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DOE OSTI2022

Open Hardware in Science: The Benefits of Open Electronics

Abstract Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.

Oellermann, Michael (ORCID:0000000153926737)↗

DOE OSTI2023

Language Barriers in Organismal Biology: What Can Journals Do Better?

Synopsis In the field of organismal biology, as in much of academia, there is a strong incentive to publish in internationally recognized, highly regarded, English-language journals to promote career advancement. This expectation has created a linguistic hegemony in scientific publishing, whereby scholars for whom English is an additional language face additional barriers to achieving the same scientific recognition as scholars who speak English as a first language. Here, we surveyed the author guidelines of 230 journals in organismal biology with impact factors of 1.5 or greater for linguistically inclusive and equitable practices and policies. We looked for efforts that reflect first steps toward reducing barriers to publication for authors globally, including the presence of statements that encouraged submissions from authors of diverse nationalities and backgrounds, policies regarding manuscript rejection based on perceived inadequacies of the English language, the existence of bias-conscious reviewer practices, whether translation and editing resources or services are available, allowance for non-English abstracts, summaries, or translations, and whether journals offer license options that would permit authors (or other scholars) to translate their work and publish it elsewhere. We also directly contacted a subset of journals to verify whether the information on their author guidelines page accurately reflects their policies and the accommodations they would make. We reveal that journals and publishers have made little progress toward beginning to recognize or reduce language barriers. Counter to our predictions, journals associated with scientific societies did not appear to have more inclusive policies compared to non-society journals. Many policies lacked transparency and clarity, which can generate uncertainty, result in avoidable manuscript rejections, and necessitate additional time and effort from both prospective authors and journal editors. We highlight examples of equitable policies and summarize actions that journals can take to begin to alleviate barriers to scientific publishing.

Nolde-Lopez, B.↗

DOE OSTI2023

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Abstract Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation

ABSTRACT The decline in abundance of Lyman-α (Lyα) emitting galaxies at z ≳ 6 is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CoDaII simulation, which is a radiation hydrodynamic simulation featuring a box of ∼94 comoving Mpc side length, to compute the Lyα transmission properties of the intergalactic medium (IGM) at z ∼ 5.8 to 7. Our results mainly confirm previous studies, i.e. we find a declining Lyα transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Lyα peaks at high redshift, we also analyse the IGM transmission on the blue side, which shows a rapid decline at z ≳ 6 of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as $n_{\rm HI}\sim 10^{-9}\, \mathrm{cm}^{-3}$ (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that $\sim 1{{\ \rm per\ cent}}$ of sightlines towards M1600AB ∼ −21 galaxies at z ∼ 7 are transparent enough to allow a transmission of a blue Lyα peak. We discuss our results in the context of the interpretation of observations.

Gronke, Max (ORCID:000000032491060X)↗

DOE OSTI2025

Mapping the cosmic gamma-ray horizon: the 1CGH catalogue of Fermi -LAT detections above 10 GeV

ABSTRACT We present the First Cosmic Gamma-ray Horizon (1CGH) catalogue, featuring $\gamma$-ray detections above 10 GeV based on 16 yr of observations with the Fermi Large Area Telescope (Fermi-LAT) satellite. After carefully selecting a sample of blazars and blazar candidates from catalogues in the literature, we performed a binned likelihood analysis and identified 2791 $\gamma$-ray emitters above 10 GeV, at >3$\sigma$ level, including 62 that are new $\gamma$-ray detections. For each source, we estimated the mean energy of the highest energy bin and analysed them in the context of the cosmic gamma-ray horizon. By adopting a reference model for the extragalactic background light (EBL), we identified a subsample of 525 sources where moderate to severe $\gamma$-ray absorption could be detected across the redshift range of 0–3. This work provides the most up-to-date compilation of detections above 10 GeV, along with their redshift information. We condense extensive results from the literature, including reports on observational campaigns dedicated to blazars and $\gamma$-ray sources, thereby delivering an unprecedented review of the redshift information for sources detected above 10 GeV. Additionally, we highlight key 1CGH sources where redshift information remains incomplete, offering guidance for future optical observation campaigns. The 1CGH catalogue aims to track the most significant sources for studying the $\gamma$-ray transparency of the Universe. Furthermore, it provides a targeted subsample where the EBL optical depth, $\tau _{(E,z)}$, can be robustly measured using Fermi-LAT data.

