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DOE OSTI2026

Fluorescence Signatures of Rare Earth Metals during Precipitation in Various Conditions

Fluorescence spectroscopy is a widely used sensor methodology that analyzes light emitted from a compound or element as it decays from an excited state. This technique is very sensitive and selective, which is ideal to characterize analytes at lower limits of detection. Key example targets of significant industry and research interest include rare earth elements (REEs) such as dysprosium (Dy) and europium (Eu). These are widely used in advanced technologies including semiconductors, electric vehicle motors, lasers, and permanent magnets. Identifying new sources and responsible reutilization of REEs is essential, and new approaches to extract and recycle REEs could be notably enhanced through the integration of on-line sensors. The sensors can support faster process design, informed scale-up, and cost-effective deployment. This study covers the initial exploration of applying fluorescence-based on-line monitoring to REEs within a precipitation process. This study demonstrates the successful scale-up of a fluorescence -based sensing approach, from stationary cuvettes and small-volume microfluidic devices to continuous flow systems operating at the bench scale (10-25mL). This work also provides initial insight into the challenges of signal’s effects and utility within a turbid environment. Using a modular design for monitoring flowing solutions in a flow tube, fluorescence can be characterized for a variety of analytical targets. In this study, detection performance parameters between the cuvette and flow tube system were compared. Additionally, the response of Dy during precipitation by sodium bicarbonate in the two measurement designs was explored. This letter represents a starting point to bridge the gap between traditional fluorescence sensor measurements in a cuvette to future developments that explore the ability to integrate fluorescence sensors into extraction and separation processes at industrially relevant scales.

fluorescence↗

DOE OSTI2024

fluxfinder: An R Package for Reproducible Calculation and Initial Processing of Greenhouse Gas Fluxes From Static Chamber Measurements

Fluxes of greenhouse gases are a critical component of the earth's natural climate, but anthropogenic emissions have created an imbalance and resulted in global climate change. Quantifying the emission of these gases is vital to our understanding of their sources and sinks, both natural and anthropogenic. The static chamber method, in which a system of interest is enclosed, and gas concentrations are measured over time, is widely used to estimate fluxes of greenhouse gases. With the development of instruments such as infrared gas analyzers (IRGAs) supporting high-frequency concentration data, there is a growing need for open-source workflows to calculate fluxes. Here we present fluxfinder, an R package designed to support reproducible calculations and processing of greenhouse gas fluxes measured with the static chamber method. The package includes raw data file parsing from widely used IRGAs, metadata matching, unit conversion, flux estimations, and initial quality assurance/quality control (QA/QC). Diagnostic graphical plots provide a transparent way to differentiate between measurement issues and nonlinear behavior. The package is also designed to be easily integrated with the gasfluxes package for further fitting of nonlinear concentration-time models, allowing alternative or additional flux QA/QC. The fluxfinder package offers a flexible workflow that is easily adaptable to promote open and reproducible greenhouse gas flux estimations.

Wilson, Stephanie J.↗

DOE OSTI2023

Improving Mathematical Exposition of an Industrial-Scale Linear Program

Industrial-scale models require considerable setup time; hence, once built, they are used in myriad ways to consider closely related cases. In practice, the code for these models frequently evolves without appropriate notational choices, largely as a result of the lengthy development time of, and the number of individuals contributing to, their formulation. This leads to inefficiencies and obfuscates model structures that might be leveraged to expedite solutions. In this paper, we advocate for an emerging literature on model formulation “best practices” and present the reformulation of a widely used industrial-scale linear program. The efficient mathematical expression of this linear program, used to plan capacity expansion in the energy sector, allows for greater transparency of model structures and enhanced ability to identify computational performance improvements, as well as a lucid interpretation of its solutions. This type of formulation is employed in several mathematical programming courses at our university as an example of the advantages of best practices; the model more broadly is used widely to inform policy in the U.S. energy sector.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Materials and technological processes for High-Gradient accelerating structures: new results from mechanical tests of an innovative braze-free cavity.

