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We uncover late-time gravitational-wave tails in fully nonlinear 3+1 dimensional numerical relativity simulations of merging black holes, using the highly accurate SpEC code. We achieve this result by exploiting the strong magnification of late-time tails due to binary eccentricity, recently observed in perturbative evolutions, and showcase here the tail presence in head-on configurations for several mass ratios close to unity. We validate the result through a large battery of numerical tests and detailed comparison with perturbative evolutions, which display striking agreement with full nonlinear ones. Our results offer yet another confirmation of the highly predictive power of black hole perturbation theory in the presence of a source, even when applied to nonlinear solutions. The late-time tail signal is much more prominent than anticipated until recently, and possibly within reach of gravitational-wave detectors measurements, unlocking observational investigations of an additional set of general relativistic predictions on the long-range gravitational dynamics., Comment: 5+7 pages, 2+5 figures, 1+1 tables

We present successful evolutions of binary black hole mergers using a novel numerical-relativity technique known as Cauchy-characteristic matching (CCM). This approach eliminates systematic errors associated with boundary conditions, effectively extending the computational domain to infinity. As an important application, we use CCM to resolve a late-time power-law tail in the gravitational wave from a head-on collision, and show that the tail is highly suppressed in a quasi-circular binary. Our results for the two extreme cases (orbital eccentricity $=0,1$) support the fact that tails increase with orbital eccentricity. Therefore, CCM paves the way for a detailed understanding of tails in eccentric systems. For the head-on case, we find that the tail behavior is consistent with predictions in the intermediate regime from black hole linear perturbation theory. However, we also raise the possibility that the power-law tail could be generated nonlinearly by quasinormal modes. The nonlinear contribution is expected to decay slower than predicted by Price's law, potentially dominating the signal at late times. If confirmed as nonlinear, this would be an example where nonlinearity prevails over linearity in the late-time regime of black hole dynamics.

Using high-accuracy numerical relativity waveforms, we confirm the presence of numerous overtones of the $\ell=2$, $m=2$ quasinormal mode early in the ringdown of binary black hole mergers. We do this by demonstrating the stability of the mode amplitudes at different fit times, ruling out the possibility that a linear superposition of modes unphysically fits a highly nonlinear part of the waveform. We also find a number of previously unidentified subdominant second-order quasinormal modes in the $(2,2)$ mode. Even though these modes are mathematically nonlinear, they nevertheless confirm the validity of perturbation theory as a good approximation for describing much of the ringdown., Comment: 17 pages, 14 figures

We assess the prospects for detecting gravitational wave echoes arising due to the quantum nature of black hole horizons with LISA. In a recent proposal, Bekenstein's black hole area quantization is connected to a discrete absorption spectrum for black holes in the context of gravitational radiation. Consequently, for incoming radiation at the black hole horizon, not all frequencies are absorbed, raising the possibility that the unabsorbed radiation is reflected, producing an echo-like signal closely following the binary coalescence waveform. In this work, we further develop this proposal by introducing a robust, phenomenologically motivated model for black hole reflectivity. Using this model, we calculate the resulting echoes for an ensemble of Numerical Relativity waveforms and examine their detectability with the LISA space-based interferometer. Our analysis demonstrates promising detection prospects and shows that, upon detection, LISA provides a direct probe of the Bekenstein-Hawking entropy. In addition, we find that the information extractable from LISA data offers valuable constraints on a wide range of quantum gravity theories., Comment: 9 pages, 8 Figures

Binary black holes are the most abundant source of gravitational-wave observations. Gravitational-wave observatories in the next decade will require tremendous increases in the accuracy of numerical waveforms modeling binary black holes, compared to today's state of the art. One approach to achieving the required accuracy is using spectral-type methods that scale to many processors. Using the SpECTRE numerical-relativity code, we present the first simulations of a binary black hole inspiral, merger, and ringdown using discontinuous Galerkin methods. The efficiency of discontinuous Galerkin methods allows us to evolve the binary through ~18 orbits at reasonable computational cost. We then use SpECTRE's Cauchy Characteristic Evolution (CCE) code to extract the gravitational waves at future null infinity. The open-source nature of SpECTRE means this is the first time a spectral-type method for simulating binary black hole evolutions is available to the entire numerical-relativity community., Comment: 32 pages, 12 figures, 28 ancillary input files