Arsioli, Bruno (ORCID:0000000181666602)↗

DOE OSTI2022

A DE1 BINDING FACTOR 1–GLABRA2 module regulates rhamnogalacturonan I biosynthesis in Arabidopsis seed coat mucilage

Abstract The mucilage surrounding hydrated Arabidopsis thaliana seeds is a specialized extracellular matrix composed mainly of the pectic polysaccharide rhamnogalacturonan I (RG-I). Although, several genes responsible for RG-I biosynthesis have been identified, the transcriptional regulatory mechanisms controlling RG-I production remain largely unknown. Here we report that the trihelix transcription factor DE1 BINDING FACTOR 1 (DF1) is a key regulator of mucilage RG-I biosynthesis. RG-I biosynthesis is significantly reduced in loss-of-function mutants of DF1. DF1 physically interacts with GLABRA2 (GL2) and both proteins transcriptionally regulate the expression of the RG-I biosynthesis genes MUCILAGE MODIFIED 4 (MUM4) and GALACTURONOSYLTRANSFERASE-LIKE5 (GATL5). Through chromatin immunoprecipitation-quantitative PCR and transcriptional activation assays, we uncover a cooperative mechanism of the DF1–GL2 module in activating MUM4 and GATL5 expression, in which DF1 binds to the promoters of MUM4 and GATL5 through interacting with GL2 and facilitates the transcriptional activity of GL2. The expression of DF1 and GL2 is directly regulated by TRANSPARENT TESTA GLABRA2 (TTG2) and, in turn, DF1 directly represses the expression of TTG2. Taken together, our data reveal that the transcriptional regulation of mucilage RG-I biosynthesis involves a regulatory module, comprising DF1, GL2, and TTG2.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Ethical considerations in infectious disease modelling for public health policy: the case of school closures

Mathematical models of infectious diseases are frequently used as a tool to support public health policy and decisions around the implementation of interventions such as school closures. However, most publications on policy-relevant modelling lack an ethical framework and do not explicitly consider the ethical implications of the work. This creates a risk that the unintended consequences of interventions are overlooked or that models are used to justify decisions that are inconsistent with public health ethics. In this article, we focus on the case study of school closures as a commonly modelled intervention against pandemic influenza, COVID-19 and other infectious disease threats. We briefly review some of the key concepts in public health ethics and describe approaches to modelling the effects of school closures. We then identify a series of ethical considerations involved in modelling school closures. These include accounting for population heterogeneity and inequalities; including a diversity of viewpoints and expertise in model design; considering the distribution of benefits and harms; and model transparency and contextualization. Furthermore, we conclude with some recommendations to ensure that policy-relevant modelling is consistent with some key ethics values.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Why don't we share data and code? Perceived barriers and benefits to public archiving practices

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2026

New framework for extracting GPDs from exclusive photon electroproduction

Recently, a new framework for studying generic 2 → 3 hard exclusive reactions, referred to as single-diffractive hard exclusive processes, has been introduced to provide a cleaner separation of the underlying physical mechanisms. In this work, we expand this formalism to the case of exclusive real-photon electroproduction off a nucleon, 𝑒⁡(ℓ) +𝑁⁡(𝑝) →𝑒⁡(ℓ′) +𝑁⁡(𝑝′) + 𝛾⁡(𝑞′), which represents the classical channel for accessing generalized parton distributions (GPDs) in nucleons and nuclei. This extension enables a more systematic and physically transparent formulation of the reaction dynamics, paving the way for improved extractions of GPDs from experimental data as compared to existing approaches.

Qiu, Jian-Wei [Thomas Jefferson National Accelerat↗

DOE OSTI2026

Insulating ground state and 2−𝑘 magnetic structure of candidate Weyl hydrogen-atom K2⁢Mn3⁢(AsO4)3