Pure oxygen-free high-conductivity copper is a widely used material for manufacturing accelerating cavities working at room temperature. Several studies attempted to explain limitations associated with the maximum allowed field gradients and the behaviour of vacuum RF breakdown in copper accelerating structures through generation and movement of dislocations under stresses associated with RF electric and magnetic fields. Pure copper and also copper alloys undergo mechanical and thermal treatments to be hardened and strengthened during manufacturing, although their mechanical properties significantly change after heating above 590°C. High temperature brazing and diffusion bonding are assembly methods widely used to manufacture ultra-high vacuum accelerating devices. However, these processes, occurring at about 800–1000°C, significantly affect the mechanical properties of copper and copper alloys. We introduce here a novel Tungsten Inert Gas welding procedure, which is fast and keeps the high-gradient surfaces of the cavity and other components well below the copper annealing temperature. This process may be successfully used to manufacture copper-based accelerating components. This technology further preserves the hardness and cleanliness of copper in order to achieve the maximum accelerating gradient.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Suppressing ion migration in metal halide perovskite via interstitial doping with a trace amount of multivalent cations

Cations with suitable sizes to occupy an interstitial site of perovskite crystals have been widely used to inhibit ion migration and promote the performance and stability of perovskite optoelectronics. However, such interstitial doping inevitably leads to lattice microstrain that impairs the long-range ordering and stability of the crystals, causing a sacrificial trade-off. Here, we unravel the evident influence of the valence states of the interstitial cations on their efficacy to suppress the ion migration. Incorporation of a trivalent neodymium cation (Nd 3+ ) effectively mitigates the ion migration in the perovskite lattice with a reduced dosage (0.08%) compared to a widely used monovalent cation dopant (Na + , 0.45%). As a result, the photovoltaic performances and operational stability of the prototypical perovskite solar cells are enhanced with a trace amount of Nd 3+ doping while minimizing the sacrificial trade-off.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Gasoline Compression Ignition (GCI) on a Light-Duty Multi-Cylinder Engine Using a Wide Range of Fuel Reactivities and Heavy Fuel Stratification

Many research studies have focused on utilizing gasoline in modern compression ignition engines to reduce emissions and improve efficiency. Collectively, this combustion mode has become known as gasoline compression ignition (GCI). One of the biggest challenges with GCI operation is maintaining control over the combustion process through the fuel injection strategy, such that the engine can be controlled on a cycle-by-cycle basis. Research studies have investigated a wide variety of GCI injection strategies (i.e., fuel stratification levels) to maintain control over the heat release rate while achieving low temperature combustion (LTC). This work shows that at loads relevant to light-duty engines, partial fuel stratification (PFS) with gasoline provides very little controllability over the timing of combustion. On the contrary, heavy fuel stratification (HFS) provides very linear and pronounced control over the timing of combustion. However, the HFS strategy has challenges achieving LTC operation due to the air handling burdens associated with the high EGR rates that are required to reduce NOx emissions to near zero levels. In this work, a wide variety of gasoline fuel reactivities (octane numbers ranging from < 40 to 87) were investigated to understand the engine performance and emissions of HFS-GCI operation on a multi-cylinder light-duty engine. The results indicate that over an EGR sweep at 4 bar BMEP, the gasoline fuels can achieve LTC operation with ultra-low NOx and soot emissions, while conventional diesel combustion (CDC) is unable to simultaneously achieve low NOx and soot. At 10 bar BMEP, all the gasoline fuels were compared to diesel, but using mixing controlled combustion and not LTC.

Dempsey, Adam↗

DOE OSTI2020

Structural and functional characterization of the dominant negative P-loop lysine mutation in the dy

Explore the source record for details and available documents.

