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At least 91 records · Page 5

TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria

In this tutorial narrative, we introduce a novel template developed to enable the creation of stoichiometric genome-scale metabolic models for iron-oxidizing bacteria. We demonstrate the development of this template by applying it to Sideroxydans lithotrophicus ES-1, and validate our model using transcriptomic data (Published in Zhou et al., 2022 AEM). Below, we further show that our template facilitates the modeling of mixotrophic iron-oxidizing bacteria and metagenome-assembled genomes (MAGs), by applying our template to the MAG of the mixotrophic iron oxidizer Leptothrix ochracea (Published in Tothero et al, 2024). This work represents the first instance of a generalized and adaptable template for modeling diverse iron-oxidizing microbial systems, expanding the accessibility and applicability of metabolic modeling in this field.

genome-scale model↗

Enabling Early Transient Discovery in LSST via Difference Imaging with DECam

We present SLIDE, a pipeline that enables transient discovery in data from the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST), using archival images from the Dark Energy Camera as templates for difference imaging. We apply this pipeline to the recently released Data Preview 1 (DP1; the first public release of Rubin commissioning data) and search for transients in the resulting difference images. The image subtraction, photometry extraction, and transient detection are all performed on the Rubin Science Platform. We demonstrate that SLIDE effectively extracts clean photometry by circumventing poor or missing LSST templates. We identified 29 previously unreported transients, 12 of which would not have been detected based on the DP1 DiaObject catalog. SLIDE will be especially useful for transient analysis in the early years of LSST, when template coverage will be largely incomplete or when templates may be contaminated by transients present at the time of acquisition. We present multiband light curves for a sample of known transients, along with new transient candidates identified through our search. Finally, we discuss the prospects of applying this pipeline during the main LSST survey. Our pipeline is broadly applicable and will support studies of all transients with slowly evolving phases.

Dong, Yize 一泽董 [Harvard-Smithsonian Center for Ast↗

Ultrathin Boron Growth onto Nanodiamond Surfaces via Electrophilic Boron Precursors

Diamond as a templating substrate is largely unexplored, and the unique properties of diamond, including its large bandgap, thermal conductance, and lack of cytotoxicity, makes it versatile in emergent technologies in medicine and quantum sensing. Surface termination of an inert diamond substrate and its chemical reactivity are key in generating new bonds for nucleation and growth of an overlayer material. Oxidized high-pressure high temperature (HPHT) nanodiamonds (NDs) are largely terminated by alcohols that act as nucleophiles to initiate covalent bond formation when an electrophilic reactant is available. In this work, we demonstrate a templated synthesis of ultrathin boron on ND surfaces using trigonal boron compounds. Boron trichloride (BCl 3 ), boron tribromide (BBr 3 ), and borane (BH 3 ) were found to react with ND substrates at room temperature in inert conditions. BBr 3 and BCl 3 were highly reactive with the diamond surface, and sheet-like structures were produced and verified with electron microscopy. Surface-sensitive spectroscopies were used to probe the molecular and atomic structure of the ND constructs’ surface, and quantification showed the boron shell was less than 1 nm thick after 1–24 h reactions. Observation of the reaction supports a self-terminating mechanism, similar to atomic layer deposition growth, and is likely due to the quenching of alcohols on the diamond surface. X-ray absorption spectroscopy revealed that boron-termination generated midgap electronic states that were originally predicted by density functional theory (DFT) several years ago. DFT also predicted a negative electron surface, which has yet to be confirmed experimentally here. The boron-diamond nanostructures were found to aggregate in dichloromethane and were dispersed in various solvents and characterized with dynamic light scattering for future cell imaging or cancer therapy applications using boron neutron capture therapy (BNCT). The unique templating mechanism based on nucleophilic alcohols and electrophilic trigonal precursors allows for covalent bond formation and will be of interest to researchers using diamond for quantum sensing, additive manufacturing, BNCT, and potentially as an electron emitter.

