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DOE OSTI2024

Searching for beyond the Standard Model physics using the improved description of 100 Mo $2\nu \beta \beta$ decay spectral shape with CUPID-Mo

The current experiments searching for neutrinoless double-β ($0\nu \beta \beta$) decay also collect large statistics of Standard Model allowed two-neutrino double-β ($2\nu \beta \beta$ ) decay events. These can be used to search for Beyond Standard Model (BSM) physics via $2\nu \beta \beta$ decay spectral distortions. 100 Mo has a natural advantage due to its relatively short half-life, allowing higher $2\nu \beta \beta$ decay statistics at equal exposures compared to the other isotopes. We demonstrate the potential of the dual read-out bolometric technique exploiting a 100 Mo exposure of 1.47 kg years, acquired in the CUPID-Mo experiment at the Modane underground laboratory (France). We set limits on $0\nu \beta \beta$ decays with the emission of one or more Majorons, on $2\nu \beta \beta$ decay with Lorentz violation, and $2\nu \beta \beta$ decay with a sterile neutrino emission. In this analysis, we investigate the systematic uncertainty induced by modeling the $2\nu \beta \beta$ decay spectral shape parameterized through an improved model, an effect never considered before. This work motivates searches for BSM processes in the upcoming CUPID experiment, which will collect the largest amount of $2\nu \beta \beta$ decay events among the next-generation experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Cold freeze out of superheavy dark matter and Hubble tension

We present a unified framework, the "X miracle", in which dark matter consists of superheavy, nonthermal X particles whose relic abundance is determined not by the conventional weak-scale, semi-relativistic ("hot") freeze-out of WIMPs, but by annihilation or decay occurring within the smallest and earliest gravitationally bound objects. Unlike thermal WIMPs, which decouple at velocities of order 0.3c with relic abundance ρ∞ set by weak-scale interactions, X particles are produced nonthermally with an initial overabun dance ρ ini >> ρ ∞ . They become nonrelativistic extremely early, redshift to ultra-cold velocities, allowing collapse into compact bound structures characterized by a novel quantum gravitational scale, r X = 4$\hbar$ 2 $/Gm^3_X$ = 10 −13 m $\hbar$$/m_Xc$, much larger than the Compton wavelength. The framework predicts a particle mass of 10 12 GeV and an enhanced cross section of 10 −21 m 3 /s. Overlapping particle wavefunctions in these compact structures drive annihilation or decay into additional radiation, leading to a "cold" freeze-out that converts most of ρ ini into radiation while leaving a relic density ρ ∞ . Solutions to the Boltzmann equation indicate that an extreme ("big") depletion, with only one particle in a billion surviving, yields an additional radiation contribution $ΔN_{eff}$ ≈ 0.4, which could help alleviate the Hubble tension. For particles of 10 12 GeV, the scenario predicts a dark coupling constant α X = 0.09 that is responsible for an instanton-induced decay process, consistent with current UHECR bounds. Early collapse at 10 −6 s may release binding energy as high-frequency (100kHz) gravitational waves or ultralight GUT-scale axions (10 −9 eV). Superheavy sterile neutrinos provide a natural particle realization, linking dark matter to neutrino mass and baryogenesis. If gravitationally produced, this framework favors high-scale inflation and effi cient reheating. The "X miracle" thus demonstrates that dark matter need not be weak-scale: gravitational dynamics can control freeze-out and evolution, producing multi-messenger observational signatures in UHECRs, axions, gravitational waves, and small-scale structures.