Tornabene, Bryan A.↗

DOE OSTI2023

Model validation and selection in metabolic flux analysis and flux balance analysis

13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. These fluxes can shed light on basic biology and have been successfully used to inform metabolic engineering strategies. Several approaches have been taken to test the reliability of estimates and predictions from constraint-based methods and to compare alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, such as the quantification of flux estimate uncertainty, validation and model selection methods have been underappreciated and underexplored. We review the history and state-of-the-art in constraint-based metabolic model validation and model selection. Applications and limitations of the χ 2 -test of goodness-of-fit, the most widely used quantitative validation and selection approach in 13C-MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C-MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how adopting robust validation and selection procedures can enhance confidence in constraint-based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Optimal Estimation Retrievals and Their Uncertainties: What Every Atmospheric Scientist Should Know

Remote sensing instruments are heavily used to provide observations for both the operational and research communities. These sensors do not provide direct observations of the desired atmospheric variables, but instead, retrieval algorithms are necessary to convert the indirect observations into the variable of interest. It is critical to be aware of the underlying assumptions made by many retrieval algorithms, including that the retrieval problem is often ill posed and that there are various sources of uncertainty that need to be treated properly. In short, the retrieval challenge is to invert a set of noisy observations to obtain estimates of atmospheric quantities. The problem is often complicated by imperfect forward models, by imperfect prior knowledge, and by the existence of nonunique solutions. Optimal estimation (OE) is a widely used physical retrieval method that combines measurements, prior information, and the corresponding uncertainties based on Bayes’s theorem to find an optimal solution for the atmospheric state. Furthermore, OE also allows the relative contributions of the different sources of error to the uncertainty in the final retrieved atmospheric state to be understood. Here, we provide a novel Python library to illustrate the use of OE for inverse problems in the atmospheric sciences. We introduce two example problems: how to retrieve drop size distribution parameters from radar observations and how to retrieve the temperature profile from ground-based microwave sensors. Using these examples, we discuss common pitfalls, how the various error sources impact the retrieval, and how the quality of the retrieval results can be quantified.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Gasoline Compression Ignition on a Light-Duty Multi-Cylinder Engine Using a Wide Range of Fuel Reactivities and Heavy Fuel Stratification

Many research studies have focused on utilizing gasoline in modern compression ignition engines to reduce emissions and improve efficiency. Collectively, this combustion mode has become kn+own as gasoline compression ignition (GCI). One of the biggest challenges with GCI operation is maintaining control over the combustion process through the fuel injection strategy, such that the engine can be controlled on a cycle-by-cycle basis. Research studies have investigated a wide variety of GCI injection strategies (i.e., fuel stratification levels) to maintain control over the heat release rate while achieving low-temperature combustion (LTC). This work shows that at loads relevant to light-duty engines, partial fuel stratification (PFS) with gasoline provides very little controllability over the timing of combustion. On the contrary, heavy fuel stratification (HFS) provides very linear and pronounced control over the timing of combustion. However, the HFS strategy has challenges achieving LTC operation due to the air handling burdens associated with the high exhaust gas recirculation (EGR) rates that are required to reduce NOx emissions to near zero levels. In this work, a wide variety of gasoline fuel reactivities (octane numbers ranging from <40 to 87) were investigated to understand the engine performance and emissions of HFS-GCI operation on a multi-cylinder light-duty engine. Overall, the results indicate that over an EGR sweep at 4 bar brake mean effective pressure (BMEP), the gasoline fuels can achieve LTC operation with ultra-low NO x and soot emissions, while conventional diesel combustion (CDC) is unable to simultaneously achieve low NO x and soot. At 10 bar BMEP, all the gasoline fuels were compared to diesel, but using mixing controlled combustion and not LTC.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Benchmarking Variables for Checkpointing in HPC Applications

Checkpoint/Restart (C/R) is a widely used fault tolerance mechanism in converged systems of cloud, edge, and HPC. However, users often rely on their experience to determine which variables to checkpoint, as there is currently no benchmark that can provide a reference. This can result in checkpointing redundant or even incorrect variables. To address this issue, we propose a benchmark suite that includes critical variables for checkpointing, which have been manually identified, and a method for identifying those critical variables, with 20 representative HPC applications. Our method involves analyzing data dependency between variables to identify critical variables analytically. We verify the identified variables' correctness with a widely used C/R library FTI by an ablation study. With our benchmark suite and data dependency analysis, HPC practitioners now have a reference for identifying checkpointing variables and better knowledge of what kind of variables to checkpoint.

