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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2010

ABSTRACTION OF INFORMATION FROM 2- AND 3-DIMENSIONAL PORFLOW MODELS INTO A 1-D GOLDSIM MODEL - 11404

The Savannah River National Laboratory has developed a 'hybrid' approach to Performance Assessment modeling which has been used for a number of Performance Assessments. This hybrid approach uses a multi-dimensional modeling platform (PorFlow) to develop deterministic flow fields and perform contaminant transport. The GoldSim modeling platform is used to develop the Sensitivity and Uncertainty analyses. Because these codes are performing complementary tasks, it is incumbent upon them that for the deterministic cases they produce very similar results. This paper discusses two very different waste forms, one with no engineered barriers and one with engineered barriers, each of which present different challenges to the abstraction of data. The hybrid approach to Performance Assessment modeling used at the SRNL uses a 2-D unsaturated zone (UZ) and a 3-D saturated zone (SZ) model in the PorFlow modeling platform. The UZ model consists of the waste zone and the unsaturated zoned between the waste zone and the water table. The SZ model consists of source cells beneath the waste form to the points of interest. Both models contain 'buffer' cells so that modeling domain boundaries do not adversely affect the calculation. The information pipeline between the two models is the contaminant flux. The domain contaminant flux, typically in units of moles (or Curies) per year from the UZ model is used as a boundary condition for the source cells in the SZ. The GoldSim modeling component of the hybrid approach is an integrated UZ-SZ model. The model is a 1-D representation of the SZ, typically 1-D in the UZ, but as discussed below, depending on the waste form being analyzed may contain pseudo-2-D elements. A waste form at the Savannah River Site (SRS) which has no engineered barriers is commonly referred to as a slit trench. A slit trench, as its name implies, is an unlined trench, typically 6 m deep, 6 m wide, and 200 m long. Low level waste consisting of soil, debris, rubble, wood, etc. is disposed within the trench which is then covered with soil and a cap. The filled trench resembles the surrounding soil, albeit with a higher porosity. As a result, the flow field through the trench is essentially 1-dimensional. This dimensionality makes the abstraction of information from this waste form fairly simple. Engineered waste forms present challenges not seen in the slit trench because of their higher dimensionality. Flow fields must conform to the barriers and are therefore subject to changes in direction. This paper will examine one case and show how this multidimensional flow field can be abstracted into a 1-dimensional flow field while retaining characteristics important to the transport of radioactive contaminants. One complication not addressed by the two preceding examples is that of multiple sources. This presents quite a challenge to the benchmarking exercise, but a fairly robust method has been developed to deal with it. While the PorFlow analyses can treat all sources as independent in space, this is not possible with a 1-D model. This problem has been addressed by constructing multiple 1-D models of the waste forms and using plume overlaps at the assessment points to address the multiple sources which can contribute to a distinct assessment point.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Data-Driven Smoothers for Extreme-Scale Computing

Patch-based relaxation refers to a family of methods for solving linear systems which partitions the matrix into smaller pieces often corresponding to groups of adjacent degrees of freedom residing within patches of the computational domain. The two most common families of patch-based methods are block-Jacobi and Schwarz methods, where the former typically corresponds to non-overlapping domains and the later implies some overlap. We focus on cases where each patch consists of the degrees of freedom on a finite element method mesh cell. Patch methods often capture complex local physics much more effectively than simpler point-smoothers such as Jacobi; however, forming, inverting, and applying each patch can be prohibitively expensive in terms of both storage and computation time. To this end, we propose several approaches for performing analysis on these patches and constructing a reduced representation. The compression techniques rely on either matrix norm comparisons or unsupervised learning via a clustering approach. We illustrate how it is frequently possible to retain/factor less than 5% of all patches and still develop a method that converges only a little slower than when all patches are stored/factored.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Background: Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent ‘natural’ phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. Results: Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. Conclusions: The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. The ontology release files associated with the ontology merge described in this manuscript are available at: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ Current ontology release files are available always available at: http://purl.obolibrary.org/obo/uberon/releases/

