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  1. The neutral atom array has gained prominence in quantum computing for its scalability and operation fidelity. Previous works focus on fixed atom arrays (FAAs) that require extensive SWAP operations for long-range interactions. This work explores a novel architecture reconfigurable atom arrays (RAAs), also known as field programmable qubit arrays (FPQAs), which allows for coherent atom movements during circuit execution under some constraints. Such atom movements, which are unique to this architecture, could reduce the cost of longrange interactions significantly if the atom movements could be scheduled strategically. In this work, we introduce Atomique, a compilation framework designed for qubit mapping, atom movement, and gate scheduling for RAA. Atomique contains a qubit-array mapper to decide the coarse-grained mapping of the qubits to arrays, leveraging MAX k-Cut on a constructed gate frequency graph to minimize SWAP overhead. Subsequently, a qubit-atom mapper determines the fine-grained mapping of qubits to specific atoms in the array and considers load balance to prevent hardware constraint violations. We further propose a router that identifies parallel gates, schedules them simultaneously, and reduces depth. We evaluate Atomique across 20+ diverse benchmarks, including generic circuits (arbitrary, QASMBench, SupermarQ), quantum simulation, and QAOA circuits. Atomique consistently outperforms IBM Superconducting, FAA with long-range gates, and FAA with rectangular and triangular topologies, achieving significant reductions in depth and the number of two-qubit gates. 
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    Free, publicly-accessible full text available July 3, 2025
  2. Quantum Hamiltonian simulation, which simulates the evolution of quantum systems and probes quantum phenomena, is one of the most promising applications of quantum computing. Recent experimental results suggest that Hamiltonian-oriented analog quantum simulation would be advantageous over circuit-oriented digital quantum simulation in the Noisy Intermediate-Scale Quantum (NISQ) machine era. However, programming analog quantum simulators is much more challenging due to the lack of a unified interface between hardware and software. In this paper, we design and implement SimuQ, the first framework for quantum Hamiltonian simulation that supports Hamiltonian programming and pulse-level compilation to heterogeneous analog quantum simulators. Specifically, in SimuQ, front-end users specify the target quantum system with Hamiltonian Modeling Language, and the Hamiltonian-level programmability of analog quantum simulators is specified through a new abstraction called the abstract analog instruction set (AAIS) and programmed in AAIS Specification Language by hardware providers. Through a solver-based compilation, SimuQ generates executable pulse schedules for real devices to simulate the evolution of desired quantum systems, which is demonstrated on superconducting (IBM), neutral-atom (QuEra), and trapped-ion (IonQ) quantum devices. Moreover, we demonstrate the advantages of exposing the Hamiltonian-level programmability of devices with native operations or interaction-based gates and establish a small benchmark of quantum simulation to evaluate SimuQ's compiler with the above analog quantum simulators.

     
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    Free, publicly-accessible full text available January 5, 2025
  3. ABSTRACT

    We report results from 8 h of JWST/MIRI low resolution spectroscopic (LRS) monitoring directly followed by 7 h of JWST/NIRSpec prism spectroscopic monitoring of the benchmark binary brown dwarf WISE 1049AB, the closest, brightest brown dwarfs known. We find water, methane, and CO absorption features in both components, including the 3.3 μm methane absorption feature and a tentative detection of small grain ($\lt $ 1μm) silicate absorption at $\gt $8.5 μm in WISE 1049A. Both components vary significantly ($\gt 1~{{\rm per\ cent}}$), with WISE 1049B displaying larger variations than WISE 1049A. Using K-means clustering, we find three main transition points in wavelength for both components of the binary: (1) change in behaviour at $\sim$2.3 μm coincident with a CO absorption bandhead, (2) change in behaviour at 4.2 μm, close to the CO fundamental band at $\lambda \gt $ 4.4 µm, and (3) change in behaviour at 8.3–8.5 µm, potentially corresponding to silicate absorption. We interpret the light curves observed with both NIRSpec and MIRI as likely stemming from (1) a deep pressure level driving the double-peaked variability seen in WISE 1049B at wavelengths $\lt $2.3 and $\gt $8.5 µm, (2) an intermediate pressure level shaping the light-curve morphology between 2.3 and 4.2 µm, and (3) a higher altitude pressure level producing single-peaked and plateaued light-curve behaviour between 4.2 and 8.5 µm.

