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Nov 20

MolSpectLLM: A Molecular Foundation Model Bridging Spectroscopy, Molecule Elucidation, and 3D Structure Generation

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at https://github.com/Eurekashen/MolSpectLLM{https://github.com/Eurekashen/MolSpectLLM}.

  • 9 authors
·
Sep 26

MSA-3D: Metallicity Gradients in Galaxies at $z\sim1$ with JWST/NIRSpec Slit-stepping Spectroscopy

The radial gradient of gas-phase metallicity is a powerful probe of the chemical and structural evolution of star-forming galaxies, closely tied to disk formation and gas kinematics in the early universe. We present spatially resolved chemical and dynamical properties for a sample of 25 galaxies at 0.5 lesssim z lesssim 1.7 from the \msasd survey. These innovative observations provide 3D spectroscopy of galaxies at a spatial resolution approaching JWST's diffraction limit and a high spectral resolution of Rsimeq2700. The metallicity gradients measured in our galaxy sample range from -0.03 to 0.02 dex~kpc^{-1}. Most galaxies exhibit negative or flat radial gradients, indicating lower metallicity in the outskirts or uniform metallicity throughout the entire galaxy. We confirm a tight relationship between stellar mass and metallicity gradient at zsim1 with small intrinsic scatter of 0.02 dex~kpc^{-1}. Our results indicate that metallicity gradients become increasingly negative as stellar mass increases, likely because the more massive galaxies tend to be more ``disky". This relationship is consistent with the predictions from cosmological hydrodynamic zoom-in simulations with strong stellar feedback. This work presents the effort to harness the multiplexing capability of JWST NIRSpec/MSA in slit-stepping mode to map the chemical and kinematic profiles of high-redshift galaxies in large samples and at high spatial and spectral resolution.

  • 17 authors
·
Sep 3, 2024

RUBIES: a complete census of the bright and red distant Universe with JWST/NIRSpec

We present the Red Unknowns: Bright Infrared Extragalactic Survey (RUBIES), providing JWST/NIRSpec spectroscopy of red sources selected across ~150 arcmin^2 from public JWST/NIRCam imaging in the UDS and EGS fields. RUBIES novel observing strategy offers a well-quantified selection function: the survey is optimised to reach high (>70%) completeness for bright and red (F150W-F444W>2) sources that are very rare. To place these rare sources in context, we simultaneously observe a reference sample of the 2<z<7 galaxy population, sampling sources at a rate that is inversely proportional to their number density in the 3D space of F444W magnitude, F150W-F444W colour, and photometric redshift. In total, RUBIES observes ~3000 targets across 1<z_{phot}<10 with both the PRISM and G395M dispersers, and ~1500 targets at z_{phot}>3 using only the G395M disperser. The RUBIES data reveal a highly diverse population of red sources that span a broad redshift range (z_{spec}sim1-9), with photometric redshift scatter and outlier fraction that are 3 times higher than for similarly bright sources that are less red. This diversity is not apparent from the photometric SEDs. Only spectroscopy reveals that the SEDs encompass a mixture of galaxies with dust-obscured star formation, extreme line emission, a lack of star formation indicating early quenching, and luminous active galactic nuclei. As a first demonstration of our broader selection function we compare the stellar masses and rest-frame U-V colours of the red sources and our reference sample: red sources are typically more massive (M_*sim10^{10-11.5} M_odot) across all redshifts. However, we find that the most massive systems span a wide range in U-V colour. We describe our data reduction procedure and data quality, and publicly release the reduced RUBIES data and vetted spectroscopic redshifts of the first half of the survey through the DJA.

  • 28 authors
·
Sep 9, 2024

The dark side of early galaxies: $\texttt{geko}$ uncovers dark-matter fractions at $z\sim4-6$

JWST/NIRCam slitless spectroscopy enables dynamical mass measurements for typical star-forming galaxies only a billion years after the Big Bang. We model the Halpha morpho-kinematics of 163 galaxies at redshift zapprox4-6 from FRESCO and CONGRESS (with JADES imaging), using the geko code, and infer rotational velocities and dispersions within r_{rm e}. Our sample spans log M_{star}approx7-10 and log M_{rm dyn}approx9-11. Gas masses are estimated via scaling relations, yielding baryonic masses and dark-matter (DM) fractions f_{rm DM}(r<r_{rm e}) within the Halpha half-light radius. We find high median fractions of langle f_{rm gas}rangle=0.77 and langle f_{rm DM}rangle=0.73, where f_{rm gas} is measured with respect to the baryonic mass and f_{rm DM} with respect to the DM+baryonic mass. About two-thirds of systems are DM-dominated within r_{rm e}sim0.5-1 kpc. Both f_{rm gas} and f_{rm DM} decrease with stellar mass, consistent with simulations. The stellar Tully-Fisher relation shows a tentative offset to higher v_{rm circ} at fixed M_{star} and substantial intrinsic scatter, suggesting that the relation is only beginning to emerge at zsim5. We measure a negative correlation between f_{rm DM} and baryonic surface density Sigma_{rm bar}, weaker but broadly consistent with trends at cosmic noon and at zsim0. Qualitatively comparing with modified NFW profiles coupled to an empirical stellar-to-halo mass relation suggests that the lowest f_{rm DM} (lesssim0.4) require cored inner DM profiles, while the highest fractions favour cuspier profiles, potentially reflecting adiabatic contraction. Overall, the elevated f_{rm gas} and f_{rm DM} at zgtrsim4 are compatible with progenitors of baryon-dominated systems at zsim2 and naturally anticipate overmassive black holes at fixed M_{star}.