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A mass–momentum consistent coupling for mesh-adaptive two-phase flow simulations

Here, we present a novel mass-momentum consistent coupling between a geometric volume-of-fluid scheme and an incompressible flow solver with differing directional-splitting approaches. The advection of the volume fraction is performed using a direction-split algorithm, whereas the momentum advection algorithm uses a traditional unsplit, fractional-step approach. Both algorithms employ finite-volume discretizations based on Cartesian meshes. In solving the mass-momentum consistency problem, momentum fluxes at the cell faces are weighted by the density fluxes based on the already advected volume fraction. The success of our approach lies on introducing a Favre-averaged velocity interpolation at the liquid/gas interface along with a minmod slope limiter. Mesh-convergence studies show that when the minmod slope limiter is used, the two-phase solver retains an accuracy between first and second order, but when a purely upwind scheme is considered, its accuracy drops to first order. Finally, after considering several validation problems, the solver is shown to agree well with reference numerical and experimental data while retaining its robustness and efficiency.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Generic FEPs Catalogue and Salt Knowledge Archive

This report describes the development of a comprehensive catalogue of generic features, events, and processes (FEPs) that are potentially important for the post-closure performance of a repository for high-level radioactive waste (HLW) and spent nuclear fuel (SNF) in salt (halite) host rock. The FEPs and other supporting information have been entered into a “SaltFEP” Database. The generic salt repository FEPs include consideration of relevant FEPs from a number of U.S., Dutch, German, and international FEP lists and should be a suitable starting point for any repository program in salt host rock. The salt FEP catalogue and database employ a FEP classification matrix approach that is based on the concept that a FEP is typically a process or event acting upon or within a feature. The FEP matrix provides a two-dimensional structure consisting of a Features/Components axis that defines the “rows” and a Processes/Events axis that defines the “columns” of the matrix. The design of the FEP classification matrix is consistent with repository performance assessment – the Features/Components axis is organized vertically to generally correspond to the direction of potential radionuclide migration (from the waste to the biosphere) and the Processes/Events axis is designed to represent the common two-way couplings between thermal processes and other processes (such as thermal-mechanical or thermal-hydrologic processes). Related FEPs can be easily identified – related FEPs will typically be grouped in a single matrix cell or aligned along a common row (Feature/Component) or column (Process/Event). The online SaltFEP database can be downloaded from www.saltfep.org. It contains the FEP matrix, the FEPs, and the associated processes for each FEP. It provides a starting point to create and document site-specific individual FEPs. Furthermore, the FEP matrix is connected to the Salt Knowledge Archive (SKA), a database of about 20,000 references and documents representing the historical knowledge on radioactive disposal in salt. This work is the result of an ongoing collaboration between researchers in the U.S., the Netherlands, and Germany, and supports the NEA Salt Club Mandate. It builds upon prior work which is documented.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Mathematical Modeling of Hydroxide-Exchange-Membrane Water Electrolyzer