     
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  4. Abstract

    Establishing the host range for novel viruses remains a challenge. Here, we address the challenge of identifying non-human animal coronaviruses that may infect humans by creating an artificial neural network model that learns from spike protein sequences of alpha and beta coronaviruses and their binding annotation to their host receptor. The proposed method produces a human-Binding Potential (h-BiP) score that distinguishes, with high accuracy, the binding potential among coronaviruses. Three viruses, previously unknown to bind human receptors, were identified: Bat coronavirus BtCoV/133/2005 and Pipistrellus abramus bat coronavirus HKU5-related (both MERS related viruses), andRhinolophus affiniscoronavirus isolate LYRa3 (a SARS related virus). We further analyze the binding properties of BtCoV/133/2005 and LYRa3 using molecular dynamics. To test whether this model can be used for surveillance of novel coronaviruses, we re-trained the model on a set that excludes SARS-CoV-2 and all viral sequences released after the SARS-CoV-2 was published. The results predict the binding of SARS-CoV-2 with a human receptor, indicating that machine learning methods are an excellent tool for the prediction of host expansion events.

     
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  5. Individual-level interactions shape societal or economic processes, such as infectious diseases spreading, stock prices fluctuating and public opinion shifting. Understanding how the interaction of different individuals affects collective outcomes is more important than ever, as the internet and social media develop. Social networks representing individuals' influence relations play a key role in understanding the connections between individual-level interactions and societal or economic outcomes. Recent research has revealed how the topology of a social network affects collective decision-making in a community. Furthermore, the traits of individuals that determine how they process received information for making decisions also change a community's collective decisions. In this work, we develop stochastic processes to generate networks of individuals with two simple traits: Being a conformist and being an anticonformist. We introduce a novel deterministic voter model for a trait-attributed network, where the individuals make binary choices following simple deterministic rules based on their traits. We show that the simple deterministic rules can drive unpredictable fluctuations of collective decisions which eventually become periodic. We study the effects of network topology and trait distribution on the first passage time for a sequence of collective decisions showing periodicity.

     
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  6. Falcão de Oliveira, Everton (Ed.)
    Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical location and movement of pathogens from the evolutionary relationships among sampled pathogen sequences, can inform policy decisions related to viral movement among jurisdictions. However, phylogeographic reconstruction is impacted by the fact that the sampling and virus sequencing policies differ among jurisdictions, and these differences can cause bias in phylogeographic reconstructions. Here we assess the potential impacts of geographic-based sampling bias on estimated viral locations in the past, and on whether key viral movements can be detected. We quantify the effect of bias using simulated phylogenies with known geographic histories, and determine the impact of the biased sampling and of the underlying migration rate on the accuracy of estimated past viral locations. We find that overall, the accuracy of phylogeographic reconstruction is high, particularly when the migration rate is low. However, results depend on sampling, and sampling bias can have a large impact on the numbers and nature of estimated migration events. We apply these insights to the geographic spread of Ebolavirus in the 2014-2016 West Africa epidemic. This work highlights how sampling policy can both impact geographic inference and be optimized to best ensure the accuracy of specific features of geographic spread. 
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  7. We introduce a graph polynomial that distinguishes tree structures to represent dependency grammar and a measure based on the polynomial representation to quantify syntax similarity. The polynomial encodes accurate and comprehensive information about the dependency structure and dependency relations of words in a sentence, which enables in-depth analysis of dependency trees with data analysis tools. We apply the polynomial-based methods to analyze sentences in the ParallelUniversal Dependencies treebanks. Specifically, we compare the syntax of sentences and their translations in different languages, and we perform a syntactic typology study of available languages in the Parallel Universal Dependencies treebanks. We also demonstrate and discuss the potential of the methods in measuring syntax diversity of corpora. 
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  8. Abstract