Cauchy-characteristic evolution (CCE) is a powerful method for accurately extracting gravitational waves at future null infinity. In this work, we extend the previously implemented CCE system within the numerical relativity code SpECTRE by incorporating a scalar field. This allows the system to capture features of beyond-general-relativity theories. We derive scalar contributions to the equations of motion, Weyl scalar computations, Bianchi identities, and balance laws at future null infinity. Our algorithm, tested across various scenarios, accurately reveals memory effects induced by both scalar and tensor fields and captures Price's power-law tail ($u^{-l-2}$) in scalar fields at future null infinity, in contrast to the $t^{-2l-3}$ tail at future timelike infinity.

Highly precise and robust waveform models are required as improvements in detector sensitivity enable us to test general relativity with more precision than ever before. In this work, we introduce a spin-aligned surrogate ringdown model. This ringdown surrogate, NRSur3dq8_RD, is built with numerical waveforms produced using Cauchy-characteristic evolution. In addition, these waveforms are in the superrest frame of the remnant black hole allowing us to do a correct analysis of the ringdown spectrum. The novel prediction of our surrogate model is complex-valued quasinormal mode (QNM) amplitudes, with median relative errors of $10^{-2}-10^{-3}$ over the parameter space. Like previous remnant surrogates, we also predict the remnant black hole's mass and spin. The QNM mode amplitude errors translate into median errors on ringdown waveforms of $10^{-4}$. The high accuracy and QNM mode content provided by our surrogate will enable high-precision ringdown analyses such as tests of general relativity. Our ringdown model is publicly available through the python package surfinBH., Comment: 11+2 pages, 13 figures, 1 table. This new model is publicly available through surfinBH https://pypi.org/project/surfinBH/

We present a discontinuous Galerkin-finite difference hybrid scheme that allows high-order shock capturing with the discontinuous Galerkin method for general relativistic magnetohydrodynamics in dynamical spacetimes. We present several optimizations and stability improvements to our algorithm that allow the hybrid method to successfully simulate single, rotating, and binary neutron stars. The hybrid method achieves the efficiency of discontinuous Galerkin methods throughout almost the entire spacetime during the inspiral phase, while being able to robustly capture shocks and resolve the stellar surfaces. We also use Cauchy-Characteristic evolution to compute the first gravitational waveforms at future null infinity from binary neutron star mergers. The simulations presented here are the first successful binary neutron star inspiral and merger simulations using discontinuous Galerkin methods., Comment: 31 pages, 8 figures, minor wording updates

Gravitational memory effects and the BMS freedoms exhibited at future null infinity have recently been resolved and utilized in numerical relativity simulations. With this, gravitational wave models and our understanding of the fundamental nature of general relativity have been vastly improved. In this paper, we review the history and intuition behind memory effects and BMS symmetries, how they manifest in gravitational waves, and how controlling the infinite number of BMS freedoms of numerical relativity simulations can crucially improve the waveform models that are used by gravitational wave detectors. We reiterate the fact that, with memory effects and BMS symmetries, not only can these next-generation numerical waveforms be used to observe never-before-seen physics, but they can also be used to test GR and learn new astrophysical information about our universe., Comment: 22 pages, 8 figures. Matches published version in CGQ's focus issue: Gravitational-Wave Memory Effects: From Theory to Observation