Water electrolyzers can transform intermittent renewable energy like solar energy and wind energy into the chemical energy of hydrogen with zero greenhouse-gas emissions. The hydroxide-exchange membrane electrolyzer (HEME) combines the capability to produce pressurized hydrogen with the advantage of being able to use low or non-platinum group metal (PGM) electrocatalysts in the alkaline environment.1 Hydroxide salts, for example, KOH, are added to the HEME water feed on both anode and cathode to improve its performance. However, the specific mechanism of performance improvement still needs to be further understood. In addition, at high current densities, bubble evolution can result in mass-transport limitations, a less well studied phenomena. Mathematical modeling is ideal to explore these issues as it is cost and time efficient and can deconvolute the physics, processes, and observed phenomena and study the applied-voltage breakdown. In this work, we extend our previously developed 1D two-phase continuum model2 to study the varies processes in the HEME and provide insights on performance optimizations. First, the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) kinetics at different hydroxide concentrations have been studied by rotating disk electrodes (RDE) and implemented in the model. Then, the model is calibrated and validated against experimental HEME polarization curves for different KOH concentrations as a liquid electrolyte. The model clearly shows a performance increase with increasing KOH concentrations, which is consistent with the experimental results. The reduced ohmic resistance and increased electrochemical active surface area (ECSA) are the two main reasons for performance increase. The large amount of hydroxide in the liquid electrolyte not only helps to distribute the reactant hydroxide throughout the catalyst layer (CL), which reduces ohmic loss, but also enables reaction at the interface between the liquid electrolyte and electrocatalyst, which increases the ECSA. Applied-voltage breakdown demonstrates that the electrolyzer performance is dominated by anode kinetics and ohmic loss. A comparison with the DI water feed shows a more uniform current distribution in the anode CL when KOH is added, which indicates a higher utilization of the CL. Second, we present modeling on the effects of bubble coverage. As gas evolves, part of the ECSA is minimized due to bubble coverage. To account for this effect, an empirical relationship between the fractional bubble coverage and the current density is implemented in the model.3 The model shows this bubble coverage effect is more pronounced at large current densities with DI water feed. Acknowledgements This work was funded under the HydroGEN Consortium by the Energy Efficiency and Renewable Energy, Hydrogen and Fuel Cell Technologies Office, of the U. S. Department of Energy under contract number DE-AC02-05CH11231. References R. Abbasi, B. P. Setzler, S. Lin, J. Wang, Y. Zhao, H. Xu, B. Pivovar, B. Tian, X. Chen, G. Wu and Y. Yan, 31, 1805876 (2019). L. N. Stanislaw, M. R. Gerhardt and A. Z. Weber, ECS Transactions, 92, 767 (2019). H. Vogt and R. J. Balzer, Electrochimica Acta, 50, 2073 (2005).

Liu, Jiangjin↗
DOE OSTI2014

Reliable wet-chemical cleaning of natively oxidized high-efficiency Cu(In,Ga)Se{sub 2} thin-film solar cell absorbers

Currently, Cu-containing chalcopyrite-based solar cells provide the highest conversion efficiencies among all thin-film photovoltaic (PV) technologies. They have reached efficiency values above 20%, the same performance level as multi-crystalline silicon-wafer technology that dominates the commercial PV market. Chalcopyrite thin-film heterostructures consist of a layer stack with a variety of interfaces between different materials. It is the chalcopyrite/buffer region (forming the p-n junction), which is of crucial importance and therefore frequently investigated using surface and interface science tools, such as photoelectron spectroscopy and scanning probe microscopy. To ensure comparability and validity of the results, a general preparation guide for “realistic” surfaces of polycrystalline chalcopyrite thin films is highly desirable. We present results on wet-chemical cleaning procedures of polycrystalline Cu(In{sub 1-x}Ga{sub x})Se{sub 2} thin films with an average x = [Ga]/([In] + [Ga]) = 0.29, which were exposed to ambient conditions for different times. The hence natively oxidized sample surfaces were etched in KCN- or NH{sub 3}-based aqueous solutions. By x-ray photoelectron spectroscopy, we find that the KCN treatment results in a chemical surface structure which is – apart from a slight change in surface composition – identical to a pristine as-received sample surface. Additionally, we discover a different oxidation behavior of In and Ga, in agreement with thermodynamic reference data, and we find indications for the segregation and removal of copper selenide surface phases from the polycrystalline material.