36 MATERIALS SCIENCE↗

Heteroepitaxial control of thickness, strain, and domain architecture in few-layer ferroelectric tin monochalcogenides

Thin-film epitaxy and epitaxial strain have been widely exploited to tune domain configurations, switching behavior, and ferroic properties in conventional three-dimensional ferroelectric thin films; however, its application to controlling the properties of two-dimensional (2D) ferroelectrics has remained largely unexplored. Here, using SnX (X = Se, S) as a model system, we demonstrate heteroepitaxial control of thickness, strain state, and domain architecture in few-layer ferroelectric SnX via growth on monolayer MoS2 van der Waals (vdW) templates. Compared with conventional growth, MoS2-templated heteroepitaxy promotes epitaxial alignment, yielding ultrathin SnSe films with improved crystalline quality, full areal coverage, and enlarged lateral dimensions. Strong interfacial epitaxial coupling induces pronounced in-plane strain and stabilizes a hierarchical ferroelastic domain architecture, in which long-range 90° stripe domains are further subdivided into nanoscale rotational variants, as revealed by scanning transmission electron microscopy and synchrotron X-ray microscopy. Piezoresponse force microscopy and second-harmonic polarimetry confirm robust in-plane polarization, while ferroelectricity in SnSe is established through polarization-electric field hysteresis and nonvolatile ferroelectric resistive switching with on/off ratios approaching 1000. A nonvolatile, switchable ferroelectric diode effect further evidences direct coupling between polarization and charge transport. Notably, ferroelectric switchability exhibits a strong thickness dependence and is preserved only below ∼10 layers. This vdW heteroepitaxial strategy is further extended to ferroelectric SnS. The seamless heteroepitaxial integration of 2D ferroelectrics with CMOS-compatible, wafer-scale MoS2 templates provides a general and scalable route for strain-enabled structural and ferroelectric engineering in emerging memory and low-power optoelectronic applications.

Wang, Yueyin↗

Mosaic lateral heterostructures in two-dimensional perovskite

Lateral heterostructures are important for exploring exotic physics, developing new devices and achieving device miniaturization. Endo-epitaxial growth occurring in patterned templates presents a promising strategy to realize extensive patterned areas in heterostructures, as recently demonstrated with two-dimensional (2D) covalent materials. However, the conventional lithography and etching processes used to prepare patterned templates are too aggressive for 2D lead halide perovskites, owing to their inherently soft and unstable ionic lattice. Here we create square holes of controllable size within 2D lead halide perovskites, enabling the fabrication of continuous lateral heterostructures over large areas. We demonstrate that the square holes form through spontaneous etching, a process initiated by internal strain and stabilized along the [100]/[010] crystallographic direction. Furthermore, the size of the square holes can be controlled by adjusting the etching time and temperature. Moreover, by incorporating a rapid solvent evaporation growth technique, the edges of the square holes act as templates for epitaxial growth of another type of perovskite, incorporating different halide or metal ions. Finally, we realized a series of mosaic lateral heterostructures that can emit various colours for light-emitting devices. As a result, this synthesis of diverse 2D perovskite mosaic lateral heterostructures provides valuable insights into the structural characteristics of perovskites and offers a versatile material platform for the development of complex integrated emitting devices.

Organic–inorganic nanostructures↗

Orientation-tunable local crystallization of Si films enabled by atomic imprint crystallization

Here, in this paper, we demonstrate area-selective crystallization of amorphous Si into tunable crystal orientations enabled by atomic imprint crystallization (AIC), where an amorphous Si layer is crystallized by solid phase epitaxy (SPE) from an externally impressed single-crystalline Si template. Using micro-patterned single-crystalline Si templates, a limited area of an amorphous Si film, where the film surface and patterned template surface are in contact, is crystallized via SPE to create an array of crystallographically aligned dots embedded in amorphous matrix. Combining AIC from the top surface and conventional SPE from the substrate, we demonstrate the fabrication of an array of crystalline dots embedded in single-crystalline matrix with tunable in-plane rotation angle. The results indicate the high tunability of the crystallization process enabled by AIC, allowing precise control of crystallographic properties of thin films with area-selectivity; such capability opens opportunities for the design of new materials for a wide range of applications in materials science.

Amorphous↗

Nonenzymatic RNA copying with a potentially primordial genetic alphabet

Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U because of the stronger G:C vs. A:U base pair and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s 2 U) and inosine (I) form by deamination of 2-thiocytidine (s 2 C) and A, respectively. We used thermodynamic and crystallographic analyses to compare the I:s 2 C and A:s 2 U base pairs. We find that the I:s 2 C base pair is isomorphic and isoenergetic with the A:s 2 U base pair. The I:s 2 C base pair is weaker than a canonical G:C base pair, while the A:s 2 U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s 2 U, s 2 C, I, and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s 2 C and s 2 U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s 2 U, s 2 C, I, and A and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying.