Xu, Zhijie Jay [Pacific Northwest National Laborat↗

DOE OSTI2022

Probing neutrino mass models through resonances at neutrino telescopes

We study the detection prospects of relatively light charged scalars in radiative Majorana neutrino mass models, such as the Zee model and its variants using scalar leptoquarks, at current and future neutrino telescopes. In particular, we show that these scalar mediators can give rise to Glashow-like resonance features in the ultrahigh energy (UHE) neutrino event spectrum at the IceCube neutrino observatory and its high-energy upgrade IceCube-Gen2. The same scalars can also give rise to observable nonstandard neutrino interactions (NSIs), and we show that the UHE neutrinos provide a complementary probe of NSI. We also discuss an interesting possibility of producing such resonances by incoming sterile neutrino components in the case where neutrinos are pseudo-Dirac particles.

Physics↗

DOE OSTI2022

Assessment of Spoilage Microbiota of Rainbow Trout (Oncorhynchus mykiss) during Storage by 16S rDNA Sequencing

Due to the high contents of protein and fat in rainbow trout, it is highly susceptible to spoilage, which limits the storage and transportation processes. Exploring the spoilage microbial community during rainbow trout storage is essential to develop an effective preservation method. Here, the changes in the total bacterial colony and total volatile base nitrogen (TVB-N) during the storage of rainbow trout were investigated. Storage at 0 °C can effectively slow down the spoilage process with bacterial counts and TVB-N contents decreased from 8.7 log CFU/g and 18.7 mg/100 g obtained at 4 °C to 5.6 log CFU/g and 14.5 mg/100 g, respectively. 16S rDNA high-throughput sequencing results showed that the diversity of microbial genera decreased during storage. Acinetobacter, Pseudomonas, and Shewanells gradually became the dominant spoilage genera with contents of 59.9%, 18.6%, and 1.7%, respectively, in the late stage of storage. The spoilage abilities of bacteria belonging to the Pseudomonas and Shewanells genera were analyzed. Shewanella sp. S5-52 showed the highest level of TVB-N content (100.6 mg/100 g) in sterile fish juice, indicating that it had a strong spoilage ability. This study confirmed the dominant spoilage bacterial genera and evaluated the spoilage abilities of isolated strains during the storage of rainbow trout, which laid the foundation for further investigation of the spoilage mechanism of rainbow trout and other aquatic products.

Du, Guangqing↗

DOE OSTI2021

Improved node culture methods for rapid vegetative propagation of switchgrass (Panicum virgatum L.)

Abstract Background Switchgrass ( Panicum virgatum L.) is an important bioenergy and forage crop. The outcrossing nature of switchgrass makes it infeasible to maintain a genotype through sexual propagation. Current asexual propagation protocols in switchgrass have various limitations. An easy and highly-efficient vegetative propagation method is needed to propagate large natural collections of switchgrass genotypes for genome-wide association studies (GWAS). Results Micropropagation by node culture was found to be a rapid method for vegetative propagation of switchgrass. Bacterial and fungal contamination during node culture is a major cause for cultural failure. Adding the biocide, Plant Preservative Mixture (PPM, 0.2%), and the fungicide, Benomyl (5 mg/l), in the incubation solution after surface sterilization and in the culture medium significantly decreased bacterial and fungal contamination. In addition, “shoot trimming” before subculture had a positive effect on shoot multiplication for most genotypes tested. Using the optimized node culture procedure, we successfully propagated 330 genotypes from a switchgrass GWAS panel in three separate experiments. Large variations in shoot induction efficiency and shoot growth were observed among genotypes. Separately, we developed an in planta node culture method by stimulating the growth of aerial axillary buds into shoots directly on the parent plants, through which rooted plants can be generated within 6 weeks. By circumventing the tissue culture step and avoiding application of exterior hormones, the in planta node culture method is labor- and cost-efficient, easy to master, and has a high success rate. Plants generated by the in planta node culture method are similar to seedlings and can be used directly for various experiments. Conclusions In this study, we optimized a switchgrass node culture protocol by minimizing bacterial and fungal contamination and increasing shoot multiplication. With this improved protocol, we successfully propagated three quarters of the genotypes in a diverse switchgrass GWAS panel. Furthermore, we established a novel and high-throughput in planta node culture method. Together, these methods provide better options for researchers to accelerate vegetative propagation of switchgrass.

