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DOE OSTI2025

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species

Abstract We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom experimental data and/or from publicly available datasets, and is species agnostic. A range of functions can be used to find topological distances between biological entities, determine relationships within sets of interest, search for topological context around sets of interest, and statistically evaluate the strength of relationships within and between sets. The command-line interface is designed for parallelization on high-performance cluster systems, which enables high-throughput analysis such as permutation testing. Several tools in the package have also been made available for use in reproducible workflows via the KBase web application.

Kainer, David (ORCID:0000000172714676)↗

DOE OSTI2025

LATTE: open-source, high-performance traveltime computation, tomography and source location in acoustic and elastic media

Traveltime-based tomography and source location are fundamental approaches for imaging subsurface structures and understanding the spatiotemporal distribution of seismicity from local to global scales. We present an open-source, high-performance framework integrating eikonal equation solvers and adjoint-state theory for traveltime computation, velocity tomography, source location and joint tomography-location in 2-D/3-D acoustic and elastic media. We introduce novel regularization schemes based on total generalized p-variation, structural similarity and multitask machine learning to enhance the fidelity and interpretability of inverted models and source locations. Key features of our implementation also include the ability to leverage both absolute-difference and double-difference traveltime misfits for high-fidelity velocity tomography and source parameter estimation; support for traveltime computation and inversion in diverse 2-D/3-D scenarios with arbitrary source and receiver distributions; and a perturbation-based optimal step-size estimation method to reduce computational costs. In addition, our implementation employs shared-memory and distributed-memory parallelization to provide an efficient solution for traveltime computation, tomography, and source location. In conclusion, we validate the efficacy and accuracy of our approach through multiple synthetic data examples.

58 GEOSCIENCES↗

DOE OSTI2025

MTUQ: a framework for estimating moment tensors, point forces, and their uncertainties

SUMMARY We introduce MTUQ, an open-source Python package for seismic source estimation and uncertainty quantification, emphasizing flexibility and operational scalability. MTUQ provides MPI-parallelized grid search and global optimization capabilities, compatibility with 1-D and 3-D Green’s function database formats, customizable data processing, C-accelerated waveform and first-motion polarity misfit functions, and utilities for plotting seismic waveforms and visualizing misfit and likelihood surfaces. Applicability to a range of full- and constrained-moment tensor, point force, and centroid inversion problems is possible via a documented application programming interface, accompanied by example scripts and integration tests. We demonstrate the software using three different types of seismic events: (1) a 2009 intraslab earthquake near Anchorage, Alaska; (2) an episode of the 2021 Barry Arm landslide in Alaska; and (3) the 2017 Democratic People’s Republic of Korea underground nuclear test. With these events, we illustrate the well-known complementary character of body waves, surface waves, and polarities for constraining source parameters. We also convey the distinct misfit patterns that arise from each individual data type, the importance of uncertainty quantification for detecting multimodal or otherwise poorly constrained solutions, and the software’s flexible, modular design.

58 GEOSCIENCES↗

DOE OSTI2024

The 4D Camera: An 87 kHz Direct Electron Detector for Scanning/Transmission Electron Microscopy

We describe the development, operation, and application of the 4D Camera—a 576 by 576 pixel active pixel sensor for scanning/transmission electron microscopy which operates at 87,000 Hz. The detector generates data at ~480 Gbit/s which is captured by dedicated receiver computers with a parallelized software infrastructure that has been implemented to process the resulting 10–700 Gigabyte-sized raw datasets. The back illuminated detector provides the ability to detect single electron events at accelerating voltages from 30 to 300 kV. Through electron counting, the resulting sparse data sets are reduced in size by 10--300× compared to the raw data, and open-source sparsity-based processing algorithms offer rapid data analysis. The high frame rate allows for large and complex scanning diffraction experiments to be accomplished with typical scanning transmission electron microscopy scanning parameters.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Revealing Phase Heterogeneity in Vertically Aligned Nanocomposites via Plan-View Electron Energy Loss Spectroscopy

