Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource
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U.S. industry is expected to deploy tristructural isotropic (TRISO) particle fuel technologies for commercial reactors within the next decade. In our previous work, we defined a preliminary transient design space for TRISO fuels, identified potential gaps in the available data, and began to develop multiphysics modeling tools that could be applied to design targeted Transient Reactor Test Facility (TREAT) experiments to fill these gaps. This work builds on that foundation by (1) updating BISON fuel performance and Griffin reactor physics models to reflect the current TREAT experiment tube and capsule designs,(2) coupling the codes to improve the accuracy and usability of the transient design analyses, and (3) demonstrating their use over an expanded design space that includes fuel burnup. The simulated mechanical responses of the TRISO particles were complex functions of fission product accumulation, fission gas release, and irradiation-induced dimensional change in the pyrolytic carbon layers. Predicted tangential stresses in particle silicon carbide layers were least compressive for preheated tests involving fresh fuels but remained compressive throughout the ranges of temperature, heat rate, and burnup considered in this work. Finally, comparisons between the potential TREAT transients and historical test reactor irradiations showed that the TREAT tests would produce significantly lower average energy deposition rates, yielding less severe transients with greater relevance to near-term commercial applications. Use of these predictive capabilities has the potential to increase the value of each test, improving the overall efficiency and cost effectiveness of transient testing for TRISO and other advanced fuels.
Immunoprecipitation is one of the most effective methods for enrichment of lysine-acetylated peptides for comprehensive acetylome analysis using mass spectrometry. Manual acetyl peptide enrichment method using non-conjugated antibodies and agarose beads has been developed and applied in various studies. However, it is time consuming, and can introduce contaminants and variability that leads to potential sample loss and decreased sensitivity and robustness of the analysis. Here we describe a fast, automated enrichment protocol that enables reproducible and comprehensive acetylome analysis using a magnetic bead-based immunoprecipitation reagent.
Device-to-device variability in experimental noise critically impacts reproducibility, especially in automated, high-throughput systems like additive manufacturing farms. While manageable in small labs, such variability can escalate into serious risks at larger scales, such as architectural 3D printing, where noise may cause structural or economic failures. This contribution presents a noise-aware decision-making algorithm that quantifies and models device-specific noise profiles to manage variability adaptively. It uses distributional analysis and pairwise divergence metrics with clustering to choose between single-device and robust multi-device Bayesian optimization strategies. Unlike conventional methods that assume homogeneous devices or enforce generic robustness, the proposed framework explicitly determines whether shared optimization across devices is appropriate based on the degree of inter-device noise heterogeneity. This enables improved performance, reproducibility, and efficiency. An experimental case study involving three nominally identical 3D printers (same brand, model, and close serial numbers) demonstrates reduced redundancy, lower resource usage, and improved reliability, along with improved convergence stability and solution quality through the selection of the appropriate optimization strategy based on the degree of inter-device noise heterogeneity. Overall, this framework establishes a general approach for precision- and resource-aware optimization in scalable, automated experimental platforms, demonstrated here on a representative multi-device 3D printing case study.
Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering, DNA synthesis, and genomic editing. However, to access the massive potential of microbial production, a vast parametric space remains to be investigated to optimize these biobased processes for a robust bioeconomy. Here, we review the current state of the art, some key challenges and possible solutions. We see a critical role of automation, high-throughput technologies, self-driving and cloud labs, and data management to enable Artificial Intelligence/Machine Learning and mechanistic models to overcome the design space challenges and accelerate the development of novel bio-based solutions. Accurate models will expedite the development and scale-up of engineered microbes for a range of final products from many starting materials.
Enzymes have shown promise in various industries due to their functional specificity, catalytic efficiency, and environmental sustainability. These biological catalysts can be a pivotal component of manufacturing pipelines like continuous flow chemistry. For this, there exists a need to robustly immobilize enzymes on solid supports and assess the effects of the solid supports on catalytic performance and stability. Here, we use an industrially relevant model enzyme, C. ensiformis (Jack bean) urease, to demonstrate immobilization and assess performance in the context of continuous flow manufacturing. Various immobilization strategies were screened focusing on immobilization efficiency, protocol simplicity, and urease biocatalyst kinetics. Based on this, CDI-agarose and NHS-agarose resins were identified as the best-performing immobilization strategies for urease. CDI-agarose-urease and NHS-agarose-urease were then scaled up and applied to a large-scale continuous flow reactor to evaluate product yields, operational stability, and long-term stability. These experiments identified differences in stability and performance depending on the immobilization method tested. This highlights the importance of screening immobilization methods and subsequent enzyme performance for each candidate biocatalyst used in manufacturing to promote optimal performance and stability. As such, this work provides a framework for evaluating enzyme biocatalyst immobilization approaches to improve performance and enable transition into industrial processes.