  • 18 authors
·
Oct 16

Imaging and controlling electron motion and chemical structural dynamics of biological system in real time and space

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

  • 7 authors
·
Oct 2

NMR-Solver: Automated Structure Elucidation via Large-Scale Spectral Matching and Physics-Guided Fragment Optimization

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful and widely used tools for molecular structure elucidation in organic chemistry. However, the interpretation of NMR spectra to determine unknown molecular structures remains a labor-intensive and expertise-dependent process, particularly for complex or novel compounds. Although recent methods have been proposed for molecular structure elucidation, they often underperform in real-world applications due to inherent algorithmic limitations and limited high-quality data. Here, we present NMR-Solver, a practical and interpretable framework for the automated determination of small organic molecule structures from ^1H and ^{13}C NMR spectra. Our method introduces an automated framework for molecular structure elucidation, integrating large-scale spectral matching with physics-guided fragment-based optimization that exploits atomic-level structure-spectrum relationships in NMR. We evaluate NMR-Solver on simulated benchmarks, curated experimental data from the literature, and real-world experiments, demonstrating its strong generalization, robustness, and practical utility in challenging, real-life scenarios. NMR-Solver unifies computational NMR analysis, deep learning, and interpretable chemical reasoning into a coherent system. By incorporating the physical principles of NMR into molecular optimization, it enables scalable, automated, and chemically meaningful molecular identification, establishing a generalizable paradigm for solving inverse problems in molecular science.

  • 9 authors
·
Aug 30

Strain-Balanced Low-Temperature-Grown Beryllium-Doped InGaAs/InAlAs Superlattices for High-Performance Terahertz Photoconductors under 1550 nm Laser Excitation

This study systematically investigates the photoconductive properties of low-temperature-grown Beryllium (Be)-doped InGaAs/InAlAs strain-balanced superlattices (SLs) grown by molecular beam epitaxy under stationary growth conditions on semi-insulating InP:Fe substrates. The stationary growth approach enabled precise control over lateral gradients in layer strain, composition, and thickness across a single wafer, while strain-balancing facilitated pseudomorphic growth to explore a wide range of structural parameters, providing a robust platform to study their influence on photoconductive performance. Structural characterization confirmed high crystalline quality and smooth surface morphology in all samples. Time-resolved pump-probe spectroscopy revealed subpicosecond carrier lifetimes, validating the effectiveness of strain balancing and Be doping in tuning ultrafast recombination dynamics. Hall effect measurements supported by 8-band k.p modeling revealed enhanced carrier mobility in strain-balanced SLs compared to lattice-matched structures, primarily due to reduced electron and hole effective masses and stronger quantum confinement. Additionally, optical absorption under 1550 nm excitation showed improved absorption coefficients for the strain-balanced structure, consistent with the reduction in bandgap energy predicted by theoretical modeling, thereby enhancing photon-to-carrier conversion efficiency. Furthermore, transmission electron microscopy provided first-time evidence of significant Be-induced interdiffusion at the strained SL interfaces, an important factor influencing carrier transport and dynamics. These findings position low-temperature-grown Be-doped InGaAs/InAlAs strain-balanced SLs as promising materials for high-performance broadband THz photoconductive detectors operating at telecom-compatible wavelengths.

  • 6 authors
·
May 3

Zapped then Napped? A rapidly quenched remnant leaker candidate with a steep spectroscopic $β_{UV}$ slope at z=8.5