Wang, Yongqin↗

DOE OSTI2022

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10 5 cfu/m 2 . Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data for Physiological Controls on Carbon Fluxes and Biomass Production in Miscanthus: Insights From a Process- Based Agroecosystem Model

Biomass crops serve as essential feedstocks for renewable energy and bioproducts and play a critical role in achieving lower emissions in the transportation sector. However, dedicated perennial biomass crops such as Miscanthus × giganteus (Miscanthus) remain underrepresented in process- based agroecosystem models, limiting robust evaluation of their economic and environmental performance. In this study, we developed a data- constrained representation of the sterile triploid Miscanthus (IL clone) within the process- based model ecosys, integrating global sensitivity analysis, ensemble simulation, and parameter calibration. Planting, harvesting, and fertilization practices consistent with field management were incorporated, and phenology was constrained using PhenoCam- derived Green Chromatic Coordinate (GCC) data. Using the Morris global sensitivity analysis method, we identified 11 key physiological parameters governing plant carbon, water, and nutrient relations, particularly processes associated with CO2 assimilation. We then conducted ensemble simulations by perturbing these parameters and calibrated the model against eddy covariance fluxes and field- measured biomass. Building on the calibrated operating state, parameter- response analyses show that different photosynthetic processes influence productivity in different ways. Protein allocation determines whether productivity increases toward a higher level, whereas electron transport capacity controls additional gains once protein allocation approaches saturation. These findings demonstrate that parameter importance depends on physiological context and on which photosynthetic processes remain limiting. Calibration and validation against observations show that ecosys can reliably reproduce carbon and water fluxes, as well as both above- and belowground biomass, with post- calibration GPP R2 improving from 0.67 to 0.95 during the calibration period and remaining high during validation (R2 = 0.95). These results provide a mechanistic foundation for regional simulations and sustainable bioenergy assessments.

Carbon↗

DOE OSTI2026

Data for Miscanthus giganteus Biolistic Transformation Using the Visible RUBY Red Marker Gene to Monitor Transformation Efficiency

Miscanthus × giganteus ( M × g ) is a high- yielding perennial C4 bioenergy crop, but genetic improvement by breeding is constrained by triploid sterility and clonal propagation. Improving genetic transformation methods for M × g would provide opportunities for advantageous trait introgression. Use of an easy to phenotype reporter gene is a promising strategy to improve transformation processes and efficiency. This study presents an efficient novel method for biolistic transformation of inflorescence- derived callus in M × g and demonstrates its efficacy using RUBY, a betalain-based noninvasive reporter that is visible throughout the transformation process. RUBY expression ( Zea mays codon optimized) was visible from callus stage through plantlet development into maturity. RUBY expressing independently transformed plants were confirmed by hygromycin phosphotransferase ELISA and by genomic PCR demonstrating that the RUBY phenotype is sufficient for screening transformants. The Zea mays codon optimized hygromycin selection marker was driven by previously established promoters for Miscanthus, ZmUBI and 2×35S, while the RUBY gene expression was controlled by a known Zea mays C4 promoter, Brachypodium UBI10, newly employed in Miscanthus. The construct containing the 2×35S promoter for hygromycin had a 15.1% transformation efficiency while the ZmUBI promoter had a 20.5% transformation efficiency. This study provides a novel, highly efficient protocol for successful biolistic transformation of M × g for stable expression. This study also demonstrates that RUBY expression can be used as a convenient and powerful monitor of transformation in ongoing and future work to engineer M × g into an improved bioproduct feedstock. **NOTE: in "TableS2_ProtocolComparison.csv", the data from row 665 to 971 should be removed.