The ideal Weyl "hydrogen-atom" semimetal exhibits only a single pair of Weyl nodes and no other trivial states at the Fermi energy. Such a material would be a panacea in the study of Weyl quasi-particles, allowing direct unambiguous observation of their topological properties. The alluaudite-like K2⁢Mn3⁢(AsO4)3 compound was recently proposed as such a material. Here, we use comprehensive experimental work and first-principle calculations to assess this prediction. We find K2⁢Mn3⁢(AsO4)3 crystallizes in the 𝐶⁢2/𝑐 symmetry with a quasi-one-dimensional Mn sublattice, growing as small needle-like crystals. Bulk property measurements reveal magnetic transitions at ≈8 and ≈4 K, which neutron scattering experiments show correspond to two distinct magnetic orders, first a partially ordered ferrimagnetic 𝐤𝟏=(0,0,0) structure at 8 K and a second transition of 𝐤𝟐=(1,0,0) at 4 K to a fully ordered state. Below the second transition, both ordering vectors are necessary to describe the complex magnetic structure with modulated spin magnitudes. Both of the best-fit magnetic structures in this work are found to break the symmetry necessary for the generation of Weyl nodes, though one of the magnetic structures allowed by 𝐤𝟏 does preserve this symmetry. However, the crystals are optically transparent and ellipsometry measurements reveal a large band gap, undermining expectations of semimetallic behavior. Density functional theory calculations predict an insulating antiferromagnetic ground state, in contrast to previous reports, and suggest potential frustration on the magnetic sublattice. Given the wide tunability of the alluaudite structure, we consider ways to push the system closer to a semimetallic state.

Taddei, Keith M [Argonne National Laboratory]↗

DOE OSTI2025

Symmetry-Energy Dependence of the Bulk Viscosity of Nuclear Matter

We clarify how the weak-interaction-driven bulk viscosity ζ and the bulk relaxation time τ Π of neutrino-transparent n p e matter depend on the nuclear symmetry energy. We show that, at saturation density, the equation-of-state dependence of these transport quantities is fully determined by the experimentally constrained nuclear symmetry energy S and its slope L . Variations of L can change the bulk viscosity by orders of magnitude, which can affect both the dissipative and the conservative tidal response of neutron stars. Furthermore, this suggests that both conservative and dissipative effects encoded in the gravitational-wave signatures of binary neutron star inspirals may help constrain nuclear symmetry-energy properties.

Neutron stars & pulsars↗

DOE OSTI2026

Autler-Townes spectroscopy of a Rydberg ladder

Ladder-type two-photon excitation of an atom from a ground state $|g\rangle$, to an intermediate excited state $|e\rangle$, and finally, to a Rydberg state $|r\rangle$ has a variety of uses from quantum information to sensing. A common scheme for detecting this transition optically is through electromagnetically induced transparency (EIT). However, in inverted wavelength schemes, where the ground-to-excited transition wavelength is shorter than the excited-to-Rydberg transition wavelength, the strength of the EIT feature on the lower-leg beam is strongly reduced in a Doppler-broadened medium. Here, in this study, we report on an alternative two-photon spectroscopic feature, which we term the two-photon Autler-Townes resonance, observed on the upper-leg beam. Compared to the EIT signal, this feature's superior signal-to-noise ratio allows one to resolve Rydberg resonances with principal quantum number as high as n=80. We also show that such a feature can be utilized to generate an error signal for stabilizing the frequency of the upper-leg beam.

Xiang, Tai [University of California, Berkeley, CA↗

DOE OSTI2026

Agentic artificial intelligence for multistage physics experiments at a large-scale user facility particle accelerator

We present a language-model-driven agentic artificial intelligence (AI) system to autonomously execute multistage physics experiments on a production synchrotron light source. Implemented at the Advanced Light Source particle accelerator, the system translates natural language user prompts into structured execution plans that combine archive data retrieval, control-system channel resolution, automated script generation, controlled machine interaction, and analysis. In a representative machine physics task, we show that preparation time was reduced by 2 orders of magnitude relative to manual scripting even for a system expert, while operator-standard safety constraints were strictly upheld. Core architectural features, plan-first orchestration, bounded tool access, and dynamic capability selection, enable transparent, auditable execution with fully reproducible artifacts. These results establish a blueprint for the safe integration of agentic AI into accelerator experiments and demanding machine physics studies, as well as routine operations, with direct portability across accelerators worldwide and, more broadly, to other large-scale scientific infrastructures.

Accelerator/storage ring control systems↗

DOE OSTI2020

Resonant propagation of x rays from the linear to the nonlinear regime

We present a theoretical study of temporal, spectral, and spatial reshaping of intense, ultrafast x-ray pulses propagating through a resonant medium. Our calculations are based on the solution of a three-dimensional time-dependent Schrodinger-Maxwell equation, with the incident x-ray photon energy on resonance with the core-level is-3p transition in neon. We study the evolution of the combined incident and medium-generated field, including the effects of stimulated emission, absorption, ionization, and Auger decay, as a function of the input pulse energy and duration. We find that stimulated Raman scattering between core-excited states 1s -1 3p and 2p -1 3p occurs at high x-ray intensity, and that the emission around this frequency is strongly enhanced when also including the similar 1s -1 -2p -1 response of the ion. We also explore the dependence of x-ray self-induced transparency (SIT) and self-focusing on the pulse intensity and duration, and we find that the stimulated Raman scattering plays an important role in both effects. Finally, we discuss how these nonlinear effects may potentially be exploited as control parameters for pulse properties of x-ray free-electron laser sources.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Singularities in nearly uniform one-dimensional condensates due to quantum diffusion