We use NIRSpec MSA spectroscopy and NIRCam Photometry to explore the properties of JADES-GS8-RL-1, a rapidly quenched, z=8.5 galaxy with a stellar mass of 10^{8.9}M_odot, a steep blue UV slope, a Balmer break, and no sign of strong emission lines. With a beta_{UV}=-2.8pm 0.2, as measured from the NIRSpec spectrum, JADES-GS8-RL-1 is consistent with negligible dust attenuation and little to no contribution from the nebular continuum alongside a probable high escape fraction. The beta_{UV} slope measured from photometry varies from -3.0 in the central regions to -2.2 at the outskirts suggesting possible regional differences in the escape fraction. There are no high-ionisation emission lines, only a tentative 2.9\sig detection of [OII]. Using photometry, this emission appears to be extended, possibly corresponding to weakly ionised gas expelled during or after the quenching process. JADES-GS8-RL-1 is spatially resolved with a half-light radius of 240 pc and has an exponential, disc-like morphology. It appears to have formed all its stars in a short burst within the past 100 Myr with a formation time of approx70 Myr and a quenching time of approx30 Myr. This quenching would have occurred rapidly, making it a more distant example of the kind of low-mass "mini-quenched" galaxies previously observed at high-z. Due to the extremely blue beta_{UV} slope, our best-fit model predicts a high value for \fesc of >10\%, consistent with the value derived from the beta_{UV} slope, which when combined with our extraordinarily low O32 upper limit suggests JADES-GS8-RL-1 is a fascinating example of a high-z "remnant leaker" in one of its earliest phases, deep in the epoch of reionisation.

  • 20 authors
·
Jan 15

Quantifying spectroscopic Ca II exocomet transit occurrence in two decades of HARPS data

The field of exocomets has been built around the unmatched number of detections made in the circumstellar disc of the archetypal star Beta Pictoris. An exocomet detection in spectroscopy is identified by variable atomic absorption features in a stellar spectrum, associated with transiting gas in and trailing an exocomet coma. This paper presents the largest spectroscopic search for exocomet transits to date, which overcomes the limitations of biased samples of stars with debris discs, and instead looks through the approx7500 stars in the HARPS archive for signs of exocomets in the CaII doublet (H:396.847nm and K:393.366nm). The search resulted in 155 candidate stars, which after filtering for false positives (e.g. binaries, stellar activity, etc.), were cut down to 22 stars. These 22 stars are classified into Tier1, 2, and 3 exocomet candidates, reflecting the confidence level of their exocomet detection. Our two best candidates (Tier1: Beta Pictoris, HD172555) and four lower confidence candidates (Tier2: Gl1, HIP5158, HD94771, HR1996) are discussed, yielding a detection rate of 0.03% (Tier1 only) and 0.1% (Tier1 & 2) in the HARPS sample. Both Tier1 stars are known exocomet host stars. These two young A-type stars correspond to 0.4% of all A-types in the sample, suggesting that detecting signs of exocomet transits using CaII is more likely around young A-type stars. Reanalysing a past HARPS study, we found no evidence to support the previously claimed four exocomet detections, indicating either that those detections are not robust or that we are only sensitive to the strongest signals.

  • 4 authors
·
Dec 17, 2024

Isotopic effects in molecular attosecond photoelectron interferometry

Isotopic substitution in molecular systems can affect fundamental molecular properties including the energy position and spacing of electronic, vibrational and rotational levels, thus modifying the dynamics associated to their coherent superposition. In extreme ultraviolet spectroscopy, the photoelectron leaving the molecule after the absorption of a single photon can trigger an ultrafast nuclear motion in the cation, which can lead, eventually, to molecular fragmentation. This dynamics depends on the mass of the constituents of the cation, thus showing, in general, a significant isotopic dependence. In time-resolved attosecond photoelectron interferometry, the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional quantum of energy (typically in the infrared spectral range) with the photoelectron-photoion system, offering the opportunity to investigate in time the influence of isotopic substitution on the characteristics of the photoionisation dynamics. Here we show that attosecond photoelectron interferometry is sensitive to isotopic substitution by investigating the two-color photoionisation spectra measured in a mixture of methane (CH_4) and deuteromethane (CD_4). The isotopic dependence manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks generated in the two-color field with the two isotopologues. The observed effects are interpreted considering the differences in the time evolution of the nuclear autocorrelation functions in the two molecules.