Hydrogen utilization in clean energy technologies is challenged by limited storage and transport within materials, owing to the complex hydrogen kinetics at interfaces [1]. Understanding these interfacial mechanisms at the nanoscale is crucial for developing improved materials for hydrogen applications, particularly proton-conducting fuel cells (PCFCs). Vertically aligned nanocomposites (VANs) grown by pulsed laser deposition (PLD) offer a unique platform for investigating the interfacial effects on hydrogen transport due to their well-defined interfaces parallel to the direction of charge transport [2-4]. To investigate hydrogen transport, the two phases within the VANs were chosen as BaZr 0.9 Y 0.1 O 3-x (BZY), a known proton conductor, and Pr 0.1 Ce 0.9 O 2-x (PCO), a mixed ionic-electronic conductor [5]. This PCO-BZY VANs architecture allows the investigation of how the interface between a proton conductor and a mixed conductor influences hydrogen transport. However, because of the small size of hydrogen, it is difficult to discern the nature of its interactions with interfaces from bulk measurements at the macroscale, thus necessitating nanoscale measurements [6]. Electron energy loss spectroscopy (EELS) allows for nanometer-resolution probing of the local atomic structure and chemistry at the BZY/PCO interface. In this study, plan-view analysis of PCO-BZY VANs films was employed to characterize the structure and phase distribution of the VANs and investigate the interface between the nanostructures. The films were imaged using scanning electron microscopy (SEM) in the Hitachi S-4800 SEM, collecting secondary electron images using mixed upper and lower detectors. Then, plan-view transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) EELS were employed using a JEOL ARM300 microscope operated at 300kV with a Gatan K3 GIF Continuum detector to study the distribution of the BZY and PCO phases through the film. As a result, spectrum images were acquired at a dispersion of 0.18eV per channel and denoised afterward by principal component analysis (PCA) method.

Griffin, Elizabeth [Northwestern University, Evans↗

DOE OSTI2024

Uncovering the truth about M101, NGC 3938, and their significant others through radiative transfer

ABSTRACT Solving the inverse problem in spiral galaxies, that allows the derivation of the spatial distribution of dust, gas, and stars, together with their associated physical properties, directly from panchromatic imaging observations, is one of the main goals of this work. To this end, we used radiative transfer models to decode the spatial and spectral distributions of the nearby face-on galaxies M101 and NGC 3938. In both cases, we provide excellent fits to the surface-brightness distributions derived from GALEX, SDSS, 2MASS, Spitzer, and Herschel imaging observations. Together with previous results from M33, NGC 628, M51, and the Milky Way, we obtain a small statistical sample of modelled nearby galaxies that we analyse in this work. We find that in all cases Milky Way-type dust with Draine-like optical properties provide consistent and successful solutions. We do not find any ‘submm excess’, and no need for modified dust-grain properties. Intrinsic fundamental quantities like star-formation rates (SFR), specific SFR (sSFR), dust opacities, and attenuations are derived as a function of position in the galaxy and overall trends are discussed. In the SFR surface density versus stellar mass surface density space, we find a structurally resolved relation (SRR) for the morphological components of our galaxies, that is steeper than the main sequence (MS). Exception to this is for NGC 628, where the SRR is parallel to the MS.

Pricopi, D.↗

DOE OSTI2024

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries

Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Thermal and kinematic properties of ejecta in SN1987A revealed by XRISM

