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DOE OSTI2025

Granger causal inference for climate change attribution

Abstract Climate change detection and attribution (D&A) is concerned with determining the extent to which anthropogenic activities have influenced specific aspects of the global climate system. D&A fits within the broader field of causal inference, the collection of statistical methods that identify cause and effect relationships. There are a wide variety of methods for making attribution statements, each of which require different types of input data and focus on different types of weather and climate events and each of which are conditional to varying extents. Some methods are based on Pearl causality (direct experimental interference) while others leverage Granger (predictive) causality, and the causal framing provides important context for how the resulting attribution conclusion should be interpreted. However, while Granger-causal attribution analyses have become more common, there is no clear statement of their strengths and weaknesses relative to Pearl-causal attribution and no clear consensus on where and when Granger-causal perspectives are appropriate. In this prospective paper, we provide a formal definition for Granger-based approaches to trend and event attribution and a clear comparison with more traditional methods for assessing the human influence on extreme weather and climate events. Broadly speaking, Granger-causal attribution statements can be constructed quickly from observations and do not require computationally-intesive dynamical experiments. These analyses also enable rapid attribution, which is useful in the aftermath of a severe weather event, and provide multiple lines of evidence for anthropogenic climate change when paired with Pearl-causal attribution. Confidence in attribution statements is increased when different methodologies arrive at similar conclusions. Moving forward, we encourage the D&A community to embrace hybrid approaches to climate change attribution that leverage the strengths of both Granger and Pearl causality.

Risser, Mark D. (ORCID:0000000319561783)↗

DOE OSTI2024

Application of functional genomics for domestication of novel non-model microbes

Abstract With the expansion of domesticated microbes producing biomaterials and chemicals to support a growing circular bioeconomy, the variety of waste and sustainable substrates that can support microbial growth and production will also continue to expand. The diversity of these microbes also requires a range of compatible genetic tools to engineer improved robustness and economic viability. As we still do not fully understand the function of many genes in even highly studied model microbes, engineering improved microbial performance requires introducing genome-scale genetic modifications followed by screening or selecting mutants that enhance growth under prohibitive conditions encountered during production. These approaches include adaptive laboratory evolution, random or directed mutagenesis, transposon-mediated gene disruption, or CRISPR interference (CRISPRi). Although any of these approaches may be applicable for identifying engineering targets, here we focus on using CRISPRi to reduce the time required to engineer more robust microbes for industrial applications. One-Sentence Summary The development of genome scale CRISPR-based libraries in new microbes enables discovery of genetic factors linked to desired traits for engineering more robust microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway

Abstract Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars after cell wall polysaccharide hydrolysis. Understanding how plants respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we acquired fundamental knowledge on lignin-modified poplar expressing 3-dehydroshikimate dehydratase using RNA-seq and metabolomics. The data clearly demonstrate that changes in gene expression and metabolite abundance can occur in a strict spatiotemporal fashion, revealing tissue-specific responses in the xylem, phloem, or periderm. In the poplar line that exhibited the strongest reduction in lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolites had differential abundance in the xylem from older stems. The changes affected predominantly the shikimate and phenylpropanoid pathways as well as secondary cell wall metabolism, and resulted in significant accumulation of hydroxybenzoates derived from protocatechuate and salicylate.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Relaxing Direct Ptychography Sampling Requirements via Parallax Imaging Insights

Direct ptychography enables the retrieval of information encoded in the phase of an electron wave passing through a thin sample by deconvolving the interference effects of a converged probe with known aberrations. Under the weak phase object approximation, this permits the optimal transfer of information using noniterative techniques. However, the achievable resolution of the technique is traditionally limited by the probe step size—setting stringent Nyquist sampling requirements. At the same time, parallax imaging has emerged as a dose-efficient phase technique which relaxes sampling requirements and enables scan-upsampling. Here, we formulate parallax imaging as a quadratic approximation to part of the direct ptychography kernel and use this insight to enable upsampling in direct ptychography. We validate our analytical results numerically using simulated and experimental reconstructions.

direct ptychography, parallax imaging, scan Nyquis↗

DOE OSTI2024

An attractive model: simulating fuzzy dark matter with attractive self-interactions