Gene Editing↗

DOE OSTI2025

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Novak, Vlastimil↗

DOE OSTI2021

Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution

When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to cryptic evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F 1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F 1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a “faster male” model for Haldane’s rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a “large-X effect” for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to demasculinization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected to arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Optode performance data associated with: Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments

This data package is associated with the publication “Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments”, submitted to PlosONE (Kaufman et al. 2023; 10.1101/2023.03.28.534656).We carried out many testing and calibration experiments on a system of small oxygen consumption batch reactors designed for use with water and sediment samples for environmental questions. The oxygen sensing system is based very directly on the work of Larsen, et al. [2011], and similar oxygen sensing technology is widely used in the literature. Our primary focus was on practical considerations, such as temperature effects, lighting angle effects, sterilization, and other similar situations that a user may find useful. Most of the tests required comparing “base” calibration curves to “treatment” calibration curves to determine the extent to which the treatment impacted the reported measurements. This data package contains the performance and calibration data collected for that purpose.This dataset is comprised of one data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; (4) diffusion test result files; (5) limit of detection test result files; (6) temperature impact files; (7) a main data file that contains test results for all other tests; and (8) an R script that uses Kolmogorov-Smirnov tests to determine whether treatment calibrations are significantly different from their respective base calibrations. All files are .csv, .txt, .Rmd, or .pdf.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Recent developments in filtration media and respirator technology in response to COVID-19

Abstract The COVID-19 pandemic triggered a surge in demand for N95 or equivalent respirators that the global supply chain was unable to satisfy. This shortage in critical equipment has inspired research that addresses the immediate problems and has accelerated the development of the next-generation filtration media and respirators. This article provides a brief review of the most recent work with regard to face respirators and filtration media. We discuss filtration efficiency of the widely utilized cloth masks. Next, the sterilization of and reuse of existing N95 respirators to extend the existing stockpile is discussed. To expand near-term supplies, optimization of current manufacturing methods, such as melt-blown processes and electrospinning, has been explored. Future manufacturing methods have been investigated to address long-term supply shortages. Novel materials with antiviral and sterilizable properties with the ability for multiple reuses have been developed and will contribute to the development of the next generation of longer lasting multi-use N95 respirators. Finally, additively manufactured respirators are reviewed, which enable a rapidly deployable source of reusable respirators that can use any filtration fabric. Graphic abstract

36 MATERIALS SCIENCE↗

DOE OSTI2021

nuSTORM Accelerator Challenges and Opportunities

The nuSTORM facility uses a stored muon beam to generate a neutrino source. Muons are captured and stored in a storage ring using stochastic injection. The facility will aim to measure neutrino-nucleus scattering cross-sections with uniquely well-characterized neutrino beams; to facilitate the search for sterile neutrino and other Beyond Standard Model processes with exquisite sensitivity, and to provide a muon source that makes an excellent technology test-bed required for the development of muon beams capable of serving as a multi-TeV collider. In this paper, we describe the latest status of the development of nuSTORM, the R&D needs, and the potential for nuSTORM as a Muon Collider test facility.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Development of a compact electron cyclotron resonance accelerator for industrial and security applications

We describe the development of a novel accelerator, an electron Cyclotron Resonance Accelerator (eCRA) [1], to produce high power electron beams and X-ray beams for medical, research, sterilization, and national security applications. The several attractive features of eCRA include: a compact robust room-temperature single-cell RF cavity as the accelerating structure; continuous ampere-level high current output; and production of a self-rastering electron beam, thus eliminating the need for a separate beam scanner. Progress on the eCRA development, including numerical simulation, engineering design, and on-going experimental efforts will be reported here.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Compact, High-Power Superconducting Electron Linear Accelerators for MW Industrial Applications