We present an analysis of high-resolution spectra from the shock-heated plasmas in SN 1987A, based on an observation using the Resolve instrument onboard the X-Ray Imaging and Spectroscopy Mission (XRISM). The 1.7–10 keV Resolve spectra are accurately represented by a single-component, plane-parallel shock plasma model, with a temperature of $2.84_{-0.08}^{+0.09}$ keV and an ionization parameter of $2.64_{-0.45}^{+0.58}$ × $10^{11}\,\,{\rm s\,\, cm}^{-3}$. The Resolve spectra are also well reproduced by the 3D magneto-hydrodynamic simulation presented by Orlando et al. (2020, A&A, 636, A22) suggesting substantial contribution from the ejecta. The metal abundances obtained with Resolve align with the Large Magellanic Cloud value, indicating that the X-rays in 2024 originate from “non-metal-rich” shock-heated ejecta and the reverse shock has not reached the inner metal-rich region of ejecta. Doppler widths of the atomic lines from Si, S, and Fe correspond to velocities of 1500–1700 km s$^{-1}$, where the thermal broadening effects in this non-metal-rich plasma are negligible. Therefore, the line broadening seen in Resolve spectra is determined by the large bulk motion of ejecta. For reference, we determined a $90\%$ upper limit on non-thermal emission from a pulsar wind nebula at $4.3 \times 10^{-13}$ erg cm$^{-2}$ s$^{-1}$ in the 2–10 keV range, aligning with NuSTAR findings by Greco et al. (2022, ApJ, 931, 132). Additionally, we searched for the $^{44}$Sc K line feature and found a $1\sigma$ upper limit of $1.0 \times 10^{-6}$ photons cm$^{-2}$ s$^{-1}$, which translates to an initial $^{44}$Ti mass of approximately $2 \times 10^{-4}\, M_{\odot }$, consistent with previous X-ray to soft gamma-ray observations (Boggs et al. 2015, Science, 348, 670; Grebenev et al. 2012, Nature, 490, 373; Leising 2006, ApJ, 651, 1019).

ISM: supernova remnants↗

DOE OSTI2025

Enhancing lipid production in plant cells through automated high-throughput genome engineering and phenotyping

Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. Furthermore, these innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Arabidopsis cytochrome b 5 proteins support fatty acid ω-3 but not ω-6 desaturation

Fatty acids are primary components of lipids, which serve as major energy sources in cells and play essential roles in membrane structure, signaling, and metabolic regulation (Shanklin and Cahoon 1998). The degree of fatty acid unsaturation critically influences lipid physicochemical properties, thereby affecting membrane fluidity and biological function (Nguyen et al. 2019). In Arabidopsis thaliana, fatty acid desaturation occurs via 2 parallel pathways: the “prokaryotic pathway” in plastids, involving glycosylglycerides, such as monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), and phospholipid phosphatidylglycerol (PG); and the “eukaryotic pathway” in the endoplasmic reticulum (ER), involving phosphatidylcholine (PC) (Lou et al. 2014) (Supplementary Figure S1). Seven fatty acid desaturases (FADs) in Arabidopsis differentially desaturate each glycerolipid class in the plastid and ER (Nguyen et al. 2019). FAD2, an ER-resident ω-6 fatty acid desaturase, catalyzes the conversion of oleic acid (18:1) to linoleic acid (18:2), which can be further desaturated to α-linolenic acid (18:3) by FAD3, an ER-resident ω-3 fatty acid desaturase. In plastids, FAD6 catalyzes the desaturation of 18:1/16:1 to produce 18:2/16:2, while FAD7 and FAD8 redundantly convert 18:2/16:2 to 18:3/16:3 (Li-Beisson et al. 2013; Nguyen et al. 2019). Additionally, fatty acids synthesized in the ER can also be reimported into plastids to their site of de novo synthesis (Xu et al. 2010). All FADs require reducing power, in the form of 2 electrons, for catalysis, but the sources of the electrons vary between their subcellular localizations. In the ER, FAD2 and FAD3 receive electrons from a cytochrome b 5 (CB5)-based electron transfer chain comprising cytochrome b 5 reductase (CBR) and CB5. In contrast, ferredoxin serves as the electron donor for plastid-localized FAD6, FAD7, and FAD8 (Ohlrogge and Browse 1995; Andreu et al. 2007). While the relative contributions of the 2 pathways to total cellular desaturation products vary across tissues and species, most polyunsaturated FA biosynthesis in seeds occurs via ER-resident FAD2 and FAD3 (Miquel and Browse 1992; Ohlrogge and Browse 1995).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

StarDICE III: characterization of the photometric instrument with a collimated beam projector