Numerical relativists can now produce gravitational waveforms with memory effects routinely and accurately. The gravitational-wave memory effect contains very low-frequency components, including a persistent offset. The presence of these components violates basic assumptions about time-shift behavior underpinning standard data-analysis techniques in gravitational-wave astronomy. This poses a challenge to the analysis of waveform spectra: How to preserve the low-frequency characteristics when transforming a time-domain waveform to the frequency domain. To tackle this challenge, we revisit the preprocessing procedures applied to the waveforms that contain memory effects. We find inconsistency between the zero-frequency limit of displacement memory and the low- frequency spectrum of the same memory preprocessed using the common scheme in literature. To resolve the inconsistency, we propose a new robust preprocessing scheme that produces the spectra of memory waveforms more faithfully. Using this new scheme, we inspect several characteristics of the spectrum of a memory waveform. In particular, we find a discernible beating pattern formed by the dominant oscillatory mode and the displacement memory. This pattern is absent in the spectrum of a waveform without memory. The difference between the memory and no-memory waveforms is too small to be observed by current-generation detectors in a single binary-black-hole event. Detecting the memory in a single event is likely to occur in the era of next-generation detectors., Comment: 24 pages, 11 figures, 5 tables

The ringdown portion of a binary black hole merger consists of a sum of modes, each containing an infinite number of tones that are exponentially damped sinusoids. In principle, these can be measured as gravitational-waves with observatories like LIGO/Virgo/KAGRA, however in practice it is unclear how many tones can be meaningfully resolved. We investigate the consistency and resolvability of the overtones of the quadrupolar $\ell = m = 2$ mode by starting at late times when the gravitational waveform is expected to be well-approximated by the $\ell m n = 220$ tone alone. We present a Bayesian inference framework to measure the tones in numerical relativity data. We measure tones at different start times, checking for consistency: we classify a tone as stably recovered if and only if the 95\% credible intervals for amplitude and phase at time $t$ overlap with the credible intervals at all subsequent times. We test a set of tones including the first four overtones of the fundamental mode and the 320 tone and find that the 220 and 221 tones can be measured consistently with the inclusion of additional overtones. The 222 tone measurements can be stabilised when we include the 223 tone, but only in a narrow time window, after which it is too weak to measure. The 223 tone recovery appears to be unstable, and does not become stable with the introduction of the 224 tone. We find that $N=3$ tones can be stably recovered simultaneously. However, when analysing $N \geq 4$ tones, the amplitude of one tone is consistent with zero. Thus, within our framework, one can identify only $N=3$ tones with non-zero amplitude that are simultaneously stable., Comment: 14 pages, 8 figures, 2 tables. Published in PRD

We investigate quadratic quasinormal mode coupling in black hole spacetime through numerical simulations of single perturbed black holes using both numerical relativity and second-order black hole perturbation theory. Focusing on the dominant $\ell=|m|=2$ quadrupolar modes, we find good agreement (within $\sim10\%$) between these approaches, with discrepancies attributed to truncation error and uncertainties from mode fitting. Our results align with earlier studies extracting the coupling coefficients from select binary black hole merger simulations, showing consistency for the same remnant spins. Notably, the coupling coefficient is insensitive to a diverse range of initial data, including configurations that led to a significant (up to $5\%$) increase in the remnant black hole mass. These findings present opportunities for testing the nonlinear dynamics of general relativity with ground-based gravitational wave observatories. Lastly, we provide evidence of a bifurcation in coupling coefficients between counter-rotating and co-rotating quasinormal modes as black hole spin increases.

The spectroscopic study of black hole quasinormal modes in gravitational-wave ringdown observations is hindered by our ignorance of which modes should dominate astrophysical signals for different binary configurations, limiting tests of general relativity and astrophysics. In this work, we present a description of the quasinormal modes that are excited in the ringdowns of comparable mass, quasi-circular precessing binary black hole coalescences -- a key region of parameter space that has yet to be fully explored within the framework of black hole spectroscopy. We suggest that the remnant perturbation for precessing and non-precessing systems is approximately the same up to a rotation, which implies that the relative amplitudes of the quasinormal modes in both systems are also related by a rotation. We present evidence for this by analyzing an extensive catalog of numerical relativity simulations. Additional structure in the amplitudes is connected to the system's kick velocity and other asymmetries in the orbital dynamics. We find that the ringdowns of precessing systems need not be dominated by the ${(\ell,m)=(2,\pm 2)}$ quasinormal modes, and that instead the $(2,\pm 1)$~or~$(2,0)$ quasinormal modes can dominate. Our results are consistent with a ringdown analysis of the LIGO-Virgo gravitational wave signal GW190521, and may also help in understanding phenomenological inspiral-merger-ringdown waveform model systematics., Comment: Data Release and Analysis Scripts: https://github.com/HengruiPrinceton/precession_ringdown