14 SOLAR ENERGY↗
DOE OSTI2024

Laboratory Testing of the Temperature Sensor Qualification Device

The Temperature sensor Qualification Device (TQD) has been developed and tested under laboratory conditions to evaluate its thermal performance and the reliability of its retractable sensor system. The TQD is designed to provide an isothermal environment for temperature sensors in both test and reference zones during irradiation experiments. Initial testing revealed minimal radial and azimuthal temperature variations but identified a significant axial gradient. To address this, design modifications were implemented, including enhanced insulation and the addition of a small heater at the device's top. These changes are expected to produce a more uniform axial temperature profile, though further testing is recommended prior to irradiation. The retractable sensor mechanism was rigorously tested, achieving 1,350 cycles at room temperature and 332 cycles at 400°C before failure. The primary failure mechanism was the thermocouple becoming stuck in the wire guide or capillary tube. Based on these results, design improvements were proposed, such as incorporating a load cell for force monitoring and a stepper motor for precise sensor positioning.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Functionalized Embedded Monometallic Nickel Catalysts for Enhanced Hydrogen Evolution: Performance and Stability

Viable anionic exchange membrane (AEM) electrolysis for H 2 production requires highly active hydrogen evolution reaction (HER) catalysts that are also robust and cost-effective. Traditionally juxtaposition of two transition metals with one being more oxophilic is necessary for easier access to water in the inner Helmholtz plane as a source of protons in the crucial Volmer step for enhanced HER activity. However, they are prone to passivation at anodic potentials or deactivation via the formation of sub-surface metal hydrides at high cathodic overpotentials. Here we report a method of enabling close juxtaposition of Ni-Ni-oxide surfaces by functionalizing Ni-based catalysts via the careful thermal treatment of carbon-supported Ni nano-particles chelated with a select organic chelating compound referred to as cupferron. This functionalization results in an embedded Ni surface with a clear graphitic coating engendering long-term stability for passivation and subsurface hydride formation. The stability and activity of the functionalized Ni catalyst are demonstrated in half-cell RDE and full-cell AEM membrane-based hydrogen pump experiments. In the case of the latter, the functionalized Ni outperforms carbon-supported Pt.

25 ENERGY STORAGE↗
DOE OSTI2021

Atomic-scale Imaging of PGM-free Catalyst Active Sites by 30 keV 4D-STEM

Platinum group metal (PGM)-free catalysts have attracted a large amount of attention due to their potential for enabling low-cost, commercially viable hydrogen fuel cells and electrolyzers [1]. Degradation of cell performance remains a significant challenge, however, currently limiting implementation of devices that utilize PGM-free materials [2]. Controlling degradation in these materials requires a better understanding of the atomic structure of active sites, thought to be FeN4 structures within a graphitic carbon lattice, which would enable more accurate prediction of the associated degradation pathways. The exact structural arrangement of active sites in these materials is still debated since a range of structures have been computationally predicted and methods to directly validate these models are still needed [1,3-5].While scanning transmission electron microscopy (STEM) has provided initial glimpses into the nature of the proposed active sites, detailed evaluation of the structure of these sites is challenging since they involve defects, edges, and nitrogen dopants in the graphitic lattice, which are susceptible to beam damage [6,7]. Conventional STEM imaging and spectroscopy methods exacerbate this problem with dose-inefficiency or nonideal contrast characteristics for imaging light and heavy elements simultaneously. A method that minimizes damage while generating dose-efficient, easily-interpretable contrast for both light and heavy elements is therefore needed to facilitate imaging of sensitive active site atomic structure.Here, we demonstrate direct atomic-scale imaging of PGM-free catalyst active sites by low-voltage four-dimensional (4D)-STEM. To accomplish this, we pair a 30 keV aberration-corrected probe, which minimizes knock-on damage, with a fast pixelated detector that has optimal performance at low beam energies [8]. We show how this setup enables relatively simple center-of-mass (CoM) techniques [9,10] to produce images with an increased signal-to-noise ratio (SNR) and light-element contrast over conventional imaging modes, allowing the entire active site structure to be imaged at the atomic scale. Moreover, we show how electron ptychography [11,12] enables images with further improved characteristics to be obtained, for example by minimizing residual aberrations, which provides a more accurate structural representation. The increased understanding that these low-voltage 4D-STEM techniques will provide about the atomic structure of PGM-free active sites and their associated degradation pathways will facilitate rational design of next-generation materials, promoting development of low-cost hydrogen fuel cells, electrolyzers, and other energy conversion devices [13]. References:[1] U Martinez et al., Adv. Mater. 31 (2019), p. 1806545.[2] Y Shao et al., Adv. Mater. 31 (2019), p. 1807615.[3] J Kneebone et al., J. Phys. Chem. C 121, (2017), p.16283.[4] T Mineva et al., ACS Catal. 9 (2019), p. 9359.[5] J Li et al., Nat. Catal. 4 (2021), p. 10.[6] T Susi et al., ACS Nano 6 (2012), p. 8837.[7] P Zelenay and DJ Myers, US Department of Energy Hydrogen and Fuel Cells Program 2017 Annual Merit Review and Peer Evaluation Meeting, Washington, DC (2017).[8] H Ryll et al., J. Inst. 11 (2016), p. P04006.[9] K Müller et al., Nat. Commun. 5 (2014), p. 5653.[10] I Lazic et al., Ultramicroscopy 160 (2016), p. 265.[11] H Yang et al., Nat. Commun. 7 (2016), p. 12532.[12] Y Jiang et al., Nature 559 (2018), p. 343. [13] Research sponsored by the Hydrogen and Fuel Cell Technologies Office, Office of Energy Efficiency and Renewable Energy, US Department of Energy (DOE). Research was conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

