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Small Angle-X-ray Scattering Tensor Tomography (SAS-TT) is a relatively new, but powerful technique for studying the multiscale architecture of hierarchical structures, which is of particular interest for life science applications. Currently, the technique is very demanding on synchrotron beamtime, which limits its applications, especially for cases requiring a statistically relevant amount of sample. This study reports the first SAS-TT measurement at a macromolecular X-ray crystallography beamline, PX-I at the SLS, with an improvement in data acquisition time from 96 h/Mvoxel in the pilot experiments to 6 h/Mvoxel, defining a new standard for fast SAS-TT and allowing the measurement of a full tomogram in 1.2 hours. Measurements were performed on the long and lenticular process of the incus bone, one of the three human auditory ossicles. The main orientation and degree of alignment of the mineralised collagen fibrils are characterised, as well as the size and shape of the mineral particles which show relevant variations in different tissue locations. The study reveals three distinct regions of high fibril alignment, most likely important pathways of sound throughout the ossicular chain, and highlights the potential of the technique to aid in future developments in middle ear reconstructive surgery.

We present a novel framework for jointly modelling the weak lensing source galaxy redshift distribution and the intrinsic alignment of galaxies via a shared luminosity function (LF). Considering this framework within the context of a Rubin Observatory's Legacy Survey of Space and Time (LSST) Year 1 and Year 10 cosmic shear analysis, we first demonstrate the substantial impact of the LF on both source galaxy redshift distributions and the intrinsic alignment contamination. We establish how the individual parameters of a Schechter LF model impact the redshift distribution of a magnitude-limited sample, and we demonstrate the effect of marginalising over the LF parameters as incorporated in the intrinsic alignment modelling of a standard cosmic shear analysis set-up. We forecast the impact of our joint modelling framework on cosmological parameter constraints. Our preliminary results are promising, indicating that this framework can yield cosmological constraints consistent with those expected from standard analyses, enhanced by the flexibility of not fixing LF parameters. We plan to further validate these findings with comprehensive Markov chain Monte Carlo simulations to robustly quantify bias avoidance and underscore the framework's efficacy. Taking advantage of our forecasting results and the parameter degeneracies, we identify the specific impact of the shape of the LF of source galaxies on the cosmic shear data vector. We also discuss the potential of this method in providing a way to model generic selection functions in redshift distribution estimation, as well as its possibilities for extension to a 3x2pt analysis, particularly with respect to incorporating galaxy bias in this luminosity-function-based framework. Although we consider the context of LSST cosmic shear in this work, the proposed joint modelling framework is generically applicable to weak lensing surveys., Comment: 19 pages, 16 figures, 3 tables; v2: added LSST DESC to arxiv author list

Small-angle scattering tensor tomography is a technique for studying anisotropic nanostructures of millimeter-sized samples in a volume-resolved manner. It requires the acquisition of data through repeated tomographic rotations about an axis which is subjected to a series of tilts. The tilt that can be achieved with a typical setup is geometrically constrained, which leads to limits in the set of directions from which the different parts of the reciprocal-space map can be probed. Here, we characterize the impact of this limitation on reconstructions in terms of the missing wedge problem of tomography, by treating the problem of tensor tomography as the reconstruction of a three-dimensional field of functions on the unit sphere, represented by a grid of Gaussian radial basis functions. We then devise an acquisition scheme to obtain complete data by remounting the sample, which we apply to a sample of human trabecular bone. Performing tensor tomographic reconstructions of limited data sets as well as the complete data set, we further investigate and validate the missing wedge understanding of data incompleteness by investigating reconstruction errors due to data incompleteness across both real and reciprocal space. Finally, we carry out an analysis of orientations and derived scalar quantities, to quantify the impact of this missing wedge problem on a typical tensor tomographic analysis. We conclude that the effects of data incompleteness are consistent with the predicted impact of the missing wedge problem, and that the impact on tensor tomographic analysis is appreciable but limited, especially if precautions are taken. In particular, there is only limited impact on the means and relative anisotropies of the reconstructed reciprocal space maps., Comment: Main: 32 pages, 9 figures; Supplementary: 9 pages, 7 figuers