  • 15 authors
·
Mar 2, 2023

XRISM Observations of Cassiopeia A: Overview, Atomic Data, and Spectral Models

Cassiopeia A (Cas A) is the youngest known core-collapse supernova remnant (SNR) in the Galaxy and is perhaps the best-studied SNR in X-rays. Cas A has a line-rich spectrum dominated by thermal emission and given its high flux, it is an appealing target for high-resolution X-ray spectroscopy. Cas A was observed at two different locations during the Performance Verification phase of the XRISM mission, one location in the southeastern part (SE) of the remnant and one in the northwestern part (NW). This paper serves as an overview of these observations and discusses some of the issues relevant for the analysis of the data. We present maps of the so-called ``spatial-spectral mixing'' effect due to the fact that the XRISM point-spread function is larger than a pixel in the Resolve calorimeter array. We analyze spectra from two bright, on-axis regions such that the effects of spatial-spectral mixing are minimized. We find that it is critical to include redshifts/blueshifts and broadening of the emission lines in the two thermal components to achieve a reasonable fit given the high spectral resolution of the Resolve calorimeter. We fit the spectra with two versions of the AtomDB atomic database (3.0.9 and 3.1.0) and two versions of the SPEX (3.08.00 and 3.08.01*) spectral fitting software. Overall we find good agreement between AtomDB 3.1.0 and SPEX 3.08.01* for the spectral models considered in this paper. The most significant difference we found between AtomDB 3.0.9 and 3.1.0 and between AtomDB 3.1.0 and SPEX 3.08.01* is the Ni abundance, with the new atomic data favoring a considerably lower (up to a factor of 3) Ni abundance. Both regions exhibit significantly enhanced abundances compared to Solar values indicating that supernova ejecta dominate the emission in these regions. We find that the abundance ratios of Ti/Fe, Mn/Fe, \& Ni/Fe are significantly lower in the NW than the SE.

  • 17 authors
·
Aug 1

2DNMRGym: An Annotated Experimental Dataset for Atom-Level Molecular Representation Learning in 2D NMR via Surrogate Supervision

Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties. However, accurately interpreting 2D NMR data remains labor-intensive and error-prone, requiring highly trained domain experts, especially for complex molecules. Machine Learning (ML) holds significant potential in 2D NMR analysis by learning molecular representations and recognizing complex patterns from data. However, progress has been limited by the lack of large-scale and high-quality annotated datasets. In this work, we introduce 2DNMRGym, the first annotated experimental dataset designed for ML-based molecular representation learning in 2D NMR. It includes over 22,000 HSQC spectra, along with the corresponding molecular graphs and SMILES strings. Uniquely, 2DNMRGym adopts a surrogate supervision setup: models are trained using algorithm-generated annotations derived from a previously validated method and evaluated on a held-out set of human-annotated gold-standard labels. This enables rigorous assessment of a model's ability to generalize from imperfect supervision to expert-level interpretation. We provide benchmark results using a series of 2D and 3D GNN and GNN transformer models, establishing a strong foundation for future work. 2DNMRGym supports scalable model training and introduces a chemically meaningful benchmark for evaluating atom-level molecular representations in NMR-guided structural tasks. Our data and code is open-source and available on Huggingface and Github.

  • 3 authors
·
May 16

Discovery of kiloparsec-scale semi-relativistic Fe K$α$ complex emission in NGC 5728

We present Chandra ACIS-S imaging spectroscopy results of the extended (1.5''- 8'', 300 pc-1600 pc) hard X-ray emission of NGC 5728, the host galaxy of a Compton thick active galactic nucleus (CT AGN). We find spectrally and spatially-resolved features in the Fe Kalpha complex (5.0-7.5 keV), redward and blueward of the neutral Fe line at 6.4 keV in the extended narrow line region bicone. A simple phenomenological fit of a power law plus Gaussians gives a significance of 5.4sigma and 3.7sigma for the red and blue wings, respectively. Fits to a suite of physically consistent models confirm a significance geq3sigma for the red wing. The significance of the blue wing may be diminished by the presence of rest frame highly ionized Fe XXV and Fe XXVI lines (1.4sigma - 3.7sigma range). A detailed investigation of the Chandra ACIS-S point spread function (PSF) and comparison with the observed morphology demonstrates that these red and blue wings are radially extended (~5'', ~1 kpc) along the optical bicone axis. If the wings emission is due solely to redshifted and blueshifted high-velocity neutral Fe Kalpha then the implied line-of-sight velocities are +/- ~0.1c, and their fluxes are consistent with being equal. A symmetric high-velocity outflow is then a viable explanation. This outflow has deprojected velocities ~100 times larger than the outflows detected in optical spectroscopic studies, potentially dominating the kinetic feedback power.

  • 5 authors
·
Mar 1, 2023

JWST observations of photodissociation regions III. Dust modelling at the illuminated edge of the Horsehead PDR

Carbonaceous nano-grains are a significant component of interstellar dust and dominate the mid-infrared emission of photodissociation regions (PDRs). We study the evolution of nano-grains across the illuminated edge of the Horsehead PDR, especially their abundance and size properties. This work is part of the Physics and Chemistry of PDR Fronts program studying dust and gas in PDRs with JWST. We use NIRCam+MIRI photometric bands and NIRSpec+MRS spectroscopy to map the illuminated edge. We model dust emission using the THEMIS dust model with the SOC radiative transfer code. Detailed modeling of high angular resolution JWST data allows us to obtain constraints on nano-grain properties. We find that diffuse ISM dust cannot account for the observed data, requiring evolved grains. A sharp density increase is observed at the illuminated edge, consistent with ALMA observations revealing a sharp transition between molecular and ionized gas. Although the PDR length could not be directly determined, we estimate an upper limit of approximately 0.015 pc. This implies a lower limit on small grain abundance (greater than 0.003), showing small grains are not depleted at the Horsehead edge, unlike in the Orion Bar. Our findings indicate a high-density environment and less steep size distribution for nano-grains at the illuminated edge versus the diffuse ISM. This implies nano-grain destruction mechanisms might be less efficient in the Horsehead's moderate-UV field than in more intense PDRs. These results support a model where nano-grain population recovery is slower in moderate-UV environments, leading to a unique dust size distribution at the edge of the Horsehead Nebula.