ABSTRACT Fuzzy dark matter (FDM), comprised of ultralight ($m \sim 10^{-22}\,{\rm eV}$) boson particles, has received significant attention as a viable alternative to cold dark matter (CDM), as it approximates CDM on large scales (${\gtrsim}1$ Mpc) while potentially resolving some of its small-scale problems via kiloparsec-scale quantum interference. However, the most basic FDM model, with one free parameter (the boson mass), is subject to a tension: small boson masses yield the desired cores of dwarf galaxies but underpredict structure in the Lyman-α forest, while large boson masses render FDM effectively identical to CDM. This Catch-22 problem may be alleviated by considering an axion-like particle with attractive particle self-interactions. We simulate an idealized FDM halo with self-interactions parametrized by an energy decay constant $f \sim 10^{15}~\rm {GeV}$ related to the axion symmetry-breaking conjectured to solve the strong-CP problem in particle physics. We observe solitons, a hallmark of FDM, condensing within a broader halo envelope, and find that the density profile and soliton mass depend on self-interaction strength. We propose generalized formulae to extend those from previous works to include self-interactions. We also investigate a critical mass threshold predicted for strong interactions at which the soliton collapses into a compact, unresolved state. We find that the collapse happens quickly, and its effects are initially contained to the central region of the halo.

Painter, Connor A. (ORCID:0000000235314806)↗

DOE OSTI2025

Investigation of oscillations above the acoustic cut-off frequency for a sample of Kepler stars. II. Identifying temporal frequency shifts

ABSTRACT Stellar oscillations with frequencies greater than the acoustic cut-off frequency are not trapped within the star’s interior. Geometric interference between these high-frequency waves produces a peak-like structure in the power spectrum of the star, known as the pseudo-modes. In this study, we aim to analyse 51 stars previously identified (from a sample of 91 Kepler stars) to contain statistically significant evidence for pseudo-modes, to determine if the pseudo-mode frequencies vary in time. We obtained these frequency variations and the uncertainty by the resampled periodogram approach, where periodogram realisations were created from successive, overlapping 90-d time segments, and a cross-correlation function was generated between them. The computed shifts were compared against temporal p-mode frequency shifts and a stellar magnetic activity proxy, $S_{\mathrm{ph}}$. We found that for 16 per cent of the stars pseudo-mode frequency shifts were significantly anticorrelated with p-mode shifts, as is the case for the Sun. However, we also found pseudo-mode and p-mode shifts to be significantly correlated in-phase in 8 per cent of our sample. The remainder showed no significant correlation. We also searched for trends between the maximum variation of pseudo-mode frequency shifts and stellar parameters. Whilst we found no correlation between the maximum variation and stellar photospheric and chromospheric proxies, we found frequency variations to have a greater amplitude for cooler and slower rotating stars, which is in opposition to p-mode frequency shift variation. Temporal changes to pseudo-mode frequencies may be attributable to variations in stellar magnetic activity, and therefore can contribute to our understanding of stellar activity cycles.

Millson, L. J. (ORCID:0009000342542676)↗

DOE OSTI2024

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a–RNA–DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Cosmic axions revealed via amplified modulation of the ellipticity of a laser

We propose a new axion dark matter detection strategy that employs optical readout of laser beam ellipticity modulations caused by axion-induced electric fields in a microwave cavity, using electro-optic (EO) crystals, enhanced by externally injected radio-frequency (rf) power. Building upon the variance-based probing method [Phys. Rev. D 107, 103005 (2023).], we extend this concept to the optical domain: A weak probe laser interacts with an EO crystal coupled to the resonant microwave cavity field at cryogenic temperatures, and the axion-induced electric field is revealed through induced ellipticity. The injected rf signal coherently interferes with that of the axion field, amplifying the optical response and significantly improving sensitivity. While our EO-based method employs a Fabry-Pérot resonator, we do not require Michelson interferometers. Our method, hence, enables compact, high-frequency axion searches, across the 0.5–50 GHz range. Operating at cryogenic temperatures not only suppresses thermal backgrounds, but, critically, allows the probing method to mitigate the quantum noise. This approach offers a scalable path forward for axion detection over the ∼(few−200) μ⁢eV mass range—covering the preferred parameter space for the postinflationary Peccei-Quinn axion dark matter—using compact, tunable systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Josephson dynamics in two-dimensional ring-shaped condensates