We present a systematic study of cosmological parameter bias in weak lensing and large-scale structure analyses for upcoming imaging surveys induced by the interplay of intrinsic alignments (IA) and photometric redshift (photo-z) model mis-specification error. We first examine the degeneracies between the parameters of the Tidal Alignment - Tidal Torquing (TATT) model for IA and of a photo-z model including a mean shift ($\Delta \bar{z}$) and variance ($\sigma_{z}$) for each tomographic bin of lenses and sources, under a variety of underlying true IA behaviors. We identify strong degeneracies between: (1) the redshift scaling of the tidal alignment amplitude and the mean shift and variances of source bins, (2) the redshift scaling of the tidal torquing amplitude and the variance of the lowest-$z$ source bin, and (3) the IA source density weighting and the mean shift and variance of several source bins. We then use this information to guide our exploration of the level of cosmological parameter bias which can be induced given incorrect modelling of IA, photo-z, or both. We find that marginalizing over all the parameters of TATT is generally sufficient to preclude cosmological parameter bias in the scenarios we consider. However, this does not necessarily mean that IA and photo-z parameters are themselves unbiased, nor does it mean that the best-fit model is a good fit to the data. We also find scenarios where the inferred parameters produce $\chi^2_{\rm DOF}$ values indicative of a good fit but cosmological parameter bias is significant, particularly when the IA source density weighting parameter is not marginalized over., Comment: 20 pages, 13 figures. Updated to match accepted version

In the context of cosmological weak lensing studies, intrinsic alignments (IAs) are one the most complicated astrophysical systematic to model, given the poor understanding of the physical processes that cause them. A number of modelling frameworks for IAs have been proposed in the literature, both purely phenomenological or grounded on a perturbative treatment of symmetry-based arguments. However, the accuracy with which any of these approaches is able to describe the impact of IAs on cosmic shear data, particularly on the comparatively small scales ($k\simeq 1\,{\rm Mpc}^{-1}$) to which this observable is sensitive, is not clear. Here we quantify the level of disagreement between the true underlying intrinsic alignments and the theoretical model used to describe them that can be allowed in the context of cosmic shear analyses with future Stage-IV surveys. We consider various models describing this "IA residual", covering both physics-based approaches, as well as completely agnostic prescriptions. The same qualitative results are recovered in all cases explored: for a Stage-IV cosmic shear survey, a mis-modelling of the IA contribution at the $\sim10\%$ level produces shifts of $\lesssim0.5\sigma$ on the final cosmological parameter constraints. Current and future IA models should therefore aim to achieve this level of accuracy, a prospect that is not unfeasible for models with sufficient flexibility.

We extend current models of the halo occupation distribution (HOD) to include a flexible, empirical framework for the forward modeling of the intrinsic alignment (IA) of galaxies. A primary goal of this work is to produce mock galaxy catalogs for the purpose of validating existing models and methods for the mitigation of IA in weak lensing measurements. This technique can also be used to produce new, simulation-based predictions for IA and galaxy clustering. Our model is probabilistically formulated, and rests upon the assumption that the orientations of galaxies exhibit a correlation with their host dark matter (sub)halo orientation or with their position within the halo. We examine the necessary components and phenomenology of such a model by considering the alignments between (sub)halos in a cosmological dark matter only simulation. We then validate this model for a realistic galaxy population in a set of simulations in the IllustrisTNG suite. We create an HOD mock with TNG-like correlations using our method, constraining the associated IA model parameters, with the $\chi^2_{\rm dof}$ between our model's correlations and those of Illustris matching as closely as 1.4 and 1.1 for orientation--position and orientation--orientation correlation functions, respectively. By modeling the misalignment between galaxies and their host halo, we show that the 3-dimensional two-point position and orientation correlation functions of simulated (sub)halos and galaxies can be accurately reproduced from quasi-linear scales down to $0.1~h^{-1}{\rm Mpc}$. We also find evidence for environmental influence on IA within a halo. Our publicly-available software provides a key component enabling efficient determination of Bayesian posteriors on IA model parameters using observational measurements of galaxy-orientation correlation functions in the highly nonlinear regime., Comment: 19 pages, 13 figures, 3 tables, accepted for publication by The Open Journal of Astrophysics, code available at https://github.com/astropy/halotools