  • 22 authors
·
Oct 28

Water Enrichment from Pebble Drift in Disks with Gap-forming Planets

Volatiles like H_2O are present as ice in solids in the outer cold regions of protoplanetary disks and as vapor in the warm inner regions within the water snow line. Icy pebbles drifting inwards from the outer disk sublimate after crossing the snow line, enriching the inner disk with solid mass and water vapor. Meanwhile, proto-planets forming within the disk open gaps in the disk gas, creating traps against the inward drift of pebbles and in turn reducing water enrichment in the inner disk. Recent disk observations from millimeter interferometry and infrared spectroscopy have supported this broad picture by finding a correlation between the outer radial distribution of pebbles and the properties of inner water vapor spectra. In this work, we aim at further informing previous and future observations by building on previous models to explore pebble drift in disks with multiple gaps. We systematically explore multiple gap locations and their depths (equivalent to specific masses of planets forming within), and different particle sizes to study their impact on inner disk water enrichment. We find that the presence of close-in deep gaps carved by a Jupiter-mass planet is likely crucial for blocking icy pebble delivery into the inner disk, while planets with lower masses only provide leaky traps. We also find that disks with multiple gaps show lower vapor enrichment in the inner disk. Altogether, these model results support the idea that inner disk water delivery and planet formation are regulated by the mass and location of the most massive planets.

  • 3 authors
·
Dec 5, 2024

Overview of the JWST Advanced Deep Extragalactic Survey (JADES)

We present an overview of the James Webb Space Telescope (JWST) Advanced Deep Extragalactic Survey (JADES), an ambitious program of infrared imaging and spectroscopy in the GOODS-S and GOODS-N deep fields, designed to study galaxy evolution from high redshift to cosmic noon. JADES uses about 770 hours of Cycle 1 guaranteed time largely from the Near-Infrared Camera (NIRCam) and Near-Infrared Spectrograph (NIRSpec) instrument teams. In GOODS-S, in and around the Hubble Ultra Deep Field and Chandra Deep Field South, JADES produces a deep imaging region of ~45 arcmin^2 with an average of 130 hrs of exposure time spread over 9 NIRCam filters. This is extended at medium depth in GOODS-S and GOODS-N with NIRCam imaging of ~175 arcmin^2 with an average exposure time of 20 hrs spread over 8-10 filters. In both fields, we conduct extensive NIRSpec multi-object spectroscopy, including 2 deep pointings of 55 hrs exposure time, 14 medium pointings of ~12 hrs, and 15 shallower pointings of ~4 hrs, targeting over 5000 HST and JWST-detected faint sources with 5 low, medium, and high-resolution dispersers covering 0.6-5.3 microns. Finally, JADES extends redward via coordinated parallels with the JWST Mid-Infrared Instrument (MIRI), featuring ~9 arcmin^2 with 43 hours of exposure at 7.7 microns and twice that area with 2-6.5 hours of exposure at 12.8 microns For nearly 30 years, the GOODS-S and GOODS-N fields have been developed as the premier deep fields on the sky; JADES is now providing a compelling start on the JWST legacy in these fields.

  • 76 authors
·
Jun 4, 2023

Total Nitrogen Estimation in Agricultural Soils via Aerial Multispectral Imaging and LIBS

Measuring soil health indicators is an important and challenging task that affects farmers' decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure soil health indicators (SHIs) are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing (UMS) solution to estimate total nitrogen (TN) of the soil, an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. We train two machine learning models including multi-layer perceptron and support vector machine to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red, near-infrared, and green spectral bands, computed vegetation indices, and environmental variables including air temperature and relative humidity. To generate the ground-truth data or the training data for the machine learning models, we measure the total nitrogen of the soil samples (collected from a farm) using laser-induced breakdown spectroscopy (LIBS).

  • 3 authors
·
Jul 5, 2021

Sloan Digital Sky Survey IV: Mapping the Milky Way, Nearby Galaxies, and the Distant Universe

We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and high signal-to-noise ratio in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially-resolved spectroscopy for thousands of nearby galaxies (median redshift of z = 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between redshifts z = 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGN and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5-meter Sloan Foundation Telescope at Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5-meter du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in July 2016.