Fu, Xiang↗

DOE OSTI2025

Synthesis of nanodiamonds encapsulated by zeolitic imidazole framework-8 for quantum sensing applications

Nitrogen vacancy (NV)-containing nanodiamonds are widely used in quantum sensing applications due to their high sensitivity to magnetic fields, relatively low cost, and ability to be initialized, manipulated, and read out at room temperature. Quantum sensing techniques such as optically detected magnetic resonance (ODMR) and spin relaxometry have exploited the sensitivity of the NV nanodiamonds to magnetic fields to detect a range of analytes, such as pH, metal ions, and biomolecules. However, diversifying the sensing targets accessible by NV diamond quantum sensors typically requires careful engineering of the diamond surface chemistry with stimuli-responsive functional groups. Here, a simple protocol for coating NV nanodiamonds with the zeolitic imidazole framework 8 (ZIF-8), a widely used metal-organic framework, is presented. ZIF-8 is a highly porous material that has been used as a selective sensor for gasses, metal ions, and other analytes. The material is well-characterized by x-ray diffraction, transmission electron microscopy, scanning electron microscopy, x-ray photoelectron spectroscopy, and luminescence spectroscopy. Encapsulation of NV nanodiamonds with a porous scaffold such as ZIF-8 provides a promising method for improving the selectivity for the quantum sensing of various analytes. Importantly, the ZIF-8 coating does not impact the luminescence properties of the NV diamond, which is a key readout in ODMR and spin relaxometry sensing approaches. Indeed, the ODMR spectra with and without the ZIF-8 shell is nearly identical. Moreover, the ZIF-8 coating increases the longitudinal spin relaxation time of the NV nanodiamond by a factor of 4 relative to aggregated diamond, a desirable outcome for spin relaxation-based quantum sensing. Metal-organic framework composites with nanodiamonds thus are an exciting strategy for enhancing NV nanodiamond performance in applications such as quantum sensing and quantum-enhanced nuclear magnetic resonance spectroscopy.

nitrogen vacancy nanodiamond↗

DOE OSTI2023

Ion concentration ratio measurements of ion beams generated by a commercial microwave electron cyclotron resonance plasma source

A commercially available electron cyclotron resonance (ECR) plasma source (GenII Plasma Source, tectra GmbH) is widely used for surface processing. This plasma source is compatible with ultrahigh vacuum systems, and its working pressure is relatively low, around 10 –6 –10 –4 Torr even without differential pumping. Here, we report ion flux concentration ratios for each ion species in an ion beam from this source, as measured by a mass/energy analyzer that is a combination of a quadrupole mass spectrometer, an electrostatic energy analyzer, and focusing ion optics. In this study, the examined beams were those arising from plasmas produced from feed gases of H 2 , D 2 , N 2 , O 2 , Ar, and dry air over a range of input power and working pressures. H 2 (D 2 ) plasmas are widely used for nuclear fusion applications and, hence, the ion concentration ratios of H + , H 2 + , and H 3 + reported here will be useful information for research that applies this plasma source to well-controlled plasma-material interaction studies. Ion energy distributions, stability of operation, and impurity concentrations were also assessed for each of the plasma species investigated.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Summary of Biomass Scale Cubical Triaxial Tester Results