Modern science is dependent on imaging on the nanoscale, often achieved through processes that detect secondary electrons created by a highly focused incident charged particle beam. Multiple types of measurement noise limit the ultimate trade-off between the image quality and the incident particle dose, which can preclude useful imaging of dose-sensitive samples. Existing methods to improve image quality do not fundamentally mitigate the noise sources. Furthermore, barriers to assigning a physically meaningful scale make the images qualitative. Here we introduce ion count-aided microscopy (ICAM), which is a quantitative imaging technique that uses statistically principled estimation of the secondary electron yield. With a readily implemented change in data collection, ICAM substantially reduces source shot noise. In helium ion microscopy, we demonstrate 3x dose reduction and a good match between these empirical results and theoretical performance predictions. ICAM facilitates imaging of fragile samples and may make imaging with heavier particles more attractive., Comment: Updated Introduction, Updated Discussion and Outlook, Updated Methods. Main article: 17 pages, 4 figures

4-Dimensional Einstein-Gauss-Bonnet (4DEGB) gravity has garnered significant attention in the last few years as a phenomenological competitor to general relativity. We consider the theoretical and observational implications of this theory in both the early and late universe, (re-)deriving background and perturbation equations and constraining its characteristic parameters with data from cosmological probes. Our investigation surpasses the scope of previous studies by incorporating non-flat spatial sections. We explore consequences of 4DEGB on the sound and particle horizons in the very early universe, and demonstrate that 4DEGB can provide an independent solution to the horizon problem for some values of its characteristic parameter $\alpha$. Finally, we constrain an unexplored regime of this theory in the limit of small coupling $\alpha$ (empirically supported in the post-Big Bang Nucleosynthesis era by prior constraints). This version of 4DEGB includes a geometric term that resembles dark radiation at the background level, but whose influence on the perturbed equations is qualitatively distinct from that of standard forms of dark radiation. In this limit, only one beyond-$\Lambda$CDM degree of freedom persists, which we denote as $\tilde{\alpha}_C$. Our analysis yields the estimate $\tilde{\alpha}_C = (-9 \pm 6) \times 10^{-6}$ thereby providing a new constraint of a previously untested sector of 4DEGB., Comment: 17 pages, 5 figures (excluding appendices). Updated to reflect JCAP author-accepted version

We propose and analyze an epidemiological model for vector borne diseases that integrates a multi-stage vector population and several host sub-populations which may be characterized by a variety of compartmental model types: subpopulations all include Susceptible and Infected compartments, but may or may not include Exposed and/or Recovered compartments. The model was originally designed to evaluate the effectiveness of various prophylactic measures in malaria-endemic areas, but can be applied as well to other vector-borne diseases. This model is expressed as a system of several differential equations, where the number of equations depends on the particular assumptions of the model. We compute the basic reproduction number $\mathcal R_0$, and show that if $\mathcal R_0\leqslant 1$, the disease free equilibrium (DFE) is globally asymptotically stable (GAS) on the nonnegative orthant. If $\mathcal R_0>1$, the system admits a unique endemic equilibrium (EE) that is GAS. We analyze the sensitivity of $R_0$ and the EE to different system parameters, and based on this analysis we discuss the relative effectiveness of different control measures., Comment: 42 pages, 3 figures. arXiv admin note: substantial text overlap with arXiv:1808.07574