  • 353 authors
·
Feb 28, 2017

MatQnA: A Benchmark Dataset for Multi-modal Large Language Models in Materials Characterization and Analysis

Recently, large language models (LLMs) have achieved remarkable breakthroughs in general domains such as programming and writing, and have demonstrated strong potential in various scientific research scenarios. However, the capabilities of AI models in the highly specialized field of materials characterization and analysis have not yet been systematically or sufficiently validated. To address this gap, we present MatQnA, the first multi-modal benchmark dataset specifically designed for material characterization techniques. MatQnA includes ten mainstream characterization methods, such as X-ray Photoelectron Spectroscopy (XPS), X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), etc. We employ a hybrid approach combining LLMs with human-in-the-loop validation to construct high-quality question-answer pairs, integrating both multiple-choice and subjective questions. Our preliminary evaluation results show that the most advanced multi-modal AI models (e.g., GPT-4.1, Claude 4, Gemini 2.5, and Doubao Vision Pro 32K) have already achieved nearly 90% accuracy on objective questions in materials data interpretation and analysis tasks, demonstrating strong potential for applications in materials characterization and analysis. The MatQnA dataset is publicly available at https://huggingface.co/datasets/richardhzgg/matQnA.

  • 4 authors
·
Sep 14

Precision measurement of the last bound states in H$_2$ and determination of the H + H scattering length

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

  • 3 authors
·
Feb 3

Robust Spectral Anomaly Detection in EELS Spectral Images via Three Dimensional Convolutional Variational Autoencoders

We introduce a Three-Dimensional Convolutional Variational Autoencoder (3D-CVAE) for automated anomaly detection in Electron Energy Loss Spectroscopy Spectrum Imaging (EELS-SI) data. Our approach leverages the full three-dimensional structure of EELS-SI data to detect subtle spectral anomalies while preserving both spatial and spectral correlations across the datacube. By employing negative log-likelihood loss and training on bulk spectra, the model learns to reconstruct bulk features characteristic of the defect-free material. In exploring methods for anomaly detection, we evaluated both our 3D-CVAE approach and Principal Component Analysis (PCA), testing their performance using Fe L-edge peak shifts designed to simulate material defects. Our results show that 3D-CVAE achieves superior anomaly detection and maintains consistent performance across various shift magnitudes. The method demonstrates clear bimodal separation between normal and anomalous spectra, enabling reliable classification. Further analysis verifies that lower dimensional representations are robust to anomalies in the data. While performance advantages over PCA diminish with decreasing anomaly concentration, our method maintains high reconstruction quality even in challenging, noise-dominated spectral regions. This approach provides a robust framework for unsupervised automated detection of spectral anomalies in EELS-SI data, particularly valuable for analyzing complex material systems.

  • 3 authors
·
Dec 16, 2024

The DESI PRObabilistic Value-Added Bright Galaxy Survey (PROVABGS) Mock Challenge

The PRObabilistic Value-Added Bright Galaxy Survey (PROVABGS) catalog will provide measurements of galaxy properties, such as stellar mass (M_*), star formation rate ({rm SFR}), stellar metallicity (Z_{rm MW}), and stellar age (t_{rm age, MW}), for >10 million galaxies of the DESI Bright Galaxy Survey. Full posterior distributions of the galaxy properties will be inferred using state-of-the-art Bayesian spectral energy distribution (SED) modeling of DESI spectroscopy and Legacy Surveys photometry. In this work, we present the SED model, Bayesian inference framework, and methodology of PROVABGS. Furthermore, we apply the PROVABGS SED modeling on realistic synthetic DESI spectra and photometry, constructed using the L-GALAXIES semi-analytic model. We compare the inferred galaxy properties to the true galaxy properties of the simulation using a hierarchical Bayesian framework to quantify accuracy and precision. Overall, we accurately infer the true M_*, {rm SFR}, Z_{rm MW}, and t_{rm age, MW} of the simulated galaxies. However, the priors on galaxy properties induced by the SED model have a significant impact on the posteriors. They impose a {rm SFR}{>}10^{-1} M_odot/{rm yr} lower bound on {rm SFR}, a {sim}0.3 dex bias on log Z_{rm MW} for galaxies with low spectral signal-to-noise, and t_{rm age, MW} < 8,{rm Gyr} upper bound on stellar age. This work also demonstrates that a joint analysis of spectra and photometry significantly improves the constraints on galaxy properties over photometry alone and is necessary to mitigate the impact of the priors. With the methodology presented and validated in this work, PROVABGS will maximize information extracted from DESI observations and provide a probabilistic value-added galaxy catalog that will extend current galaxy studies to new regimes and unlock cutting-edge probabilistic analyses.