Science & Technology - Other Topics↗

Compressed baryon acoustic oscillation analysis is robust to modified-gravity models

Abstract We study the robustness of the baryon acoustic oscillation (BAO) analysis to the underlying cosmological model. We focus on testing the standard BAO analysis that relies on the use of a template. These templates are constructed assuming a fixed fiducial cosmological model and used to extract the location of the acoustic peaks. Such “compressed analysis” had been shown to be unbiased when applied to the ΛCDM model and some of its extensions. However, it has not been known whether this type of analysis introduces biases in a wider range of cosmological models where the template may not fully capture relevant features in the BAO signal. In this study, we apply the compressed analysis to noiseless mock power spectra that are based on Horndeski models, a broad class of modified-gravity theories specified with eight additional free parameters. We study the precision and accuracy of the BAO peak-location extraction assuming DESI, DESI II, and MegaMapper survey specifications. We find that the bias in the extracted peak locations is negligible; for example, it is less than 10% of the statistical error for even the proposed future MegaMapper survey. Our findings indicate that the compressed BAO analysis is remarkably robust to the underlying cosmological model.

Astronomy & Astrophysics↗

Impact of systematic redshift errors on the cross-correlation of the Lyman-α forest with quasars at small scales using DESI Early Data

The Dark Energy Spectroscopic Instrument (DESI) will measure millions of quasar spectra by the end of its 5 year survey. Quasar redshift errors impact the shape of the Lyman-α forest correlation functions, which can affect cosmological analyses and therefore cosmological interpretations. Here, using data from the DESI Early Data Release and the first two months of the main survey, we measure the systematic redshift error from an offset in the cross-correlation of the Lyman-α forest with quasars. We find evidence for a redshift dependent bias causing redshifts to be underestimated with increasing redshift, stemming from improper modeling of the Lyman-α optical depth in the templates used for redshift estimation. New templates were derived for the DESI Year 1 quasar sample at z > 1.6 and we found the redshift dependent bias, Δr ∥ , increased from -1.94 ± 0.15 h -1 Mpc to -0.08 ± 0.04 h -1 Mpc (-205 ± 15 km s -1 to -9.0 ± 4.0 km s -1 ). These new templates will be used to provide redshifts for the DESI Year 1 quasar sample.

Lyman alpha forest↗

Unveiling phase evolution of complex oxides toward precise solid-state synthesis

The precise synthesis of high-purity materials is crucial in accelerating materials discovery. However, the lack of theoretical understanding and practical guidance poses challenges, particularly for materials with compositional and structural complexity. Here, we propose a feasible principle toward synthesizing complex inorganic solids. This principle involves the introduction of an inducer that induces crucial intermediates, which in turn guide the synthesis pathway toward the target materials through structural templating, named inducer-facilitated assembly through structural templating (i-FAST). We validate this principle with three distinct oxides: garnet Li6.5La3Zr1.5Ta0.5O12, perovskite BaCo0.8Sn0.2O3, and pyrochlore Gd1.5La0.5Zr2O7. This structural templating approach enables synthesis along predesigned pathways, forming intermediates that are thermodynamically favored for prior formation and kinetically preferred for the final product, resulting in precisely synthesizing high-purity target materials. This study not only represents a substantial advancement in comprehending the interplay between thermodynamics/kinetics and phase evolution in complex solid synthesis but also provides an effective strategy for guiding exploratory solid-state synthesis.

Yang, Lin↗

Extrapolation of Type Ia Supernova Spectra into the Near-infrared Using Principal Component Analysis

Abstract We present a method of extrapolating the spectroscopic behavior of Type Ia supernovae (SNe Ia) in the near-infrared (NIR) wavelength regime up to 2.30 μ m using optical spectroscopy. Such a process is useful for accurately estimating K-corrections and other photometric quantities of SNe Ia in the NIR. A principal component analysis is performed on data consisting of Carnegie Supernova Project I & II optical and NIR FIRE spectra to produce models capable of making these extrapolations. This method differs from previous spectral template methods by not parameterizing models strictly by photometric light-curve properties of SNe Ia, allowing for more flexibility of the resulting extrapolated NIR flux. A difference of around −3.1% to −2.7% in the total integrated NIR flux between these extrapolations and the observations is seen here for most test cases including Branch core-normal and shallow-silicon subtypes. However, larger deviations from the observation are found for other tests, likely due to the limited high-velocity and broad-line SNe Ia in the training sample. Maximum-light principal components are shown to allow for spectroscopic predictions of the color-stretch light-curve parameter, s BV , within approximately ±0.1 units of the value measured with photometry. We also show these results compare well with NIR templates, although in most cases the templates are marginally more fitting to observations, illustrating a need for more concurrent optical+NIR spectroscopic observations to truly understand the diversity of SNe Ia in the NIR.