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is the process of determining correspondences between entities across these resources, such as gene identifiers, disease concepts, or chemical entity identifiers. Many tools have been developed to compute such mappings based on common structural features and lexical information such as labels and synonyms. Lexical approaches in particular often provide very high recall, but low precision, due to lexical ambiguity. As a consequence of this, mapping efforts often resort to a labor intensive manual mapping refinement through a human curator. Large Language Models (LLMs), such as the ones employed by ChatGPT, have generalizable abilities to perform a wide range of tasks, including question-answering and information extraction. Here we present MapperGPT, an approach that uses LLMs to review and refine mapping relationships as a post-processing step, in concert with existing high-recall methods that are based on lexical and structural heuristics. We evaluated MapperGPT on a series of alignment tasks from different domains, including anatomy, developmental biology, and renal diseases. We devised a collection of tasks that are designed to be particularly challenging for lexical methods. We show that when used in combination with high-recall methods, MapperGPT can provide a substantial improvement in accuracy, beating state-of-the-art (SOTA) methods such as LogMap.

A fully relativistic three-dimensional Cauchy-characteristic matching (CCM) algorithm is implemented for physical degrees of freedom in a numerical relativity code SpECTRE. The method is free of approximations and can be applied to any physical system. We test the algorithm with various scenarios involving smooth data, including the propagation of Teukolsky waves within a flat background, the perturbation of a Kerr black hole with a Teukolsky wave, and the injection of a gravitational-wave pulse from the characteristic grid. Our investigations reveal no numerical instabilities in the simulations. In addition, the tests indicate that the CCM algorithm effectively directs characteristic information into the inner Cauchy system, yielding higher precision in waveforms and smaller violations of Bondi-gauge constraints, especially when the outer boundary of the Cauchy evolution is at a smaller radius.

Numerical relativity simulations provide the most precise templates for the gravitational waves produced by binary black hole mergers. However, many of these simulations use an incomplete waveform extraction technique -- extrapolation -- that fails to capture important physics, such as gravitational memory effects. Cauchy-characteristic evolution (CCE), by contrast, is a much more physically accurate extraction procedure that fully evolves Einstein's equations to future null infinity and accurately captures the expected physics. In this work, we present a new surrogate model, NRHybSur3dq8$\_$CCE, built from CCE waveforms that have been mapped to the post-Newtonian (PN) BMS frame and then hybridized with PN and effective one-body (EOB) waveforms. This model is trained on 102 waveforms with mass ratios $q\leq8$ and aligned spins $\chi_{1z}, \, \chi_{2z} \in \left[-0.8, 0.8\right]$. The model spans the entire LIGO-Virgo-KAGRA (LVK) frequency band (with $f_{\text{low}}=20\text{Hz}$) for total masses $M\gtrsim2.25M_{\odot}$ and includes the $\ell\leq4$ and $(\ell,m)=(5,5)$ spin-weight $-2$ spherical harmonic modes, but not the $(3,1)$, $(4,2)$ or $(4,1)$ modes. We find that NRHybSur3dq8$\_$CCE can accurately reproduce the training waveforms with mismatches $\lesssim2\times10^{-4}$ for total masses $2.25M_{\odot}\leq M\leq300M_{\odot}$ and can, for a modest degree of extrapolation, capably model outside of its training region. Most importantly, unlike previous waveform models, the new surrogate model successfully captures memory effects., Comment: 14 pages, 11 figures. Accepted for publication in PRD

