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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2024

Cover crops and poultry litter impact on soil structural stability in dryland soybean production in southeastern United States

Abstract This study explored the efficacy of soil aggregate indices in quantifying soil structural development, utilizing 5‐year field experiment data from the Southeastern United States. The experiment utilized a split‐plot design with cover crops (native vegetation as control, cereal rye (Secale cerealeL.), winter wheat (Triticum aestivum), hairy vetch (Vicia villosa), and mustard (Brassica rapa) plus cereal rye as the main factor and fertilizer source (no fertilizer as control, inorganic fertilizer with phosphorus, potassium, and elemental sulfur, and poultry litter) as the secondary factor. Aggregate size fractions were determined using the wet‐sieving method, and aggregate stability index (ASI), mean weight diameter (MWD), geometric mean diameter (GMD), and fractal dimension (FD) were calculated to assess soil structural stability. Main effects results indicated that cereal rye (55.11%) and poultry litter (50.97%) exhibited the highest ASI values. The highest MWD, GMD, and FD were observed under mustard plus cereal rye (1.187 mm), cereal rye (0.462 mm), and hairy vetch (2.573), respectively. Principal component analysis revealed that cover crops significantly improved soil aggregate structure and stability, overcoming limitations of sole fertilization practices. Regression analysis suggested that ASI, MWD, and GWD positively correlated with soil organic carbon, whereas FD negatively correlated with MWD, GMD, and ASI. Principal component analysis exhibited that FD decreased with increasing soil organic carbon, ASI, MWD, and GMD, demonstrating that lower FD values indicate enhanced soil aggregation and structure. Assessed indices, FD included, effectively gauged soil structural stability. These metrics should be prioritized in managerial decisions to support soil productivity and health in agricultural systems.

Agriculture↗
DOE OSTI2021

Investigation of pre-cooling as a recommended measure to improve residential buildings’ thermal resilience during heat waves

More intense heat waves are expected to occur more frequently in the twenty-first century. During severe heat waves, cooling capacity shortfall and overheating are likely to occur in residential buildings, and this will adversely affect occupant's thermal comfort and productivity. We propose a strategy of pre-cooling the house during off-peak hours to mitigate overheating during heat waves. Additionally, simulation results of a prototype single-family house show that adopting the rule-based control (RBC) of pre-cooling thermostat setpoint schedule is effective in reducing thermal discomfort, and that the efficacy of pre-cooling depends upon several building characteristics. An optimized control (OC) of the thermostat setpoint schedule was developed based on the simulation of a prototype building. A simplified yet improved RBC (IRBC) pre-cooling schedule was then extracted from the OC schedule for practical implementation at a larger scale. The effects of the RBC schedule and IRBC schedule were evaluated in the King District of Fresno, which contains 814 residential buildings. Results show that both thermostat setpoint schedules can reduce overheating effectively and that IRBC is slightly better than RBC for most buildings. The findings support the California government's recommendation on pre-cooling to mitigate overheating, which can be further improved with an optimized thermostat setpoint schedule broadcast to residents through early alert messages before a heat wave.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Enabling BWR fuel rod analysis in the BISON fuel performance code

Nuclear fuel vendors around the world are pursuing approaches to sustain the existing nuclear reactor fleet consisting primarily of pressurized-water reactors (PWRs) and boiling-water reactors (BWRs). To support the industry's efforts, advanced modeling and simulation tools need to be capable of analyzing both legacy reactor concepts. BWR fuel rods are significantly different than those used in PWRs, which can affect fuel performance analysis. BWR fuel rods include: (1) an extensive use of gadolinia dopant as a burnable absorber, (2) an axial variation in fuel enrichment and gadolinia content, (3) the inclusion of a liner on the inner cladding surface to mitigate the impact of pellet-clad mechanical interaction (which impacts hydrogen and hydride distribution), (4) a lower initial fill gas pressure, (5) bottom-entry control rods, and (6) a lower coolant pressure that results in the two-phase flow boiling phenomenon. Although the primary focus of BISON has been in the area of PWR and advanced reactor fuel analyses, this paper presents the developments in BISON to support BWR fuel performance analysis. An overview of the models that account for the effects of gadolinia is highlighted. Internal mesh generation capabilities to include a liner is presented. Normal operating and transient (reactivity insertion accident) demonstration problems are presented to illustrate the impact of gadolinia, the hydrogen and hydride evolution due to the presence of the liner, and BISON's ability to simulate axially varying enrichments and dopant concentration. Bottom-entry control effects are captured by the axial power peaking factors present in the demonstration cases. Comparisons to integral experiments from the Halden IFA-681 experiments are discussed as initial validation. Reasonable comparisons are obtained for fuel centerline temperature and rod internal pressure as a function of time. In conclusion, simulations of additional experiments containing Gd 2 O 3 -bearing fuel are necessary to completely validate the code for BWR applications.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Biomass to bio-energy supply chain: Economic viability, case studies, challenges and policy implications in India