Astronomy & Astrophysics↗

Distance Estimate Method for Asymptotic Giant Branch Stars Using Infrared Spectral Energy Distributions

We present a method to estimate distances to asymptotic giant branch (AGB) stars in the Galaxy, using spectral energy distributions (SEDs) in the near- and mid-infrared. By assuming that a given set of source properties (initial mass, stellar temperature, composition, and evolutionary stage) will provide a typical SED shape and brightness, sources are color matched to a distance-calibrated template and thereafter scaled to extract the distance. The method is tested by comparing the distances obtained to those estimated from very long baseline interferometry or Gaia parallax measurements, yielding a strong correlation in both cases. Additional templates are formed by constructing a source sample likely to be close to the Galactic center, and thus with a common, typical distance for calibration of the templates. These first results provide statistical distance estimates to a set of almost 15,000 Milky Way AGB stars belonging to the Bulge Asymmetries and Dynamical Evolution (BAaDE) survey, with typical distance errors of ±35%. With these statistical distances, a map of the intermediate-age population of stars traced by AGBs is formed, and a clear bar structure can be discerned, consistent with the previously reported inclination angle of 30° to the GC–Sun direction vector. These results motivate deeper studies of the AGB population to tease out the intermediate-age stellar distribution throughout the Galaxy, as well as determining statistical properties of the AGB population luminosity and mass-loss-rate distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

An Agnostic Approach to Building Empirical Type Ia Supernova Light Curves: Evidence for Intrinsic Chromatic Flux Variation Using Nearby Supernova Factory Data

We present a new empirical Type Ia supernova (SN Ia) model with three chromatic flux variation templates: one phase dependent and two phase independent. No underlying dust extinction model or patterns of intrinsic variability are assumed. Implemented with Stan and trained using spectrally binned Nearby Supernova Factory spectrophotometry, we examine this model's 2D, phase-independent flux variation space using two motivated basis representations. In both, the first phase-independent template captures variation that appears dust-like, while the second captures a combination of effectively intrinsic variability and second-order dust-like effects. We find that ≈13% of the modeled phase-independent flux variance is not dust-like. Previous empirical SN Ia models either assume an effective dust extinction recipe in their architecture, or only allow for a single mode of phase-independent variation. The presented results demonstrate such an approach may be insufficient, because it could "leak" noticeable intrinsic variation into phase-independent templates.

79 ASTRONOMY AND ASTROPHYSICS↗

Improved Spectral Classification of Local K/M Dwarfs in SDSS Surveys. I. Chemodynamic Validation and Metallicity Calibration

An examination of 109,276 spectra of low-mass stars in the Sloan Digital Sky Survey (SDSS) data archive, collected pre-2010, provides a broad collection of K/M (sub)dwarfs tracing the local (d ≲ 250 pc) population of the thin-disk, thick-disk, and halo, based on 3D kinematics. These populations have distinct metallicities and kinematics, which should be reflected in lower-mass members. One complication is measuring metallicities of M dwarfs from low-resolution spectroscopy or photometry alone remains a challenge, even with the availability of Gaia data. To better characterize physical parameters of low-mass stars observed by SDSS, we define a set of 536 improved, empirical K/M dwarf classification templates to more accurately determine spectral subtypes (K5.5–M8.5) and morphology classes (MCs) (0.5–12.5). We select the best-fit template to every archival SDSS spectrum in the range 5000–8000 Å based on minimum χ 2 value. We then use secondary metallicity estimators to calibrate the most likely [Fe/H] values corresponding to the assigned MC. We confirm that the most metal-rich K/M dwarfs have thin-disk kinematics, and we observe the known effect of Galactic radial metallicity migration, which we confirm is strongly imprinted in the chemodynamics of the local disk M dwarfs. Confirmation of these chemodynamic trends validates the precision of our improved templates for estimating [Fe/H] for M (sub)dwarfs, notably at the low-metallicity end (–3 < [Fe/H] < –1). Substructure in the chemodynamics of the most metal-poor K/M subdwarfs begins to distinguish between local Gaia-Enceladus and local in situ halo objects. This methodology opens the door to use the ubiquitous, local K/M (sub)dwarfs to trace local Galactic chemodynamics with the highest possible resolution.