Fermilab has developed a novel concept for an industrial electron linac using Nb₃Sn coating technology and conduction cooling. We will show the range of multi-cavity linac designs targeted toward various applications. We will also discuss technology development status with results on conduction cooling of SRF cavities based on cryocoolers, which removes the need for liquid Helium, thus making SRF technology accessible to industrial applications. These conduction-cooled linacs can generate electron beam energies up to 10 MeV in continuous-wave operation and can reach higher power (>=1 MW) by combing several modules. Compact and light enough to mount on mobile platforms, our machine is anticipated to enable new in-situ environmental remediation applications such as waste-water treatment for urban areas, X-ray medical device sterilization, and innovative pavement applications. We also show cost-economics and key R&D areas that much be addressed for a practical machine.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Lessons from commissioning and operations of the ICARUS cryogenic system at Fermilab

Results and lessons from three years of commissioning and operations of the cryogenic and purificationsystems of the ICARUS neutrino detector installed at the Fermilab are described. The detector uses liquid argon stored in two separate containers of about 275 m 3 each. The liquid argon must be kept in very stable thermal conditions, and the contamination of electronegative impurities must be consistently kept at small fractions of parts per billion. Since its fill in early 2020, the detector has been commissioned and then operated in neutrino beams at Fermilab for the search of sterile neutrinos and measurements of neutrino-argon cross sections. The results of operating the cryogenic and purification systems and lessons learned, including challenges in reaching the design electron lifetime in argon bath, operating and servicing liquid nitrogen and argon circulation pumps, argon condensers and purifiers, are described. Plans for future operations and list of recommendations are presented.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

Lessons from commissioning of the cryogenic system for the Short-Baseline Neutrino Detector at Fermilab

Results from commissioning and first year of operations of the cryogenic system of the Short-Baseline Neutrino Detector (SBND) and its membrane cryostat installed at the Fermi National Accelerator Laboratory are described. The SBND detector is installed in a 200 m$^3$ membrane cryostat filled with liquid argon, which serves both as target and as active media. For the correct operation of the detector, the liquid argon must be kept in very stable thermal conditions while the contamination of electronegative impurities must be consistently kept at the level of small fractions of parts per billion. The detector is operated in Booster Neutrino Beams (BNB) at Fermilab for the search of sterile neutrinos and measurements of neutrino-argon cross sections. The cryostat and the cryogenic systems also serve as prototypes for the much larger equipment to be used for the LBNF/DUNE experiment. Since its installation in 2018-2023 and cooldown in spring of 2024, the cryostat and the cryogenic system have been commissioned to support the detector operations. The lessons learned through installation, testing, commissioning, cooldown, and initial operations are described.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Far-forward neutrinos at the Large Hadron Collider

We present a new calculation of the energy distribution of high-energy neutrinos from the decay of charm and bottom hadrons produced at the Large Hadron Collider (LHC). In the kinematical region of very forward rapidities, heavy-flavor production and decay is a source of tau neutrinos that leads to thousands of charged-current tau neutrino events in a 1 m long, 1 m radius lead neutrino detector at a distance of 480 m from the interaction region. In our computation, next-to-leading order QCD radiative corrections are accounted for in the production cross-sections. Non-perturbative intrinsic-k T effects are approximated by a simple phenomenological model introducing a Gaussian k T -smearing of the parton distribution functions, which might also mimic perturbative effects due to multiple initial-state soft-gluon emissions. The transition from partonic to hadronic states is described by phenomenological fragmentation functions. To study the effect of various input parameters, theoretical predictions for $D^{±}_s$ production are compared with LHCb data on double-differential cross-sections in transverse momentum and rapidity. The uncertainties related to the choice of the input parameter values, ultimately affecting the predictions of the tau neutrino event distributions, are discussed. We consider a 3+1 neutrino mixing scenario to illustrate the potential for a neutrino experiment to constrain the 3+1 parameter space using tau neutrinos and antineutrinos. We find large theoretical uncertainties in the predictions of the neutrino fluxes in the far-forward region. Untangling the effects of tau neutrino oscillations into sterile neutrinos and distinguishing a 3+1 scenario from the standard scenario with three active neutrino flavours, will be challenging due to the large theoretical uncertainties from QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