To fully exploit the capabilities of next-generation gravitational wave detectors, we need to significantly improve the accuracy of our models of gravitational-wave-emitting systems. This paper focuses on one way of doing so: by taking black hole perturbation theory to second perturbative order. Such calculations are critical for the development of nonlinear ringdown models and of gravitational self-force models of extreme-mass-ratio inspirals. In the most astrophysically realistic case of a Kerr background, a second-order Teukolsky equation presents the most viable avenue for calculating second-order perturbations. Motivated by this, we analyse two second-order Teukolsky formalisms and advocate for the one that is well-behaved for gravitational self-force calculations and which meshes naturally with recent metric reconstruction methods due to Green, Hollands, and Zimmerman [CQG 37, 075001 (2020)] and others. Our main result is an expression for the nonlinear source term in the second-order field equation; we make this available, along with other useful tools, in an accompanying Mathematica notebook. Using our expression for the source, we also show that infrared divergences at second order can be evaded by adopting a Bondi--Sachs gauge., Comment: 22 pages, 0 figures. Accompanying Mathematica notebook available at https://github.com/DrAndrewSpiers/NP-and-GHP-Formalisms-for-2nd-order-Teukolsky

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt., Comment: Updated 2023-12-22

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of knowledge graphs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of knowledge graphs. Features include a simple, modular extract-transform-load (ETL) pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate knowledge graphs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph machine learning, including node embeddings and training of models for link prediction and node classification.

The motion of a radiating point particle can be represented by a series of geodesics whose "constants" of motion evolve slowly with time. The evolution of these constants of motion can be determined directly from the self-force equations of motion. In the presence of spacetime symmetries, the situation simplifies: there exist not only constants of motion conjugate to these symmetries, but also conserved currents whose fluxes can be used to determine their evolution. Such a relationship between point-particle motion and fluxes of conserved currents is a flux-balance law. However, there exist constants of motion that are not related to spacetime symmetries, the most notable example of which is the Carter constant in the Kerr spacetime. In this paper, we first present a new approach to flux-balance laws for spacetime symmetries, using the techniques of symplectic currents and symmetry operators, which can also generate more general conserved currents. We then derive flux-balance laws for all constants of motion in the Kerr spacetime, using the fact that the background, geodesic motion is integrable. For simplicity, we restrict derivations in this paper to the scalar self-force problem. While generalizing the discussion in this paper to the gravitational case will be straightforward, there will be additional complications in turning these results into a practical flux-balance law in this case., Comment: 15+3 pages, 1 figure; v2: corrected typos and added appendix and figure, "matches" published version

The gravitational wave strain emitted by a perturbed black hole (BH) ringing down is typically modeled analytically using first-order BH perturbation theory. In this Letter we show that second-order effects are necessary for modeling ringdowns from BH merger simulations. Focusing on the strain's $(\ell,m)=(4,4)$ angular harmonic, we show the presence of a quadratic effect across a range of binary BH mass ratios that agrees with theoretical expectations. We find that the quadratic $(4,4)$ mode's amplitude exhibits quadratic scaling with the fundamental $(2,2)$ mode -- its parent mode. The nonlinear mode's amplitude is comparable to or even larger than that of the linear $(4,4)$ mode. Therefore, correctly modeling the ringdown of higher harmonics -- improving mode mismatches by up to 2 orders of magnitude -- requires the inclusion of nonlinear effects., Comment: 6+2 pages, 4 figures, 1 table. Matches PRL version

The Bondi-van der Burg-Metzner-Sachs (BMS) group, which uniquely describes the symmetries of asymptotic infinity and therefore of the gravitational waves that propagate there, has become increasingly important for accurate modeling of waveforms. In particular, waveform models, such as post-Newtonian (PN) expressions, numerical relativity (NR), and black hole perturbation theory, produce results that are in different BMS frames. Consequently, to build a model for the waveforms produced during the merging of compact objects, which ideally would be a hybridization of PN, NR, and black hole perturbation theory, one needs a fast and robust method for fixing the BMS freedoms. In this work, we present the first means of fixing the entire BMS freedom of NR waveforms to match the frame of either PN waveforms or black hole perturbation theory. We achieve this by finding the BMS transformations that change certain charges in a prescribed way -- e.g., finding the center-of-mass transformation that maps the center-of-mass charge to a mean of zero. We find that this new method is 20 times faster, and more correct when mapping to the superrest frame, than previous methods that relied on optimization algorithms. Furthermore, in the course of developing this charge-based frame fixing method, we compute the PN expression for the Moreschi supermomentum to 3PN order without spins and 2PN order with spins. This Moreschi supermomentum is effectively equivalent to the energy flux or the null memory contribution at future null infinity $\mathscr{I}^{+}$. From this PN calculation, we also compute oscillatory ($m\not=0$ modes) and spin-dependent memory terms that have not been identified previously or have been missing from strain expressions in the post-Newtonian literature., Comment: 16+4 pages with 2 appendices, 4 figures, 1 table