The measurement of Type Ia supernovae magnitudes provides cosmological distances, which constrain dark energy parameters. Current and upcoming large photometric surveys require improved photometric calibration precision to reduce systematic uncertainties in cosmological constraints. The StarDICE experiment aims to establish accurate broad-band flux references for these surveys, targeting sub-percent precision in magnitude measurements. Achieving this requires precise filter bandpass measurements for both StarDICE and survey instruments with sub-nanometre accuracy. To this end, we developed the Collimated Beam Projector (CBP), an optical device for calibrating the throughput of astronomical telescopes and their filters. The CBP uses a tunable laser source and a reversed telescope to emit a parallel monochromatic light beam, continuously monitored in flux and wavelength. The CBP output flux is measured with a large-area photodiode calibrated relative to a NIST photodiode. Using CBP measurements, we derive the StarDICE telescope throughput and filter transmissions, anchoring them to NIST’s absolute calibration. After analysing systematic uncertainties, we achieved sub-nanometre accuracy for filter central wavelengths, measured filter transmission with ~0.5 per cent precision per 1 nm bin, and detected out-of-band leakages at a relative level of 10 –4 ⁠. Furthermore, we synthesized equivalent transmission for full pupil illumination from four sampled positions in the StarDICE telescope mirror, with ~0.2 nm accuracy for central wavelengths and 7 mmag for broad-band fluxes. This demonstrates our ability to characterize telescope throughput down to the millimagnitude, paving the way for future developments, such as the Rubin-CBP for measuring the LSST at Vera Rubin Observatory, and a portable CBP version for in-situ transmission monitoring.

Calibration↗

DOE OSTI2024

Extending evolutionary forecasts across bacterial species

Improving evolutionary forecasting requires progressing from studying repeated evolution of a single genotype under identical conditions to formulating broad principles. These principles should enable predictions of how similar species will adapt to similar selective pressures. Evolve-and-resequence experiments with multiple species allow testing forecasts on different biological levels and elucidating the causes for failed predictions. Here, we show that forecasts for adaptation to static culture conditions can be extended to multiple species by testing previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species differ in their repertoire of biofilm regulatory genes and structural components. Consistent with predictions, both species repeatedly produced biofilm mutants with a wrinkly spreader phenotype. Predominantly, mutations occurred in the wsp operon, with less frequent promoter mutations near uncharacterized diguanylate cyclases. However, mutational patterns differed on the gene level, which was explained by a lack of conservation in relative fitness of mutants between more divergent species. The same mutation was the most frequent for both species suggesting that conserved mutation hotspots can increase parallel evolution. This study shows that evolutionary forecasts can be extended across species, but that differences in the genotype–phenotype–fitness map and mutational biases limit predictability on a detailed molecular level.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Structure of active methyl-CoM reductase, Earth’s main methane producer

Summary Our work reveals the structure of the active state of Methyl-Coenzyme M Reductase (MCR), the key and rate-limiting enzyme in biological methane formation. We find large differences between the active Ni(I) and inactive Ni(II) proteins and provide insight into how nature makes and breaks the C-H bond of methane. The Ni(II)-F430 center in inactive MCR contains four planar nitrogen ligands, a lower axial glutamine oxo, and an upper axial thiolate. The Ni(I)-enzyme replaces the axial ligands with a single water. The one-electron redox change results in movement of the Ni ion and upward swing of the β-lactam ring in the tetrapyrrole coupled to a domino-like protein quake through second sphere residues, inter-subunit interactions, a substrate tunnel, affecting even the dimensions of the unit cell. These structural changes lead Ni(I)-MCR to release a charge clamp that, in the Ni(II) state, locks down substrate Coenzyme B. Determining the Ni(I)-MCR structure required development of rigorous anaerobic crystallographic techniques. Validation of the MCR redox state was accomplished by in-line and parallel spectroscopic and unit cell analyses. This structure has large implications for developing technologies to limit methane emissions and efficiently produce biofuels. Methodology described here will enhance structural biology for other oxygen-sensitive enzymes.