Dissipative systems often exhibit wavelength-dependent loss rates. One prominent example is Rydberg polaritons formed by electromagnetically induced transparency, which have long been a leading candidate for studying the physics of interacting photons and also hold promise as a platform for quantum information. In this system, dissipation is in the form of quantum diffusion, i.e., proportional to k 2 (k being the wavevector) and vanishing at long wavelengths as k→0. Here, we show that one-dimensional condensates subject to this type of loss are unstable to long-wavelength density fluctuations in an unusual manner: after a prolonged period in which the condensate appears to relax to a uniform state, local depleted regions quickly form and spread ballistically throughout the system. We connect this behavior to the leading-order equation for the nearly uniform condensate—a dispersive analog to the Kardar-Parisi-Zhang equation—which develops singularities in finite time. Furthermore, we show that the wavefronts of the depleted regions are described by purely dissipative solitons within a pair of hydrodynamic equations, with no counterpart in lossless condensates. We close by discussing conditions under which such singularities and the resulting solitons can be physically realized.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Local chromatic correction optics for Future Circular Collider e + e −

Local chromatic correction optics are proposed for the Future Circular e + − e − Collider. These new optics assume an identical layout of the magnets at all operation energies and include a new design for the arcs, for the straight sections, and for the final focus. The arcs design is a step forward from the classic FODO lattice that achieves near cancellation up to the fourth order of chromatic and geometric aberrations. Straight sections and the final focus benefit from the application of transparency conditions and are thus minimally impacting the global beam dynamics. The final focus design includes both vertical and horizontal chromaticity correction sections, crab sextupoles, and additional specific sextupoles and decapoles for the optimization of the dynamics off-energy. Decapoles are very effective in mitigating the reduction of dynamic aperture due to synchrotron radiation. Nonlinear magnet settings are further optimized with multiobjective algorithms. The overall properties of the new optics proposed are analyzed in the presence of errors and compared to other optics designs.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Multiple Tunable Hyperbolic Resonances in Broadband Infrared Carbon-Nanotube Metamaterials

Aligned densely packed carbon-nanotube metamaterials prepared using vacuum filtration are an emerging infrared nanophotonic material. We report multiple hyperbolic plasmon resonances, together spanning the mid-infrared, in individual resonators made from aligned and densely packed carbon nanotubes. In a near-field scanning optical microscopy (NSOM) imaging study of nanotube metamaterial resonators, we observe distinct deeply subwavelength field profiles at the fundamental and higher-order resonant frequencies. The wafer-scale area of the nanotube metamaterials allows us to combine this near-field imaging with a systematic far-field spectroscopic study of the scaling properties of many resonator arrays. Thorough theoretical modeling agrees with these measurements and identifies the resonances as higher-order Fabry-Perot (FP) resonances of hyperbolic waveguide modes. Nanotube resonator arrays show broadband extinction from 1.5–10 µm and reversibly switchable extinction in the 3–5 µm atmospheric transparency window through the coexistence of multiple modes in individual ribbons. Broadband carbon-nanotube metamaterials supporting multiple resonant modes are a promising candidate for ultracompact absorbers, tunable thermal emitters, and broadband sensors in the mid-infrared.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Bound States in the Continuum on a Silicon Chip with Dynamic Tuning

Expanding bound states in the continuum (BIC) beyond photonic crystal systems may enable broader applications benefiting from the unique properties of BIC states. We use photonic integrated circuit to realize a Fabry-Pérot BIC on a silicon chip. The devices consist of cascaded ring resonators with tunable resonance frequencies and phase delays. As a result, the BIC state is dynamically tuned with electrical I/O. We analyze the mechanism of the formation of BIC states in this waveguide system and point out the fundamental differences between the BIC states and electromagnetically induced transparency states in integrated photonics. The high transmission protected by the BIC state enables versatile optical filters, which are capable of independent control over switching, peak position, and quality factor. We also demonstrate the scalability of this platform. As a result, this integrated silicon photonic platform brings opportunities for practical BIC applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