We investigate Josephson transport in a fully closed, two-dimensional superfluid circuit formed by a ring-shaped 87 Rb Bose-Einstein condensate that contains two optical barriers acting as movable weak links. Translating these barriers at controlled speeds imposes a steady bias current, enabling direct mapping of the current-chemical-potential (𝐼−Δ⁢𝜇) characteristics. For narrow junctions (𝑤 ≈ 1µ⁢m), the circuit exhibits a pronounced dc branch that terminates at a critical current 𝐼 𝑐 = 9⁢(1) × 10 3 s −1 ; above this threshold, the system switches to an ac, resistive regime. Classical-field simulations that include the moving barriers quantitatively reproduce both the nonlinear 𝐼−Δ⁢𝜇 curve and the measured 𝐼 𝑐 , validating the underlying microscopic picture. Analysis of the ensuing phase dynamics shows that dissipation is mediated by the nucleation and traversal of vortex-antivortex pairs through the junctions, while the bulk condensate remains globally phase locked—direct evidence of the ring's topological constraint enforcing quantized circulation. These results establish a cold-atom analog of a superconducting quantum interference device in which Josephson dynamics can be resolved at the single-vortex level, providing a versatile platform for atomtronic circuit elements, nonreciprocal Josephson devices, and on-chip Sagnac interferometers for multiaxis rotation sensing.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Transverse spin effects and light-quark dipole moments at lepton colliders

We propose to probe light-quark dipole interactions at lepton colliders using the azimuthal asymmetry of a collinear dihadron pair (ℎ 1 ⁡ℎ 2 ) produced in association with another hadron ℎ′. This asymmetry, arising from quantum interference in the quark spin space, is exclusively sensitive to dipole interactions at the leading power of the new physics scale and simultaneously probes both the real and imaginary components of the dipole couplings. By combining all possible channels of ℎ′, this method allows for disentangling the up and down quark dipole moments and has the potential to significantly strengthen current constraints by one to two orders of magnitude.

Wen, Xin-Kai [Peking University, Beijing (China); ↗

DOE OSTI2026

Effects of screening and pressure ionization on the electron broadening of spectral lines in dense plasmas

Collisions between electrons and radiating atoms broaden spectral absorption and emission lines in dense plasmas. High densities also introduce screening and pressure ionization effects that distort the wave functions of both bound and free electrons. In order to study how dense plasma effects influence the electron broadening of spectral lines, this paper incorporates electron wave functions from an average-atom (AA) model to calculate the linewidth of the B III 2⁢𝑝−2⁢𝑠 transition at 𝑇 = 10 eV for mass densities ranging from 𝜌 = 10 −4 to 0.4⁢ g⁡/cc. The calculation method uses the impact approximation, allowing the linewidth to be written in terms of electron-collision cross sections and an interference term. Compared to an otherwise identical calculation that uses Coulomb free wave functions, the AA method is found to modify both the cross sections and the resulting linewidth at sufficiently high density by introducing screening and pressure-ionized bound states. Screening lowers the cross sections at low energies and near electron excitation thresholds, while pressure-ionized bound states introduce resonances into the continuum. Thus, as the density increases, the relative linewidth between the AA and Coulomb calculations follows a general decrease because of screening, with sharp increases at various intervals due to pressure ionization. Finally, the AA results are also compared with a common approach to introduce screening through the interaction potential and reduced models that use the Bethe formula for the inelastic electron-collision cross sections.

electronic excitation & ionization↗

DOE OSTI2025

Continuum-electron interferometry for enhancement of photoelectron circular dichroism and measurement of bound, free, and mixed contributions to chiral response