  • 19 authors
·
Feb 3, 2022

KIC 4150611: A quadruply eclipsing heptuple star system with a g-mode period-spacing pattern Asteroseismic modelling of the g-mode period-spacing pattern

In this work, we aim to estimate the stellar parameters of the primary (Aa) by performing asteroseismic analysis on its period-spacing pattern. We use the C-3PO neural network to perform asteroseismic modelling of the g-mode period-spacing pattern of Aa, discussing the interplay of this information with external constraints from spectroscopy (T_{rm eff} and log(g)) and eclipse modelling (R). To estimate the level of uncertainty due to different frequency extraction and pattern identification processes, we consider four different variations on the period-spacing patterns. To better understand the correlations between and the uncertainty structure of our parameter estimates, we also employed a classical, parameter-based MCMC grid search on four different stellar grids. The best-fitting, externally constrained model to the period-spacing pattern arrives at estimates of the stellar properties for Aa of: M=1.51 pm 0.05 M_odot, X_c =0.43 pm 0.04, R=1.66 pm 0.1 R_odot, f_{rm ov}=0.010, Omega_c=1.58 pm 0.01 d^{-1} with rigid rotation to within the measurement errors, log(T_{rm eff})=3.856 pm 0.008 dex, log(g)=4.18 pm 0.04 dex, and log(L)=0.809 pm 0.005 dex, which agree well with previous measurements from eclipse modelling, spectroscopy, and the Gaia DR3 luminosity. We find that the near-core properties of the best-fitting asteroseismic models are consistent with external constraints from eclipse modelling and spectroscopy. Aa appears to be a typical example of a gamma Dor star, fitting well within existing populations. We find that Aa is quasi-rigidly rotating to within the uncertainties, and note that the asteroseismic age estimate for Aa (1100 pm 100 Myr) is considerably older than the young (35 Myr) age implied by previous isochrone fits to the B binary in the literature. Our MCMC parameter-based grid-search agrees well with our pattern-modelling approach.

  • 10 authors
·
Nov 27, 2024

Neural-Driven Image Editing

Traditional image editing typically relies on manual prompting, making it labor-intensive and inaccessible to individuals with limited motor control or language abilities. Leveraging recent advances in brain-computer interfaces (BCIs) and generative models, we propose LoongX, a hands-free image editing approach driven by multimodal neurophysiological signals. LoongX utilizes state-of-the-art diffusion models trained on a comprehensive dataset of 23,928 image editing pairs, each paired with synchronized electroencephalography (EEG), functional near-infrared spectroscopy (fNIRS), photoplethysmography (PPG), and head motion signals that capture user intent. To effectively address the heterogeneity of these signals, LoongX integrates two key modules. The cross-scale state space (CS3) module encodes informative modality-specific features. The dynamic gated fusion (DGF) module further aggregates these features into a unified latent space, which is then aligned with edit semantics via fine-tuning on a diffusion transformer (DiT). Additionally, we pre-train the encoders using contrastive learning to align cognitive states with semantic intentions from embedded natural language. Extensive experiments demonstrate that LoongX achieves performance comparable to text-driven methods (CLIP-I: 0.6605 vs. 0.6558; DINO: 0.4812 vs. 0.4636) and outperforms them when neural signals are combined with speech (CLIP-T: 0.2588 vs. 0.2549). These results highlight the promise of neural-driven generative models in enabling accessible, intuitive image editing and open new directions for cognitive-driven creative technologies. Datasets and code will be released to support future work and foster progress in this emerging area.

Citizen Science Identification of Isolated Blue Stellar Systems in the Virgo cluster

We present a catalog of 34 new candidate (13 high confidence) isolated, young stellar systems within the Virgo galaxy cluster identified through a citizen science search of public optical and ultraviolet imaging. "Blue blobs" are a class of blue, faint, isolated, extremely low stellar mass, and metal-rich star-forming clouds embedded in the hot intracluster medium of the Virgo cluster. Only six blue blobs were known previously and here we confirm an additional six of our candidates through velocity and metallicity measurements from follow-up optical spectroscopy on the Hobby-Eberly Telescope (HET). Our 13 high confidence candidates (including the six confirmed) have properties consistent with prior known blue blobs and are inconsistent with being low-mass galaxies. Most candidates are concentrated in relatively dense regions, roughly following filamentary structures within the cluster, but avoiding its center. Three of our candidates are likely the stellar counterparts of known 'optically dark' clouds of neutral hydrogen in the cluster, while a further four are widely separated extensions to previously known blue blobs. The properties of our new candidates are consistent with previous conclusions that blue blobs likely originated from ram pressure stripping events, however, their locations in velocity--projected cluster-centric radius phase-space imply that their parent galaxies are not on their first infall into the cluster. Through our ongoing follow-up program with HET we aim to confirm additional candidates, however, detailed understanding of the stellar populations and star formation histories of blue blobs will require JWST observations.