We propose two frequency-domain filters to analyze ringdown signals of binary black hole mergers. The first rational filter is constructed based on a set of (arbitrary) quasi-normal modes (QNMs) of the remnant black holes, whereas the second full filter comes from the transmissivity of the remnant black holes. The two filters can remove corresponding QNMs from original time-domain ringdowns, while changing early inspiral signals in a trivial way - merely a time and phase shift. After filtering out dominant QNMs, we can visualize the existence of various subdominant effects. For example, by applying our filters to a GW150914-like numerical relativity (NR) waveform, we find second-order effects in the (l = 4, m = 4), (l = 5, m = 4) and (l = 5, m = 5) harmonics; the spherical-spheroidal mixing mode in the (l = 2,m = 2) harmonic; and a mixing mode in the (l = 2,m = 1) harmonic due to a gravitational recoil. In another NR simulation where two component spins are anti-aligned with the orbital angular momentum, we also find retrograde modes. The filters are sensitive to the remnant properties (i.e., mass and spin) and thus have a potential application to future data analyses and parameter estimations. We also investigate the stability of the full filter. Its connection to the instability of QNM spectra is discussed.

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness between core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally-accepted, open-access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object-oriented classification and graph-oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates), representing biomedical entities such as gene, disease, chemical, anatomical structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

We propose a new approach toward reconstructing the late-time near-horizon geometry of merging binary black holes, and toward computing gravitational-wave echoes from exotic compact objects. A binary black-hole merger spacetime can be divided by a time-like hypersurface into a Black-Hole Perturbation (BHP) region, in which the space-time geometry can be approximated by homogeneous linear perturbations of the final Kerr black hole, and a nonlinear region. At late times, the boundary between the two regions is an infalling shell. The BHP region contains late-time gravitational-waves emitted toward the future horizon, as well as those emitted toward future null infinity. In this region, by imposing no-ingoing wave conditions at past null infinity, and matching out-going waves at future null infinity with waveforms computed from numerical relativity, we can obtain waves that travel toward the future horizon. In particular, the Newman-Penrose $\psi_0$ associated with the in-going wave on the horizon is related to tidal deformations measured by fiducial observers floating above the horizon. We further determine the boundary of the BHP region on the future horizon by imposing that $\psi_0$ inside the BHP region can be faithfully represented by quasi-normal modes. Using a physically-motivated way to impose boundary conditions near the horizon, and applying the so-called Boltzmann reflectivity, we compute the quasi-normal modes of non-rotating ECOs, as well as gravitational-wave echoes. We also investigate the detectability of these echoes in current and future detectors, and prospects for parameter estimation.

The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common software packages that export annotations in GFF3 format model the same data and metadata in different notations, which puts the burden on end-users to interpret the data model. The AgBioData consortium is a group of genomics, genetics and breeding databases and partners working towards shared practices and standards. Providing concrete guidelines for generating GFF3, and creating a standard representation of the most common biological data types would provide a major increase in efficiency for AgBioData databases and the genomics research community that use the GFF3 format in their daily operations. The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome further discussion of these recommendations. We request the genomics and bioinformatics community to utilize the github repository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) to provide feedback via issues or pull requests., Comment: 23 pages

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Are they associated in some other way? Such relationships between the mapped terms are often not documented, leading to incorrect assumptions and making them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Also, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. The Simple Standard for Sharing Ontological Mappings (SSSOM) addresses these problems by: 1. Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. 2. Defining an easy to use table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data standards. 3. Implementing open and community-driven collaborative workflows designed to evolve the standard continuously to address changing requirements and mapping practices. 4. Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases, and survey some existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable, and Reusable (FAIR). The SSSOM specification is at http://w3id.org/sssom/spec., Comment: Corresponding author: Christopher J. Mungall