Biomass supply chain (BSC) management is an integral part of renewable energy projects, which include biomass-harvesting, collection, storage, processing and transportation to the bio-energy plants. The sustainability concept identifies economy, environment, and society as the three principal pillars of bioenergy. With an effective BSC implemented, all three dimensions of sustainability can be attained. Although, there’s been extensive research on the environmental sustainability of BSC, the economic aspects are under-represented in existing literature. So, an elaborate analysis on the economic viability of BSCs developed worldwide and those in India is critical, and needs to be studied. This review conducts a detailed accounting of the economic aspects of a BSC which includes the existing challenges in designing an environmental-cum-economically efficient BSC and strategies to address the issues. The Indian context has been studied on the BSC models, highlighting their shortcomings, while encapsulating the essential insights from global BSC models for a cost-effective BSC-to-bioenergy in India. Here, this review also emphasizes the policies supporting the BSC in India and forecasts the future biomass demand and supply. This review will provide stakeholders with critical insights on BSC and related challenges and assist them to investigate and devise strategies for successful implementation of BSCs in India.

Biomass↗
DOE OSTI2024

Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model

Although implicated as deleterious in many organisms, aneuploidy can underlie rapid phenotypic evolution. However, aneuploidy will be maintained only if the benefit outweighs the cost, which remains incompletely understood. To quantify this cost and the molecular determinants behind it, we generated a panel of chromosome duplications in Saccharomyces cerevisiae and applied comparative modeling and molecular validation to understand aneuploidy toxicity. We show that 74%–94% of the variance in aneuploid strains’ growth rates is explained by the cumulative cost of genes on each chromosome, measured for single-gene duplications using a genomic library, along with the deleterious contribution of small nucleolar RNAs (snoRNAs) and beneficial effects of tRNAs. Machine learning to identify properties of detrimental gene duplicates provided no support for the balance hypothesis of aneuploidy toxicity and instead identified gene length as the best predictor of toxicity. Our results present a generalized framework for the cost of aneuploidy with implications for disease biology and evolution.

genic load↗
DOE OSTI2021

Engineering Calcium-Bearing Mineral/Hydrogel Composites for Effective Phosphate Recovery

Effectively recovering phosphate from wastewater streams and reutilizing it as a nutrient will critically support sustainability. Here, to capture aqueous phosphate, we developed novel mineral-hydrogel composites composed of calcium alginate, calcium phosphate (CaP), and calcium silicate (CSH) (CaP + CSH/Ca-Alg). The CaP + CSH/Ca-Alg composites were synthesized by dripping a sodium alginate (Na-Alg) solution with ionic precursors into a calcium chloride bath. To change the mineral seed’s properties, we varied the calcium bath concentrations and the ionic precursor (sodium dibasic phosphate (NaH 2 PO 4 ) and/or sodium silicate (Na 2 SiO 3 )) amounts and their ratios. The added CSH in the mineral-hydrogel composites resulted in the release of calcium and silicate ions in phosphate-rich solutions, increasing the saturation ratio with respect to calcium phosphate within the mineral-hydrogel composites. The CSH addition to the mineral-hydrogel composites doubled the phosphate removal rate while requiring lesser initial amounts of Ca and P materials for synthesis. Furthermore, by incorporating both CSH and CaP mineral seeds in composites, we achieved a final concentration of 0.25 mg-P/L from an initial 6.20 mg-P/L. Moreover, the mineral-hydrogel composites can remove phosphate even under CaP undersaturated conditions. This suggests their potential to be a widely applicable and environmentally-sustainable treatment and recovery method for nutrient-rich wastewater.

42 ENGINEERING↗
DOE OSTI2022

Microscale Colocalization of Cascade Enzymes Yields Activity Enhancement

Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is often challenging. This is mainly due to difficulties in establishing proper size regimes and in the analytical quantification of colocalization effect with adequate experimental systems and simulations. In this study, by taking advantage of reversible DNA-directed colocalization of enzymes on microspheres, we established a cascade system that can be used to directly evaluate the colocalization effect with exactly the same experimental settings except for the state of enzyme dispersion. In the regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared with the freely diffusing cascade, as evidenced by a shortened lag phase in the time-course production. Reaction-diffusion modeling reveals that the enhancement can be ascribed to the initial accumulation of intermediate substrate around the colocalized enzymes and is found to be carrier-size-dependent. Further, this work demonstrates the dependence of the colocalization effect of enzyme cascades on an interplay of nano-and microscales, lending theoretical support to the rational design of highly efficient multienzyme catalysts.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

What is quantum biology?