Without mitigation, the intrinsic alignment (IA) of galaxies poses a significant threat to achieving unbiased cosmological parameter constraints from precision weak lensing surveys. Here, we apply for the first time to data a method to extract the scale dependence of the IA contribution to galaxy-galaxy lensing, which takes advantage of the difference in alignment signal as measured by shear estimators with different sensitivities to galactic radii. Using data from Year 1 of the Dark Energy Survey, with shear estimators METACALIBRATION and IM3SHAPE, we investigate and address method systematics including non-trivial selection functions, differences in weighting between estimators, and multiplicative bias. We obtain a null detection of IA, which appears qualitatively consistent with existing work. We then forecast the application of this method to Rubin Observatory Legacy Survey of Space and Time (LSST) data and place requirements on a pair of shear estimators for detecting IA and constraining its 1-halo scale dependence. We find that for LSST Year 1, shear estimators should have at least a $40\%$ difference in IA amplitude, and the Pearson correlation coefficient of their shape noise should be at least $\rho=0.50$, to ensure a $1\sigma$ detection of IA and a constraint on its 1-halo scale dependence with a signal-to-noise ratio greater than $1$. For Year 10, a $1\sigma$ detection and constraint become possible for $20\%$ differences in alignment amplitude and $\rho=0.50$., Comment: Fixed formatting issue in abstract metadata

The development of small-angle scattering tensor tomography has enabled the study of anisotropic nanostructures in a volume-resolved manner. It is of great value to have reconstruction methods that can handle many different nanostructural symmetries. For such a method to be employed by researchers from a wide range of backgrounds, it is crucial that its reliance on prior knowledge about the system is minimized, and that it is robust under various conditions. Here, we present a method employing band-limited spherical functions to enable the reconstruction of reciprocal space maps of a wide variety of nanostructures. This method has been thoroughly tested and compared to existing methods in its ability to retrieve known reciprocal space maps, as well as its robustness to changes in initial conditions, using both simulations and experimental data. The anchoring of this method in a framework of integral geometry and linear algebra highlights its possibilities and limitations., Comment: Article has 11 pages and 6 figures, supplementary information has 7 pages and 4 figures

Multifunctionality as a paradigm requires materials exhibiting multiple superior properties. Integrating second-order optical nonlinearity and large bandgap with piezoelectricity could, for example, enable broadband, strain-tunable photonics. Though very different phenomena at distinct frequencies, both second-order optical nonlinearity and piezoelectricity are third-rank polar tensors present only in acentric crystal structures. However, simultaneously enhancing both phenomena is highly challenging since it involves competing effects with tradeoffs. Recently, a large switchable ferroelectric polarization of ~ 80 uC cm-2 was reported in Zn1-xMgxO films. Here, ferroelectric Zn1-xMgxO is demonstrated to be a platform that hosts simultaneously a 30% increase in the electronic bandgap, a 50% enhancement in the second harmonic generation coefficients, and a near 200% improvement in the piezoelectric coefficients over pure ZnO. These enhancements are shown to be due to a 400% increase in the electronic anharmonicity and a ~200% decrease in the ionic anharmonicity with Mg substitution. Precisely controllable periodic ferroelectric domain gratings are demonstrated down to 800 nm domain width, enabling ultraviolet quasi-phase-matched optical harmonic generation as well as domain-engineered piezoelectric devices.

High quality, ultrathin, superconducting films are required for advanced devices such as hot-electron bolometers, superconducting nanowire single photon detectors, and quantum applications. Using Hybrid Physical-Chemical Vapor Deposition (HPCVD), we show that MgB2 films as thin as 4 nm can be fabricated on the carbon terminated 6H-SiC (0001) surface with a superconducting transition temperature above 33K and a rms roughness of 0.7 nm. Remarkably, the film quality is a function of the SiC surface termination, with the C-terminated surface preferred to the Si-terminated surface. To understand the MgB2 thin film/ SiC substrate interactions giving rise to this difference, we characterized the interfacial structures using Rutherford backscattering spectroscopy/channeling, electron energy loss spectroscopy, and x-ray photoemission spectroscopy. The MgB2/SiC interface structure is complex and different for the two terminations. Both terminations incorporate substantial unintentional oxide layers influencing MgB2 growth and morphology, but with different extent, intermixing and interface chemistry. In this paper, we report measurements of transport, resistivity, and critical superconducting temperature of MgB2/SiC that are different for the two terminations, and link interfacial structure variations to observed differences. The result shows that the C face of SiC is a preferred substrate for the deposition of ultrathin superconducting MgB2 films.

