole approximation" appearing in the standard Wigner-Weisskopf analysis of spontaneous emission. On the other hand, at large times, the atomic field decays like O(1/t3) with a known constant expressed in terms of the coupling parameter and the resonant frequency of the atoms. Moreover, we show that for stronger coupling, the solutions also feature a collection of oscillatory exponentials which dominate the behavior at long times. Finally, we extend the analysis to the continuum limit in which atoms are distributed according to a given density.

DNA damage reshapes the cellular transcriptome by modulating RNA transcription and processing. In cancer cells, these changes can alter the expression of genes in the immune surveillance and cell death pathways. Here, we investigate how DNA damage impacts alternative polyadenylation (APA) using the PAPERCLIP technique. We find that APA shifts are a coordinated response for hundreds of genes to DNA damage, and we identify PCF11 as an important contributor of DNA damage-induced APA shifts. One of these APA shifts results in upregulation of the full-length MSL1 mRNA isoform, which protects cells from DNA damage-induced apoptosis and promotes cell survival from DNA-damaging agents. Importantly, blocking MSL1 upregulation enhances cytotoxicity of chemotherapeutic agents even in the absence of p53 and overcomes chemoresistance. Our study demonstrates that characterizing adaptive APA shifts to DNA damage has therapeutic implications and reveals a link between PCF11, the MSL complex, and DNA damage-induced apoptosis.

Abstract Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's cardiolipin composition to resist such types of perturbations that compromise their membrane stability. Here, we used molecular dynamics simulations to quantify the role of cardiolipin on the formation of pores in simple bacterial-like membrane models composed of phosphatidylglycerol and cardiolipin mixtures. Cardiolopin modified the structure and ordering of the lipid bilayer, making it less susceptible to mechanical changes. Accordingly, the free-energy barrier for the formation of a transmembrane pore and its kinetic instability augmented by increasing the cardiolipin concentration. This is attributed to the unfavorable positioning of cardiolipin near the formed pore, due to its small polar-head and bulky hydrophobic-body. Overall, our study demonstrates how cardiolipin prevents membrane-pore formation and this constitutes a plausible mechanism used by bacteria to act against stress perturbations and, thereby, gain resistance to antimicrobial agents.

We report on an all-sky search for continuous gravitational waves in the frequency band 20-2000\,Hz and with a frequency time derivative in the range of [−1.0,+0.1]×10−8\,Hz/s. Such a signal could be produced by a nearby, spinning and slightly non-axisymmetric isolated neutron star in our galaxy. This search uses the LIGO data from the first six months of Advanced LIGO's and Advanced Virgo's third observational run, O3. No periodic gravitational wave signals are observed, and 95\%\ confidence-level (CL) frequentist upper limits are placed on their strengths. The lowest upper limits on worst-case (linearly polarized) strain amplitude h0 are 1.7×10−25 near 200\,Hz. For a circularly polarized source (most favorable orientation), the lowest upper limits are ∼6.3×10−26. These strict frequentist upper limits refer to all sky locations and the entire range of frequency derivative values. For a population-averaged ensemble of sky locations and stellar orientations, the lowest 95\%\ CL upper limits on the strain amplitude are ∼1.×10−25. These upper limits improve upon our previously published all-sky results, with the greatest improvement (factor of ∼2) seen at higher frequencies, in part because quantum squeezing has dramatically improved the detector noise level relative to the second observational run, O2. These limits are the most constraining to date over most of the parameter space searched.

The characteristics of the stellar populations in the Galactic bulge inform and constrain the Milky Way’s formation and evolution. The metal-poor population is particularly important in light of cosmological simulations, which predict that some of the oldest stars in the Galaxy now reside in its centre. The metal-poor bulge appears to consist of multiple stellar populations that require dynamical analyses to disentangle. In this work, we undertake a detailed chemodynamical study of the metal-poor stars in the inner Galaxy. Using R ∼ 20 000 VLT/GIRAFFE spectra of 319 metal-poor (−2.55 dex ≤ [Fe/H] ≤ 0.83 dex, with [Fe/H] = −0.84 dex) stars, we perform stellar parameter analysis and report 12 elemental abundances (C, Na, Mg, Al, Si, Ca, Sc, Ti, Cr, Mn, Zn, Ba, and Ce) with precisions of ≈0.10 dex. Based on kinematic and spatial properties, we categorize the stars into four groups, associated with the following Galactic structures: the inner bulge, the outer bulge, the halo, and the disc. We find evidence that the inner and outer bulge population is more chemically complex (i.e. higher chemical dimensionality and less correlated abundances) than the halo population. This result suggests that the older bulge population was enriched by a larger diversity of nucleosynthetic events. We also find one inner bulge star with a [Ca/Mg] ratio consistent with theoretical pair-instability supernova yields and two stars that have chemistry consistent with globular cluster stars.

Problems with networks of coupled oscillators arise in multiple contexts, commonly leading to the question about the dependence of network dynamics on network structure. Previous work has addressed this question in Drosophila oogenesis, where stable cytoplasmic bridges connect the future oocyte to the supporting nurse cells that supply the oocyte with molecules and organelles needed for its development. To increase their biosynthetic capacity, nurse cells enter the endoreplication program, a special form of the cell cycle formed by the iterated repetition of growth and synthesis phases without mitosis. Recent studies have revealed that the oocyte orchestrates nurse cell endoreplication cycles, based on retrograde (oocyte to nurse cells) transport of a cell cycle inhibitor produced by the nurse cells and localized to the oocyte. Furthermore, the joint dynamics of endocycles has been proposed to depend on the intercellular connectivity within the oocyte-nurse cell cluster. We use a computational model to argue that this connectivity guides, but does not uniquely determine the collective dynamics and identify several oscillatory regimes, depending on the time scale of intercellular transport. Our results provide insights into collective dynamics of coupled cell cycles and motivate future quantitative studies of intercellular communication in the germline cell clusters.