We develop photoelectron interferometry based on laser-assisted extreme ultraviolet ionization for flexible and robust control of photoelectron circular dichroism in randomly oriented chiral molecules. A comb of XUV photons ionizes a sample of chiral molecules in the presence of a time-delayed infrared or visible laser pulse promoting interferences between components of the XUV-ionized photoelectron wave packet. In striking contrast to multicolor phase control schemes relying on pulse shaping techniques, the magnitude of the resulting chiral signal is here controlled by the time delay between the XUV and laser pulses. Furthermore, we show that the relative polarization configurations of the XUV and IR fields allow for disentangling the contributions of bound and continuum states to the chiral response. Our proposal provides a simple, robust, and versatile tool for the control of photoelectron circular dichroism and experimentally feasible protocol for probing the individual contributions of bound and continuum states to the photoelectron circular dichroism in a time-resolved manner.

atomic and molecular processes in external fields↗

DOE OSTI2026

Flux trapping in NbTiN strips

We use scanning superconducting quantum interference device (SQUID) microscopy to image vortices in superconducting structures fabricated from NbTiN thin films. We repeatedly cool superconducting strips with different width in an applied magnetic field and image the individual vortices. From these images we determine the threshold field at which the first vortex enters a strip and the number and configuration of vortices beyond this threshold field. We model the behavior of the vortices with and without considering the effect of pinning using numerical methods to minimize the Gibbs free energy of vortices in the strips. Our measurements provide a first benchmark to investigate the flux trapping properties of NbTiN thin films directly relevant to NbTiN-based superconducting digital circuits.

Bai, Ruiheng [Cornell University] (ORCID:000000025↗

DOE OSTI2025

Color glass condensate meets high twist expansion

We establish the correspondence between two well-known frameworks for quantum chromodynamics (QCD) multiple scattering in nuclear media: the color glass condensate (CGC) and the high-twist (HT) expansion formalism. We argue that a consistent matching between both frameworks, in their common domain of validity, is achieved by incorporating the subeikonal longitudinal momentum phase in the CGC formalism, which mediates the transition between coherent and incoherent scattering. We perform a detailed calculation and analysis of direct photon production in proton-nucleus scattering as a concrete example to establish the matching between HT and CGC up to twist-4, including initial- and final-state interactions, as well as their interferences. The techniques developed in this work can be adapted to other processes in electron-nucleus and proton-nucleus collisions, and they provide a potential avenue for a unified picture of dilute-dense dynamics in nuclear media.

quantum chromodynamics↗

DOE OSTI2025

Attosecond X-Ray Core-Level Chronoscopy of Aromatic Molecules

Attosecond photoemission or photoionization delays are a unique probe of the structure and the electronic dynamics of matter. However, the spectral congestion of valence photoelectron spectra sets fundamental limits to the complexity of systems that can be studied, and the delocalization of valence electron wave functions blurs the spatial origin of the photoelectron wave packet. Using attosecond x-ray pulses from LCLS, we demonstrate the key advantages of measuring core-level delays: The photoelectron spectra remain atomlike, the measurements become element specific, and the observed scattering dynamics originate from a pointlike source when multicenter interference effects are negligible. We exploit these unique features to reveal the effects of changing functional groups (C-H vs N) and symmetry on attosecond scattering dynamics by measuring and calculating the photoionization delays between N−1⁢𝑠 and C−1⁢𝑠 core shells of a series of aromatic azabenzene molecules. Remarkably, the delays increase with the number of nitrogen atoms in the molecule and reveal multiple resonances. We identify two previously unknown mechanisms regulating the associated attosecond dynamics, namely the enhanced confinement of the trapped wave function with the replacement of C-H groups by N atoms and the decrease of the coupling strength among the photoemitted partial waves with increasing symmetry. This study demonstrates the unique opportunities opened by measurements of core-level photoionization delays for unraveling attosecond electron dynamics in complex matter.