The rapidly increasing statistical power of cosmological imaging surveys requires us to reassess the regime of validity for various approximations that accelerate the calculation of relevant theoretical predictions. In this paper, we present the results of the 'N5K non-Limber integration challenge', the goal of which was to quantify the performance of different approaches to calculating the angular power spectrum of galaxy number counts and cosmic shear data without invoking the so-called 'Limber approximation', in the context of the Rubin Observatory Legacy Survey of Space and Time (LSST). We quantify the performance, in terms of accuracy and speed, of three non-Limber implementations: ${\tt FKEM (CosmoLike)}$, ${\tt Levin}$, and ${\tt matter}$, themselves based on different integration schemes and approximations. We find that in the challenge's fiducial 3x2pt LSST Year 10 scenario, ${\tt FKEM (CosmoLike)}$ produces the fastest run time within the required accuracy by a considerable margin, positioning it favourably for use in Bayesian parameter inference. This method, however, requires further development and testing to extend its use to certain analysis scenarios, particularly those involving a scale-dependent growth rate. For this and other reasons discussed herein, alternative approaches such as ${\tt matter}$ and ${\tt Levin}$ may be necessary for a full exploration of parameter space. We also find that the usual first-order Limber approximation is insufficiently accurate for LSST Year 10 3x2pt analysis on $\ell=200-1000$, whereas invoking the second-order Limber approximation on these scales (with a full non-Limber method at smaller $\ell$) does suffice., Comment: 15 pages, 8 figures. Journal-accepted version

We constrain extensions to the $\Lambda$CDM model using measurements from the Dark Energy Survey's first three years of observations and external data. The DES data are the two-point correlation functions of weak gravitational lensing, galaxy clustering, and their cross-correlation. We use simulated data and blind analyses of real data to validate the robustness of our results. In many cases, constraining power is limited by the absence of nonlinear predictions that are reliable at our required precision. The models are: dark energy with a time-dependent equation of state, non-zero spatial curvature, sterile neutrinos, modifications of gravitational physics, and a binned $\sigma_8(z)$ model which serves as a probe of structure growth. For the time-varying dark energy equation of state evaluated at the pivot redshift we find $(w_{\rm p}, w_a)= (-0.99^{+0.28}_{-0.17},-0.9\pm 1.2)$ at 68% confidence with $z_{\rm p}=0.24$ from the DES measurements alone, and $(w_{\rm p}, w_a)= (-1.03^{+0.04}_{-0.03},-0.4^{+0.4}_{-0.3})$ with $z_{\rm p}=0.21$ for the combination of all data considered. Curvature constraints of $\Omega_k=0.0009\pm 0.0017$ and effective relativistic species $N_{\rm eff}=3.10^{+0.15}_{-0.16}$ are dominated by external data. For massive sterile neutrinos, we improve the upper bound on the mass $m_{\rm eff}$ by a factor of three compared to previous analyses, giving 95% limits of $(\Delta N_{\rm eff},m_{\rm eff})\leq (0.28, 0.20\, {\rm eV})$. We also constrain changes to the lensing and Poisson equations controlled by functions $\Sigma(k,z) = \Sigma_0 \Omega_{\Lambda}(z)/\Omega_{\Lambda,0}$ and $\mu(k,z)=\mu_0 \Omega_{\Lambda}(z)/\Omega_{\Lambda,0}$ respectively to $\Sigma_0=0.6^{+0.4}_{-0.5}$ from DES alone and $(\Sigma_0,\mu_0)=(0.04\pm 0.05,0.08^{+0.21}_{-0.19})$ for the combination of all data. Overall, we find no significant evidence for physics beyond $\Lambda$CDM., Comment: Updated to match published version and fix a citation reference. 46 pages, 25 figures, data available at https://dev.des.ncsa.illinois.edu/releases/y3a2/Y3key-extensions