Brownian coating thermal noise in detector test masses is limiting the sensitivity of current gravitational-wave detectors on Earth. Therefore, accurate numerical models can inform the ongoing effort to minimize Brownian coating thermal noise in current and future gravitational-wave detectors. Such numerical models typically require significant computational resources and time, and often involve closed-source commercial codes. In contrast, open-source codes give complete visibility and control of the simulated physics, enable direct assessment of the numerical accuracy, and support the reproducibility of results. In this article, we use the open-source SpECTRE numerical relativity code and adopt a novel discontinuous Galerkin numerical method to model Brownian coating thermal noise. We demonstrate that SpECTRE achieves significantly higher accuracy than a previous approach at a fraction of the computational cost. Furthermore, we numerically model Brownian coating thermal noise in multiple sub-wavelength crystalline coating layers for the first time. Our new numerical method has the potential to enable fast exploration of realistic mirror configurations, and hence to guide the search for optimal mirror geometries, beam shapes and coating materials for gravitational-wave detectors., Comment: 15 pages, 5 figures. Results are reproducible with the ancillary input files

Elliptic partial differential equations must be solved numerically for many problems in numerical relativity, such as initial data for every simulation of merging black holes and neutron stars. Existing elliptic solvers can take multiple days to solve these problems at high resolution and when matter is involved, because they are either hard to parallelize or require a large amount of computational resources. Here we present a new solver for linear and nonlinear elliptic problems that is designed to scale with resolution and to parallelize on computing clusters. To achieve this we employ a discontinuous Galerkin discretization, an iterative multigrid-Schwarz preconditioned Newton-Krylov algorithm, and a task-based parallelism paradigm. To accelerate convergence of the elliptic solver we have developed novel subdomain-preconditioning techniques. We find that our multigrid-Schwarz preconditioned elliptic solves achieve iteration counts that are independent of resolution, and our task-based parallel programs scale over 200 million degrees of freedom to at least a few thousand cores. Our new code solves a classic initial data problem for binary black holes faster than the spectral code SpEC when distributed to only eight cores, and in a fraction of the time on more cores. It is publicly accessible in the next-generation SpECTRE numerical relativity code. Our results pave the way for highly parallel elliptic solves in numerical relativity and beyond., Comment: 25 pages, 20 figures, published version. Results are reproducible with the ancillary input files

Quasi-normal mode (QNM) modeling is an invaluable tool for characterizing remnant black holes, studying strong gravity, and testing GR. Only recently have QNM studies begun to focus on multimode fitting to numerical relativity (NR) strain waveforms. As GW observatories become even more sensitive they will be able to resolve higher-order modes. Consequently, multimode QNM fits will be critically important, and in turn require a more thorough treatment of the asymptotic frame at $\mathscr{I}^+$. The first main result of this work is a method for systematically fitting a QNM model containing many modes to a numerical waveform produced using Cauchy-characteristic extraction (CCE), an extraction technique which is known to resolve memory effects. We choose the modes to model based on their power contribution to the residual between numerical and model waveforms. We show that the all-mode strain mismatch improves by a factor of $\sim10^5$ when using multimode fitting as opposed to only fitting the $(2,\pm2,n)$ modes. Our most significant result addresses a critical point that has been overlooked in the QNM literature: the importance of matching the Bondi-van der Burg-Metzner-Sachs (BMS) frame of the numerical waveform to that of the QNM model. We show that by mapping the numerical waveforms$-$which exhibit the memory effect$-$to a BMS frame known as the super rest frame, there is an improvement of $\sim10^5$ in the all-mode strain mismatch compared to using a strain waveform whose BMS frame is not fixed. Furthermore, we find that by mapping CCE waveforms to the super rest frame, we can obtain all-mode mismatches that are, on average, a factor of $\sim4$ better than using the publicly-available extrapolated waveforms. We illustrate the effectiveness of these modeling enhancements by applying them to families of waveforms produced by NR and comparing our results to previous QNM studies., Comment: 17 + 2 pages, 11 figures, 2 tables