09 BIOMASS FUELS↗

DOE OSTI2023

Finite element modeling of biomass hopper flow

Hoppers are widely used biomass handling devices that channel bulk biomass from storage to subsequent handling equipment. Jenike’s longstanding approach, based on the Mohr-Coulomb model, has been successfully used to design hoppers handling cohesionless granular materials such as grains and other agricultural produces. However, designing a hopper to ensure reliable biomass flow is found to be challenging due to cohesion, irregular particle shape, and bulk material elastoplasticity. This study aims to address the biomass handling engineering challenge with alternative constitutive material models concerning the flow behavior of bulk solids. Finite element modeling is an approach that allows for implementation of different material models, whose underlying constitutive theories assist in investigating the origin and manifestation of bulk mechanical behavior of granular materials. This study focuses on the incipient gravity hopper flow of two types of biomass feedstocks, i.e., ground corn stover and Douglas fir wood. Three widely used constitutive material models, i.e., Mohr-Coulomb model, modified Cam-Clay model, and Drucker-Prager/Cap model, are implemented. Using the flow pattern represented by the volume of biomass exhibiting more than 7% of axial strain (Kamath and Puri, 1999), the finite element model predicts that the bulk corn stover particulate material forms an arch, which represents a hampered transition from the static state to the dynamic flow-state out of the hopper, whereas bulk Douglas fir wood particulate material develops a reliable mass flow pattern. A laboratory scale hopper was used to experimentally determine the biomass flow conditions, which were subsequently compared with the predicted onset of flow by a finite element model (FEM). The developed FEM was found to correctly predict the initiation of mass flow for the milled Douglas fir wood, whereas corn stover was predicted to establish a strong core flow suggesting an unreliable handling characteristic. This observation aligns with the reported poor handling of milled corn stover.

09 BIOMASS FUELS↗

DOE OSTI2022

How Can Construction Process Simulation Modeling Aid the Integration of Lean Principles in the Factory-Built Housing Industry?

New and existing factories that produce and deliver factory-built housing can benefit from construction process simulation modeling to explore the integration of Lean principles in their operations. Construction process simulation modeling provides digital or virtual recreations of the real-world factory environments to visualize, quantify, analyze, and optimize their underlying behavior, including factory productivity, material flow, labor dynamics, bottlenecks, and work scope. One of the key benefits of process simulation modeling is the ability to create and compare "what-if" scenarios, including integrating Lean principles such as reducing waste (for example, transportation, waiting), line balancing, and just-in-time concepts. In general, three process simulation methods are widely used: discrete event simulation (DES), agentbased modeling (ABM), and system dynamics (SD). Myriad process simulation software also is available, but depending on the industry, complexity of the system, and purposes of the simulation, some software might be more appropriate. Similar to how computer-aided design (CAD) software such as AutoCAD and Rhinoceros enable building design of modular or factory-built housing, process simulation modeling software such as jStrobe, ProModel, and AnyLogic can enable factory design of new and existing factories to deliver modular affordable housing at scale, as opposed to traditional site-built construction. Software with DES capabilities can help generate a process model that is a logical representation of resources and activities in a factory. Software with CAD-DES integration can leverage product-process data integration to help spatially visualize a DES model of the factory in the CAD environment. Software with multimethod simulation capabilities, widely used in the manufacturing industry, brings together DES, ABM, and SD in a single platform that allows visualization, quantification, analyses, and optimization at varying data fidelities. Near-real-time data from an existing factory can be directly plugged into multimethod simulation software so that the construction process simulation model is a near-accurate representation of the real-world factory conditions. This report provides insights into the use of simulation as an aid to integrate Lean concepts in factories, including guidelines for selecting the appropriate process simulation modeling method and software. These insights have been developed as part of ongoing process simulation modeling research, development, and demonstration projects at the U.S. Department of Housing and Urban Development, the U.S. Department of Energy, and the National Renewable Energy Laboratory focused on how process simulation models can enable better integration of resilience, energy efficiency, and low-carbon design strategies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing

ABSTRACT Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences. IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