    We present the characterization of the low-gravity M6 dwarf 2MASS J06195260-2903592, previously identified as an unusual field object based on its strong IR excess and variable near-IR spectrum. Multiple epochs of low-resolution (R≈ 150) near-IR spectra show large-amplitude (≈0.1–0.5 mag) continuum variations on timescales of days to 12 yr, unlike the small-amplitude variability typical for field ultracool dwarfs. The variations between epochs are well-modeled as changes in the relative extinction (ΔAV≈ 2 mag). Similarly, Panoramic Survey Telescope and Rapid Response System 1 optical photometry varies on timescales as long as 11 yr (and possibly as short as an hour) and implies comparableAVchanges. Near Earth Object Wide-field Infrared Survey Explorer mid-IR light curves also suggest changes on 6 month timescales, with amplitudes consistent with the optical/near-IR extinction variations. However, near-IR spectra, near-IR photometry, and optical photometry obtained in the past year indicate that the source can also be stable on hourly and monthly timescales. From comparison to objects of similar spectral type, the total extinction of 2MASS J0619-2903 seems to beAV≈ 4–6 mag, with perhaps epochs of lower extinction. Gaia Early Data Release 3 (EDR3) finds that 2MASS J0619-2903 has a wide-separation (1.′2 = 10,450 au) stellar companion, with an isochronal age of3110+22Myr and a mass of0.300.03+0.04M. Adopting this companion’s age and EDR3 distance (145.2 ± 0.6 pc), we estimate a mass of 0.11–0.17Mfor 2MASS J0619-2903. Altogether, 2MASS J0619-2903 appears to possess an unusually long-lived primordial circumstellar disk, perhaps making it a more obscured analog to the “Peter Pan” disks found around a few M dwarfs in nearby young moving groups.

     
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  9. Abstract

    The unprecedented medium-resolution (Rλ∼ 1500–3500) near- and mid-infrared (1–18μm) spectrum provided by JWST for the young (140 ± 20 Myr) low-mass (12–20MJup) L–T transition (L7) companion VHS 1256 b gives access to a catalog of molecular absorptions. In this study, we present a comprehensive analysis of this data set utilizing a forward-modeling approach applying our Bayesian framework,ForMoSA. We explore five distinct atmospheric models to assess their performance in estimating key atmospheric parameters:Teff, log(g), [M/H], C/O,γ,fsed, andR. Our findings reveal that each parameter’s estimate is significantly influenced by factors such as the wavelength range considered and the model chosen for the fit. This is attributed to systematic errors in the models and their challenges in accurately replicating the complex atmospheric structure of VHS 1256 b, notably the complexity of its clouds and dust distribution. To propagate the impact of these systematic uncertainties on our atmospheric property estimates, we introduce innovative fitting methodologies based on independent fits performed on different spectral windows. We finally derived aTeffconsistent with the spectral type of the target, considering its young age, which is confirmed by our estimate of log(g). Despite the exceptional data quality, attaining robust estimates for chemical abundances [M/H] and C/O, often employed as indicators of formation history, remains challenging. Nevertheless, the pioneering case of JWST’s data for VHS 1256 b has paved the way for future acquisitions of substellar spectra that will be systematically analyzed to directly compare the properties of these objects and correct the systematics in the models.

     
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    Free, publicly-accessible full text available April 25, 2025
  10. Abstract

    We present a performance analysis for the aperture masking interferometry (AMI) mode on board the James Webb Space Telescope Near Infrared Imager and Slitless Spectrograph (JWST/NIRISS). Thanks to self-calibrating observables, AMI accesses inner working angles down to and even within the classical diffraction limit. The scientific potential of this mode has recently been demonstrated by the Early Release Science (ERS) 1386 program with a deep search for close-in companions in the HIP 65426 exoplanetary system. As part of ERS 1386, we use the same data set to explore the random, static, and calibration errors of NIRISS AMI observables. We compare the observed noise properties and achievable contrast to theoretical predictions. We explore possible sources of calibration errors and show that differences in charge migration between the observations of HIP 65426 and point-spread function calibration stars can account for the achieved contrast curves. Lastly, we use self-calibration tests to demonstrate that with adequate calibration NIRISS F380M AMI can reach contrast levels of ∼9–10 mag at ≳λ/D. These tests lead us to observation planning recommendations and strongly motivate future studies aimed at producing sophisticated calibration strategies taking these systematic effects into account. This will unlock the unprecedented capabilities of JWST/NIRISS AMI, with sensitivity to significantly colder, lower-mass exoplanets than lower-contrast ground-based AMI setups, at orbital separations inaccessible to JWST coronagraphy.

     
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    Free, publicly-accessible full text available February 19, 2025