We give full details regarding the new Cauchy-characteristic evolution (CCE) system in SpECTRE. The implementation is built to provide streamlined flexibility for either extracting waveforms during the process of a SpECTRE binary compact object simulation, or as a standalone module for extracting waveforms from worldtube data provided by another code base. Using our recently presented improved analytic formulation, the CCE system is free of pure-gauge logarithms that would spoil the spectral convergence of the scheme. It gracefully extracts all five Weyl scalars, in addition to the news and the strain. The SpECTRE CCE system makes significant improvements on previous implementations in modularity, ease of use, and speed of computation.

Discontinuous Galerkin methods are popular because they can achieve high order where the solution is smooth, because they can capture shocks while needing only nearest-neighbor communication, and because they are relatively easy to formulate on complex meshes. We perform a detailed comparison of various limiting strategies presented in the literature applied to the equations of general relativistic magnetohydrodynamics. We compare the standard minmod/$\Lambda\Pi^N$ limiter, the hierarchical limiter of Krivodonova, the simple WENO limiter, the HWENO limiter, and a discontinuous Galerkin-finite-difference hybrid method. The ultimate goal is to understand what limiting strategies are able to robustly simulate magnetized TOV stars without any fine-tuning of parameters. Among the limiters explored here, the only limiting strategy we can endorse is a discontinuous Galerkin-finite-difference hybrid method., Comment: matches published version. 21 pages, 12 figures. Added KH instability, TOV runs with classical limiters. arXiv admin note: text overlap with arXiv:2109.11645

Understanding the Bondi-Metzner-Sachs (BMS) frame of the gravitational waves produced by numerical relativity is crucial for ensuring that analyses on such waveforms are performed properly. It is also important that models are built from waveforms in the same BMS frame. Up until now, however, the BMS frame of numerical waveforms has not been thoroughly examined, largely because the necessary tools have not existed. In this paper, we show how to analyze and map to a suitable BMS frame for numerical waveforms calculated with the Spectral Einstein Code (SpEC). However, the methods and tools that we present are general and can be applied to any numerical waveforms. We present an extensive study of 13 binary black hole systems that broadly span parameter space. From these simulations, we extract the strain and also the Weyl scalars using both SpECTRE's Cauchy-characteristic extraction module and also the standard extrapolation procedure with a displacement memory correction applied during postprocessing. First, we show that the current center-of-mass correction used to map these waveforms to the center-of-mass frame is not as effective as previously thought. Consequently, we also develop an improved correction that utilizes asymptotic Poincar\'e charges instead of a Newtonian center-of-mass trajectory. Next, we map our waveforms to the post-Newtonian (PN) BMS frame using a PN strain waveform. This helps us find the unique BMS transformation that minimizes the $L^{2}$ norm of the difference between the numerical and PN strain waveforms during the early inspiral phase. We find that once the waveforms are mapped to the PN BMS frame, they can be hybridized with a PN strain waveform much more effectively than if one used any of the previous alignment schemes, which only utilize the Poincar\'e transformations., Comment: 18 pages, 11 figures; Published in Physical Review D

We present a new study of remnant black hole properties from 13 binary black hole systems, numerically evolved using the Spectral Einstein Code. The mass, spin, and recoil velocity of each remnant were determined quasi-locally from apparent horizon data and asymptotically from Bondi data $(h, \psi_4, \psi_3, \psi_2, \psi_1)$ computed at future null infinity using SpECTRE's Cauchy characteristic evolution. We compare these independent measurements of the remnant properties in the bulk and on the boundary of the spacetime, giving insight into how well asymptotic data are able to reproduce local properties of the remnant black hole in numerical relativity. We also discuss the theoretical framework for connecting horizon quantities to asymptotic quantities and how it relates to our results. This study recommends a simple improvement to the recoil velocities reported in the Simulating eXtreme Spacetimes waveform catalog, provides an improvement to future surrogate remnant models, and offers new analysis techniques for evaluating the physical accuracy of numerical simulations., Comment: 14 pages, 4 figures, 1 table; published Physical Review D