Quantum biology is the field at the intersection of quantum-related physics and the biology of living systems. The goal of the field is to determine if quantum phenomena underpin biological function at the macroscale. Such results, supported by compelling experimental evidence, will be important because they will show how quantum effects can have functional relevance, even in very complex and nominally classical systems. Here, we attempt to define the scope of quantum biology with a forward-facing view to help focus the research agenda. To that end, we propose open questions fundamental to consolidating the field of quantum biology. These open questions highlight the importance of developing suitable probes at the quantum scale, the possibility that classical biological machinery might simply mimic quantum systems, and of elucidating the ways quantum function can be amplified to the macroscale.

coherence↗
DOE OSTI2023

The Second Radio Synchrotron Background Workshop: Conference Summary and Report

We summarize the second radio synchrotron background workshop, which took place on 2022 June 15–17 in Barolo, Italy. This meeting was convened because available measurements of the diffuse radio zero level continue to suggest that it is several times higher than can be attributed to known Galactic and extragalactic sources and processes, rendering it the least well-understood electromagnetic background at present and a major outstanding question in astrophysics. The workshop agreed on the next priorities for investigations of this phenomenon, which include searching for evidence of the radio Sunyaev–Zel’dovich effect, carrying out cross-correlation analyses of radio emission with other tracers, and supporting the completion of the 310 MHz absolutely calibrated sky map project.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Engineering an effective three-spin Hamiltonian in trapped-ion systems for applications in quantum simulation

Trapped-ion quantum simulators, in analog and digital modes, are considered a primary candidate to achieve quantum advantage in quantum simulation and quantum computation. The underlying controlled ion–laser interactions induce all-to-all two-spin interactions via the collective modes of motion through Cirac–Zoller or Mølmer–Sørensen schemes, leading to effective two-spin Hamiltonians, as well as two-qubit entangling gates. In this work, the Mølmer–Sørensen scheme is extended to induce three-spin interactions via tailored first- and second-order spin–motion couplings. The scheme enables engineering single-, two-, and three-spin interactions, and can be tuned via an enhanced protocol to simulate purely three-spin dynamics. Analytical results for the effective evolution are presented, along with detailed numerical simulations of the full dynamics to support the accuracy and feasibility of the proposed scheme for near-term applications. With a focus on quantum simulation, the advantage of a direct analog implementation of three-spin dynamics is demonstrated via the example of matter-gauge interactions in the U(1) lattice gauge theory within the quantum link model. The mapping of degrees of freedom and strategies for scaling the three-spin scheme to larger systems, are detailed, along with a discussion of the expected outcome of the simulation of the quantum link model given realistic fidelities in the upcoming experiments. The applications of the three-spin scheme go beyond the lattice gauge theory example studied here and include studies of static and dynamical phase diagrams of strongly interacting condensed-matter systems modeled by two- and three-spin Hamiltonians.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

A leaf-level spectral library to support high-throughput plant phenotyping: predictive accuracy and model transfer

Abstract Leaf-level hyperspectral reflectance has become an effective tool for high-throughput phenotyping of plant leaf traits due to its rapid, low-cost, multi-sensing, and non-destructive nature. However, collecting samples for model calibration can still be expensive, and models show poor transferability among different datasets. This study had three specific objectives: first, to assemble a large library of leaf hyperspectral data (n=2460) from maize and sorghum; second, to evaluate two machine-learning approaches to estimate nine leaf properties (chlorophyll, thickness, water content, nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur); and third, to investigate the usefulness of this spectral library for predicting external datasets (n=445) including soybean and camelina using extra-weighted spiking. Internal cross-validation showed satisfactory performance of the spectral library to estimate all nine traits (mean R2=0.688), with partial least-squares regression outperforming deep neural network models. Models calibrated solely using the spectral library showed degraded performance on external datasets (mean R2=0.159 for camelina, 0.337 for soybean). Models improved significantly when a small portion of external samples (n=20) was added to the library via extra-weighted spiking (mean R2=0.574 for camelina, 0.536 for soybean). The leaf-level spectral library greatly benefits plant physiological and biochemical phenotyping, whilst extra-weight spiking improves model transferability and extends its utility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Electronic structure of the kagome metal YbTi 3 Bi 4 studied using torque magnetometry