Zachman, Michael↗
DOE OSTI2019

Building Random Alloy Surfaces from Intermetallic Seeds: A General Route to Strain-Engineered Electrocatalysts with High Durability

Pt-based catalysts are common in fuel cells but suffer from high cost and poor durability. To overcome these limitations, earth-abundant metals are often incorporated with Pt in core@shell architectures or through alloy formation. In this work, the concepts of a core@shell architecture, alloyed surfaces, and high-durability intermetallics are integrated into one nanostructure platform using seed-mediated co-reduction (SMCR). Specifically, random alloy PtM (where M = Ni, Co, Cu, or Fe) shells are deposited on intermetallic PdCu B2 seeds. Control of shell thickness and Pt:M ratios is also demonstrated, providing a general route to strain-engineered alloyed surfaces. The performance of these nanocatalysts was evaluated for the oxygen reduction reaction (ORR) as a function of shell thickness and shell composition, where PtCu and PtNi shells showed a 230% and 270% activity increase, respectively, compared to the Pt reference. This evaluation is coupled with Tafel plot analysis which shows significant changes in the Tafel slopes, which indicate a shift in the rate-limiting step when a core@shell architecture is incorporated. Significantly, this work demonstrates the versatility of SMCR as a facile way to integrate a core@shell architecture, alloyed surfaces, and high-durability intermetallics within one platform.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Implementation of Gamma Transport Capability in MPACT

This paper presents the latest work on the development of the gamma transport capability for the CASL neutronics code MPACT. MPACT is capable of performing pin-resolved neutronics calculations for full-core problems and the purpose of this project is to further expand its capability for gamma transport calculations at the same level of accuracy for potential applications of interests, such as gamma heating and gamma fluence calculations. The development of the gamma transport capability reuses many existing geometrical capabilities and neutronics solvers in MPACT, because essentially the same form of Boltzmann transport equation is solved. First, 2-D gamma transport is implemented in this work by leveraging the method of characteristics (MOC) sweeper. The HELIOS library is used to provide the neutron-induced gamma production and gamma interaction cross sections. The new gamma transport capability is verified with MCNP. Both the gamma spectrum of a pin cell problem and the gamma flux distribution of 2D assembly problems are consistent with reference calculations. A 2D quarter core case is qualitatively verified by comparing MCNP and MPACT predictions of the gamma flux and thermal neutron flux to confirm the gamma smearing effects.