Ji, Jia-Bao [Eidgenoessische Technische Hochschule↗

DOE OSTI2025

Reexamining circular dichroism in photoemission from a topological insulator

The orbital angular momentum (OAM) of electron states is an essential ingredient for topological and quantum geometric quantities in solids. For example, Dirac surface states with helical spin- and orbital-angular momenta are a hallmark of a 3D topological insulator. Angle-resolved photoemission spectroscopy (ARPES) with variable circular light polarization, known as circular dichroism (CD), has been assumed to be a direct probe of OAM and, by proxy, of the Berry curvature of electronic bands in energy- and momentum-space. Indeed, topological surface states have been shown to exhibit angle-dependent CD (CDAD), and more broadly, CD is often interpreted as evidence of spin-orbit coupling. Meanwhile, it is well-established that CD originates from the photoemission matrix elements, which can have extrinsic contributions related to the experimental geometry and the inherently broken inversion symmetry at the sample surface. Therefore, it is important to broadly examine CD-ARPES to determine the scenarios in which it provides a robust probe of intrinsic material physics. We performed CD-ARPES on the canonical topological insulator Bi 2 ⁢Se 3 over a wide range of incident photon energies. Not only do we observe angle-dependent CD in the surface states, as expected, but we also find CD of a similar magnitude in virtually all bulk bands. Since OAM is forbidden by inversion symmetry in the bulk, we conclude this originates from symmetry-breaking in the photoemission process. Comparison with theoretical calculations supports this view and suggests that “hidden” OAM—localized to atomic sites within each unit cell—contributes significantly. Additional effects, including inter-atomic interference and final-state resonances, are responsible for the rapid variation of the CDAD signal with photon energy.

Sidilkover, Ittai [Tel Aviv University, Tel Aviv (↗

DOE OSTI2025

Evolution of charge correlations in the hole-doped kagome superconductor CsV 3−𝑥⁢ Ti 𝑥 ⁢Sb 5

The interplay between superconductivity and charge correlations in the kagome metal CsV 3⁢ Sb 5 can be tuned by external perturbations such as doping or pressure. Here we present a study of charge correlations and superconductivity upon hole doping via Ti substitution on the V kagome sites in CsV 3−𝑥 ⁢Ti 𝑥 ⁢Sb 5 via synchrotron x-ray diffraction and scanning superconducting quantum interference device measurements. While the superconducting phase, as viewed via the vortex structure, remains conventional and unchanged across the phase diagram, the nature of charge correlations evolves as a function of hole doping from the first superconducting dome into the second superconducting dome. For Ti doping in the first superconducting dome, competing 2×2×2 and 2×2×4 supercells form within the charge density wave state and are suppressed rapidly with carrier substitution. In the second superconducting dome, no charge correlations are detected. Here, comparing these results to those observed for CsV 3 ⁢Sb 5−𝑥 ⁢Sn 𝑥 suggests important differences between hole doping via chemical substitution on the V and Sb sites, particularly in the disorder potential associated with each dopant.

Charge density waves↗

DOE OSTI2025

Portal matter models of kinetic mixing with two light dark gauge bosons

The kinetic mixing (KM) portal mandates the existence of at least one new gauge boson, the dark photon (DP) based on the group 𝑈⁢(1) 𝐷 , which mixes with the Standard Model (SM) photon via loops of other new heavy particles carrying both SM and dark charges called portal matter (PM). Arguments exist based on the renormalization group equations running of the 𝑈⁢(1) 𝐷 gauge coupling suggesting that at higher scales 𝑈⁢(1) 𝐷 becomes part of a more complex non-Abelian group, a simple example being just the SM-like 𝐺 𝐷 =𝑆⁢𝑈⁢(2)𝐼 ×𝑈⁢(1) 𝑌 𝐼 . In our past analyses, it was always assumed that 𝐺 𝐷 broke in a SM-like manner directly to the DP’s 𝑈⁢(1) 𝐷 which then subsequently broke at low energies ≲1 GeV. However, this need not be the case, and 𝐺 𝐷 can instead break to 𝑈⁢(1) 𝑇 3⁢𝐼 ×𝑈⁢(1) 𝑌 𝐼 , with 𝑇 3⁢𝐼 being the diagonal generator of 𝑆⁢𝑈⁢(2) 𝐼 , now producing two light gauge bosons which obtain masses at the ≲1 GeV scale. In this paper, we explore the phenomenology of a very simple realization of this kind of alternative setup employing non-Abelian KM and having a minimal, leptonlike PM sector, demonstrating its distinctive nature in comparison to the previously examined symmetry breaking path. The effects of interference between these gauge bosons on thermal dark matter annihilation, the production of new heavy gauge, and Higgs and PM states at colliders, as well as the corresponding signatures for the light dark gauge bosons are examined. Collider signatures of this setup are found to be particularly challenging.

extensions of Higgs sector↗