09 BIOMASS FUELS↗

DOE OSTI2024

Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquaticWolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and foundWolffiacells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations thatWolffiahas made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizingWolffiaas a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes.Wolffiaprovides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Interface, bulk and surface structure of heteroepitaxial altermagnetic α-MnTe films grown on GaAs(111)

Epitaxial MnTe films have recently seen a surge in research into their altermagnetic semiconducting properties. However, those properties may be extremely sensitive to structural and chemical modifications. We report a detailed investigation of the synthesis of the altermagnet α-MnTe on GaAs(111), which reveals the bulk defect structure of this material, the mechanism by which it releases strain from the underlying substrate, and the impact of oxidation on its surface. X-ray diffraction measurements show that α-MnTe layers with thicknesses spanning 45 to 640 nm acquire lattice parameters different from bulk, mostly due to thermal strain caused by the substrate rather than strain from the lattice mismatch. Through high-resolution transmission electron microscopy (TEM) measurement, we then unveil a misfit dislocation array at the interface, revealing the mechanism by which lattice strain is relaxed. TEM also reveals a stacking fault in the bulk, occurring along a glide plane parallel to the interface. The combination of TEM with polarized neutron reflectometry measurements finally reveals the impact of oxidation on the chemistry of the surface of uncapped MnTe. Furthermore, or findings highlight the subtle role of epitaxy in altering the structure of α-MnTe, providing potential opportunities to tune the altermagnetic properties of this material.

Altermagnets↗

DOE OSTI2025

Weak bosons as partons below 10 TeV partonic center-of-momentum

We investigate the modeling of weak boson number densities for leptons and hadrons in practical calculations in the Standard Model. Working in the framework of the Effective $W$ Approximation (EWA) and in $R_\xi$ and axial gauges, we derive the unrenormalized, tree-level parton number density functions for weak bosons from massless leptons at next-to-leading power in the collinear expansion. Corrections exhibit a number of properties, including those conjectured but never universally derived. Parallels with heavy quark factorization are also found. We avoid pathologies through a novel set of kinematical consistency conditions. When satisfied, good agreement between the full and approximated matrix elements is achieved. Findings suggest that the EWA may be testable at the Large Hadron Collider with $450$ fb$^{-1}$ luminosity of same-sign $WW$ scattering data at $\sqrt{s}=13.6$ TeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Mode Multiplexing for Scalable Cavity-Enhanced Operations in Neutral-Atom Arrays

Neutral-atom arrays provide a versatile platform for quantum information processing. However, in large-scale arrays, efficient photon collection remains a bottleneck for key tasks such as fast, nondestructive qubit readout and remote entanglement distribution. We propose a cavity-based approach that enables fast, parallel operations over many atoms using multiple modes of a single optical cavity. By selectively shifting the relevant atomic transitions, each atom can be coupled to a distinct cavity mode, allowing independent simultaneous processing. We present practical system designs that support cavity-mode multiplexing with up to 50 modes, enabling rapid mid-circuit syndrome extraction and significantly enhancing entanglement distribution rates between remote atom arrays. This approach offers a scalable solution to core challenges in neutral-atom arrays, advancing the development of practical quantum technologies.

Aqua, Ziv [Massachusetts Institute of Technology (↗

DOE OSTI2025

Theory of tunneling between two-dimensional electron layers driven by spin pumping: Adiabatic regime and beyond

Tunneling spectroscopy between parallel two-dimensional (2D) electronic systems provides a powerful method to probe the underlying electronic properties by measuring tunneling conductance. Here, in this work, we present a theoretical framework for spin transport in 2D-to-2D tunneling systems, driven by spin pumping. This theory applies to a vertical heterostructure where two layers of metallic 2D electron systems are separated by an insulating barrier, with one layer exchange coupled to a magnetic layer driven at resonance. Utilizing a nonperturbative Floquet-Keldysh formalism, we derive general expressions for the tunneling spin and charge currents across a broad range of driving frequencies, extending beyond the traditional adiabatic pumping regime. At low frequencies, we obtain analytical results that recover the known behaviors in the adiabatic regime. However, at higher frequencies, our numerical findings reveal significant deviations in the dependence of spin and charge currents on both frequency and precession angle. This work offers fresh insights into the role of magnetization dynamics in tunneling transport, opening up new avenues for exploring nonadiabatic spin pumping phenomena.

Green's function methods↗