This study investigates the electronic structure of the kagome metal YbTi 3 ⁢Bi 4 using high-field torque magnetometry. The torque signal measured at a maximum field of 41.5 T reveals clear de Haas–van Alphen (dHvA) oscillations with a major frequency peak at F δ ~ 130 T. By rotating the sample at various tilt angles Θ, we observed that F δ exhibits a nearly 1/cos⁡Θ dependence, indicating the presence of a quasi-two-dimensional (2D) Fermi surface (FS) in YbTi 3 ⁢Bi 4 . This argument is further supported by the detection of a forward-leaning, sawtoothlike waveform in the dHvA effect, a hallmark of 2D FS characteristics. Notably, we identified two high-frequency peaks near F χ ~ 1900 T and F λ ~ 5600 T; however, these peaks quickly disappear at Θ greater than 21°. To better understand experimental observations, we computed the electronic band structure and FS using ab initio density-functional theory (DFT). The electronic bands reveal the presence of several Dirac points, flat bands, and van Hove singularities near the Fermi level. Five bands cross the Fermi level and contribute to the FS of this material. The FS comprises cylindrical sheets, with theoretical frequencies from the FS pockets aligning well with the experimental dHvA frequencies. Several FS parameters characterizing F δ were determined by analyzing the temperature and field dependence of the dHvA oscillations using the Lifshitz-Kosevich theory. Further, the detailed electronic properties presented in this work provide critical insights into the electronic structure of YbTi 3 ⁢Bi 4 and other titanium-based kagome compounds.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Dynamical model of φ meson photoproduction on the nucleon and 4 He

We investigate φ meson photoproduction on the nucleon and the 4 He targets within a dynamical model approach based on a Hamiltonian which describes the production mechanisms by the Pomeron-exchange, meson-exchanges, φ radiations, and nucleon resonance excitations mechanisms. The final φN interactions are included being described by the gluon-exchange, direct φN couplings, and the box-diagrams arising from the couplings with πN, ρN, KΛ, and KΣ channels. The parameters of the Hamiltonian are determined by the experimental data of γp → φp from the CLAS Collaboration. The resulting Hamiltonian is then used to predict the coherent φ-meson production on the 4 He targets by using the distorted-wave impulse approximation. For the proton target, the final φN rescattering effects, as required by the unitarity condition, are found to be very weak, which supports the earlier calculations in the literature. For the 4 He targets, the predicted differential cross sections are in good agreement with the data obtained by the LEPS Collaboration. Furthermore, the role of each mechanism in this reaction is discussed and predictions for a wide range of scattering angles are presented, which can be tested in future experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

The Potential of Low Molecular Weight Heparin to Mitigate Cytokine Storm in Severe COVID‐19 Patients: A Retrospective Cohort Study

On March 11, 2020, the World Health Organization declared its assessment of coronavirus disease 2019 (COVID‐19) as a global pandemic. However, specific anti‐severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) drugs are still under development, and patients are managed by multiple complementary treatments. We performed a retrospective analysis to compare and evaluate the effect of low molecular weight heparin (LMWH) treatment on disease progression. For this purpose, the clinical records and laboratory indicators were extracted from electronic medical records of 42 patients with COVID‐19 (21 of whom were treated with LMWH, and 21 without LMWH) hospitalized (Union Hospital of Huazhong University of Science and Technology) from February 1 to March 15, 2020. Changes in the percentage of lymphocytes before and after LMWH treatment were significantly different from those in the control group ( P = 0.011). Likewise, changes in the levels of D‐dimer and fibrinogen degradation products in the LMWH group before and after treatment were significantly different from those in the control group ( P = 0.035). Remarkably, IL‐6 levels were significantly reduced after LMWH treatment ( P = 0.006), indicating that, besides other beneficial properties, LMWH may exert an anti‐inflammatory effect and attenuate in part the “cytokine storm” induced by the virus. Our results support the use of LMWH as a potential therapeutic drug for the treatment of COVID‐19, paving the way for a subsequent well‐controlled clinical study.

Shi, Chen↗
DOE OSTI2021

Euclidean gravity and holography

We discuss a recent proposal that the Euclidean gravity approach to quantum gravity is correct if and only if the theory is holographic, providing several examples and general arguments to support the conjecture. This provides a natural mechanism for the low-energy gravitational effective field theory to access a host of deep ultraviolet properties, like the Bekenstein–Hawking entropy of black holes, the unitarity of black hole evaporation, and the lack of exact global symmetries.

Astronomy & Astrophysics↗