79 ASTRONOMY AND ASTROPHYSICS↗

Municipal Fleet Action Plan Guide

This action plan template and guide have been designed to support light-duty or medium-duty municipal fleet managers as they plan to adopt electric vehicles. The resource is an adaptation of content created by the National Laboratory of the Rockies (NLR), with support from World Resources Institute (WRI), for participants in the U.S. Department of Energy's Energy to Communities peer-learning cohort, Charting a Path to Municipal Fleet Electrification. Fifteen participating municipalities joined monthly cohort workshops from July through December 2024 to learn and plan for their own fleet electrification. Clean Cities and Communities coalitions supported participating municipalities throughout the cohort series by conducting fleet analysis and planning activities on their behalf. This template is an adapted version of cohort activities.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Curvilinear Magnonic Crystal Based on 3D Hierarchical Nanotemplates

Curvilinear magnetic nanostructures enable control of magnetization dynamics through geometry-induced anisotropy and chiral interactions, as well as magnetic field modulation. In this work, we report a curvilinear magnonic crystal based on large-area square arrays of truncated nanospikes fabricated by conformal coating of 3D hierarchical templates with permalloy thin films. Brillouin light scattering spectroscopy reveals an anisotropic band structure with multiple dispersive and folded Bloch-type dispersive spin-wave modes as well as nondispersive modes exhibiting direction-dependent frequency shifts and intensity asymmetries along lattice principal axes. Finite element micromagnetic simulations indicate that curvature-induced variations of the demagnetizing field govern the magnonic response, enabling the identification of modes propagating in nanochannels and others localized on nanospike apexes or along the ridges connecting adjacent nanospikes. The combination of geometric curvature and optical probing asymmetry produces directional dependence of magnonic bands, establishing 3D hierarchical templates as a versatile platform for curvature-engineered magnonics.

3D hierarchical templates↗

Sequential Infiltration Synthesis of Cadmium Sulfide Discrete Atom Clusters

Abstract Exposure of soft material templates to alternating volatile chemical precursors can produce inorganic deposition within the permeable template (e.g. a polymer thin film) in a process akin to atomic layer deposition (ALD). While such sequential infiltration synthesis (SIS) processes have now been demonstrated for many metal oxides, we report an SIS process for a transition metal sulfide – CdS. Gas phase dimethyl cadmium and hydrogen sulfide precursors infiltrated into poly(4‐vinylpyridine) thin films result in the 3D‐nucleation of clusters consistent with a cubane‐type Cd 4 S 4 core that are variably terminated with methyl, thiol and hydroxy capping ligands. First principles models and simulation of few‐atom Cd‐based clusters are consistent with electronic and vibrational spectroscopy and grazing‐incidence total X‐ray scattering measurements of 3D‐cluster‐arrays synthesized at 80 °C. The direct synthesis of few‐atom transition metal sulfide clusters within polymer thin films will provide a versatile new route to precision architectures for light‐absorbing materials including solar energy harvesting and conversion applications.

Jayaweera, Nuwanthaka P. [Material Science Divisio↗

Sequential Infiltration Synthesis of Cadmium Sulfide Discrete Atom Clusters

Exposure of soft material templates to alternating volatile chemical precursors can produce inorganic deposition within the permeable template (e.g. a polymer thin film) in a process akin to atomic layer deposition (ALD). While such sequential infiltration synthesis (SIS) processes have now been demonstrated for many metal oxides, we report an SIS process for a transition metal sulfide – CdS. Gas phase dimethyl cadmium and hydrogen sulfide precursors infiltrated into poly(4-vinylpyridine) thin films result in the 3D-nucleation of clusters consistent with a cubane-type Cd 4 S 4 core that are variably terminated with methyl, thiol and hydroxy capping ligands. First principles models and simulation of few-atom Cd-based clusters are consistent with electronic and vibrational spectroscopy and grazing-incidence total X-ray scattering measurements of 3D-cluster-arrays synthesized at 80 °C. The direct synthesis of few-atom transition metal sulfide clusters within polymer thin films will provide a versatile new route to precision architectures for light-absorbing materials including solar energy harvesting and conversion applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