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In this work, we investigated how the sequencing of laboratory analytical methods used for chemical and morphological characterization influences analytical findings for particulate materials relevant to the nuclear fuel cycle, including UO2, U3O8, studtite (UO2O2·4H2O), and β-UO3, in the context of nuclear forensic analysis. Particles of each chemistry obtained from consistent production batches were exposed to Raman spectroscopy and scanning electron microscopy in varying orders to elucidate how the order in which the techniques are applied influences morphological and chemical observations as a function of particle size. The results indicate that particles from all four chemistries exposed to high-resolution electron imaging before Raman spectral analysis demonstrate optical vibrational spectral changes that reduce accurate interpretation of the underlying chemistry via Raman spectral analysis. We hypothesize that these changes are due to the thermal load of the electron beam imparted to the sample being unable to be dissipated by materials with poor thermal conduction properties. Results from this study will aid in determining best practices for forensic analysis procedures to reduce uncertainty in chemical determination of unknown particulate samples.
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The U.S. nuclear industry is expected to deploy tristructural isotropic (TRISO) particle fuel technologies for commercial reactors within the next decade. In previous work, we defined a preliminary transient design space for TRISO fuels, identified potential gaps in the available data, and began to develop multiphysics modeling tools that could be applied to design targeted Transient Reactor Test Facility (TREAT) experiments to fill these gaps. Here, this work builds on that foundation by (1) updating BISON fuel performance and Griffin reactor physics models to reflect the current TREAT experiment tube and capsule designs, (2) coupling the codes to improve the accuracy and usability of the transient design analyses, and (3) demonstrating their use over an expanded design space that includes fuel burnup. The simulated mechanical responses of the TRISO particles were complex functions of fission product accumulation, fission gas release, and irradiation-induced dimensional change in the pyrolytic carbon layers. The predicted tangential stresses in the particles' silicon carbide layers were least compressive for preheated tests involving fresh fuels but remained compressive throughout the ranges of temperature, heat rate, and burnup considered in this work. Finally, comparisons between the potential TREAT transients and historical test reactor irradiations showed that the TREAT tests would produce significantly lower average energy deposition rates, yielding less severe transients with greater relevance to near-term commercial applications. The use of these predictive capabilities has the potential to increase the value of each test, improving the overall efficiency and cost-effectiveness of transient testing for TRISO and other advanced fuels.
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Shales are a central component of petroleum systems, as source, seal, and unconventional reservoir rocks. Unlike traditional unconventional shale, a newly emerging Caney Shale play is regarded as an unconventional of unconventional shales (UUS), due to its high content of fine-grained materials, lower reservoir porosity, dominance of nanopores, and a scarcity of visible natural fractures. Other developed unconventional shales such as the Woodford and Barnett have larger average pore size, higher porosity, and extensive natural fractures at core scale that contribute to reservoir quality. In this work, the Caney Shale was cored in entirety to characterize its interbedded ductile and reservoir intervals and establish criteria for their recognition. Representative ductile and reservoir intervals known as D2 and R3, respectively, were selected for detailed analysis including variations in elemental composition, mineralogy, facies, and the presence of natural fractures at well and core scales using X-ray fluorescence, X-ray diffraction, and thin section and core description. Characteristics of microstructure and microgeochemistry at nano- and microscales are compared using field emission scanning electron microscopy with energy dispersive spectroscopy and lowpressure nitrogen adsorption isotherms with fractal dimension analysis. The ductile (detrital clay-rich) member D2 is characterized by higher concentrations of Ti and Al and lower Si, while the reservoir R3 (possibly biogenic silica-accumulated) is characterized by lower Ti and Al and higher Si. Eight mixed carbonate–siliciclastic facies are recognized, and R3 shows a higher heterogeneity of facies stacking and average fracture abundance than D2. Further, R3 shows a more microscopically heterogeneous fabric/texture of matrix and a higher microporosity than D2 that has a higher pore surface heterogeneity. A fundamental understanding of the compositional and microstructural characteristics of UUS and further ductile/reservoir intervals will allow for a better assessment of reservoir quality, more effective production of hydrocarbons, and optimized selection of safe caprocks in carbon sequestration and subsurface hydrogen storage.
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Microkinetic models for catalytic systems require estimation of many thermodynamic and kinetic parameters that can be calculated for isolated species and transition states using ab initio methods. However, the presence of nearby coadsorbates on the surface can dramatically alter these thermodynamic and kinetic parameters causing them to be dependent on species coverage fractions. As there are combinatorially many coadsorbed configurations on the surface, computing the coverage dependence of these parameters is far less straightforward. We present a framework for generating and applying machine learning models to predict coverage-dependent parameters for microkinetic models. Our toolkit enables automatic calculation and evaluation of coadsorbed configurations allowing us to sample 2,000 coadsorbed adsorbates and transition states (TSs) for a diverse set of 9 reactions on Cu(111), a challenging surface, with four possible coadsorbates. This dataset was then used to train subgraph isomorphic decision trees (SIDTs) to predict the stability and association energy of configurations. We were able to achieve mean absolute errors (MAEs) of 0.106 eV on adsorbates, 0.172 eV on TSs, and due to natural error cancellation in SIDTs for relative properties, 0.130 eV on reaction energies and 0.180 eV on activation barriers. In conclusion, we describe how to use these models to predict coverage-dependent corrections for adsorbates and TSs and demonstrate on H*, HO*, and O* comparing the generated SIDT model with an iteratively refined version.