  • 7 authors
·
Nov 21, 2024

EIGER IV: The cool 10$^4$K circumgalactic environment of high-$z$ galaxies reveals remarkably efficient IGM enrichment

We report new observations of the cool diffuse gas around 29, 2.3<z<6.3 galaxies, using deep JWST/NIRCam slitless grism spectroscopy around the sightline to the quasar J0100+2802. The galaxies span a stellar mass range of 7.1 leq log M_{*}/M_{sun} leq 10.7, and star-formation rates of -0.1 < log ; SFR/M_{sun}yr^{-1} ; <2.3. We find galaxies for seven MgII absorption systems within 300 kpc of the quasar sightline. The MgII radial absorption profile falls off sharply with radii, with most of the absorption extending out to 2-3R_{200} of the host galaxies. Six out of seven MgII absorption systems are detected around galaxies with log M_{*}/M_{sun} >9. MgII absorption kinematics are shifted from the systemic redshift of host galaxies with a median absolute velocity of 135 km/s and standard deviation of 85 km/s. The high kinematic offset and large radial separation (R> 1.3 R_{200}), suggest that five out of the seven MgII absorption systems are gravitationally not bound to the galaxies. In contrast, most cool circumgalactic media at z<1 are gravitationally bound. The high incidence of unbound MgII gas in this work suggests that towards the end of reionization, galaxy halos are in a state of remarkable disequilibrium, and are highly efficient in enriching the intergalactic medium. Two strongest MgII absorption systems are detected at zsim 4.22 and 4.5, the former associated with a merging galaxy system and the latter associated with three kinematically close galaxies. Both these galaxies reside in local galaxy over-densities, indicating the presence of cool MgII absorption in two "proto-groups" at z>4.

  • 11 authors
·
Jul 3, 2023

First Light And Reionisation Epoch Simulations (FLARES) VI: The colour evolution of galaxies $z=5-15$

With its exquisite sensitivity, wavelength coverage, and spatial and spectral resolution, the James Webb Space Telescope is poised to revolutionise our view of the distant, high-redshift (z>5) Universe. While Webb's spectroscopic observations will be transformative for the field, photometric observations play a key role in identifying distant objects and providing more comprehensive samples than accessible to spectroscopy alone. In addition to identifying objects, photometric observations can also be used to infer physical properties and thus be used to constrain galaxy formation models. However, inferred physical properties from broadband photometric observations, particularly in the absence of spectroscopic redshifts, often have large uncertainties. With the development of new tools for forward modelling simulations it is now routinely possible to predict observational quantities, enabling a direct comparison with observations. With this in mind, in this work, we make predictions for the colour evolution of galaxies at z=5-15 using the FLARES: First Light And Reionisation Epoch Simulations cosmological hydrodynamical simulation suite. We predict a complex evolution, driven predominantly by strong nebular line emission passing through individual bands. These predictions are in good agreement with existing constraints from Hubble and Spitzer as well as some of the first results from Webb. We also contrast our predictions with other models in the literature: while the general trends are similar we find key differences, particularly in the strength of features associated with strong nebular line emission. This suggests photometric observations alone should provide useful discriminating power between different models.

  • 9 authors
·
Jul 22, 2022

Galaxy Spectra neural Networks (GaSNets). I. Searching for strong lens candidates in eBOSS spectra using Deep Learning

With the advent of new spectroscopic surveys from ground and space, observing up to hundreds of millions of galaxies, spectra classification will become overwhelming for standard analysis techniques. To prepare for this challenge, we introduce a family of deep learning tools to classify features in one-dimensional spectra. As the first application of these Galaxy Spectra neural Networks (GaSNets), we focus on tools specialized at identifying emission lines from strongly lensed star-forming galaxies in the eBOSS spectra. We first discuss the training and testing of these networks and define a threshold probability, PL, of 95% for the high quality event detection. Then, using a previous set of spectroscopically selected strong lenses from eBOSS, confirmed with HST, we estimate a completeness of ~80% as the fraction of lenses recovered above the adopted PL. We finally apply the GaSNets to ~1.3M spectra to collect a first list of ~430 new high quality candidates identified with deep learning applied to spectroscopy and visually graded as highly probable real events. A preliminary check against ground-based observations tentatively shows that this sample has a confirmation rate of 38%, in line with previous samples selected with standard (no deep learning) classification tools and follow-up by Hubble Space Telescope. This first test shows that machine learning can be efficiently extended to feature recognition in the wavelength space, which will be crucial for future surveys like 4MOST, DESI, Euclid, and the Chinese Space Station Telescope (CSST).

  • 3 authors
·
Feb 16, 2022

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.

  • 89 authors
·
Feb 3, 2019

Modeling with the Crowd: Optimizing the Human-Machine Partnership with Zooniverse

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.

  • 5 authors
·
Mar 18, 2019