Wang, Xinyan↗
DOE OSTI2018

A Porous Pyrochlore Y 2 [Ru 1.6 Y 0.4 ]O 7–δ Electrocatalyst for Enhanced Performance towards the Oxygen Evolution Reaction in Acidic Media

A robust porous structure is often needed for practical applications in electrochemical devices, such as fuel cells, batteries, and electrolyzers. While templating approach is useful for the preparation of porous materials in general, it is not effective for the synthesis of oxide-based electrocatalysts owing to the chemical instability of disordered porous materials thus created. Now the synthesis of phase-pure porous yttrium ruthenate pyrochlore oxide using an unconventional porogen of perchloric acid is presented here. The lattice oxygen defects are formed by the mixed-valence state of Ru 4+ / 5+ through the partial substitution of Ru 4+ with Y 3+ cations, leading to the formation of mixed B-site Y 2 [Ru 1.6 Y 0.4 ]O 7-δ . This porous Y 2 [Ru 1.6 Y 0.4 ]O 7-δ electrocatalyst exhibits a turnover frequency (TOF) of 560 s -1 (at 1.5 V versus RHE) for the oxygen evolution reaction, which is two orders of magnitude higher than that of the RuO 2 reference catalyst (5.41 s -1 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multi-Sourced Collaboration for the Production and Refining of Rare Elements and Critical Metals (Final Technical Report)

The project objective was to develop a feasible and cost-effective method for recovering rare earth elements (REEs) and critical materials (CMs) from coal and coal byproducts, resulting in high-purity individually separated REEs and CMs. The targeted REEs included Y, Pr, Nd, Gd, Dy, and Sm, with a purity of over 99.5%, while the CMs included Co, Mn, Ga, Sr, Li, Ni, Zn, and Ge, with a purity of over 90%. The project aimed to design a prototype facility capable of producing 1-3 tonnes/day of high-purity REO mixes. The work was divided into four designated circuits: 1) REE extraction and concentration, 2) REE separation and purification, 3) RE metal production, and 4) CM production. To achieve these goals, the project involved 11 tasks, including technology reviews, research, process flow diagram development, mass balance estimation, and preliminary technical-economic analysis. The project team included researchers from the University of Kentucky, University of Alabama and Virginia Tech as well as process specialists from Argonne National Laboratory. MP Materials provided technical support regarding rare earth markets and processing while Alliance Coal performed resource assessment. The project included a market analysis for Nd/Pr, Tb, Dy, Gd, Y, Co, Mn, Li, Sr, Ga, Ni, Zn, and Ge. These analyses provided insights into the supply and demand trends as well as historic and future projections of market price relative to purity requirements for these elements. Two coal resources were selected for the project: the West Kentucky No. 13 (Baker) Seam and an undisclosed lignite resource in the Illinois coal basin. The estimated quantities of REEs in these resources were calculated based on production samples and drilling data. It was estimated that there is adequate supply for an operation producing one metric ton daily of higher purity mixed rare earth oxides (MREO) for approximately 20 years at a site located in western Kentucky. In Circuit 1, project data was obtained from a pilot heap leach and REE concentration facility. It was concluded that the existing circuit, which generated a MREO concentrate, two types of CM mixed products, and Li- and Sr-containing waters, would be suitable feed for circuits 2-4. Data from the first-of-its-kind coal coarse refuse heap leach pilot pad played a crucial role in estimating reliable elemental concentrations of the pregnant leaching solution (PLS). The average total REE concentration in the PLS was found to be 28.6 ppm. In Circuit 2, several concepts were explored including a novel process referred to as solvent-assisted chromatography (SAC). This concept involved a novel columnar reactor that incorporated multiple mixer/settlers, thereby enabling the operation of counter-flowing aqueous and organic phases. Unfortunately, due to project time constraints, a complete fundamental modeling analysis could not be completed to fully evaluate the technology. Molten salt electrowinning was considered as an alternative for circuit 3 following circuit 2 purification circuit utilizing the novel SAC process. A mass and energy balance of Nd reduction to metal in a fluoride containing molten salt electrolyte was conducted. Comparisons were made with the current state of Asian molten salt electrorefining, and potential improvements in siphoning rare earth metals (REM) from the reactor were presented. A cost estimate was performed for the production of 1 tonne per day, which yielded a total of $2.29 million for the nine electrowinning (EW) cells required. The selected option for circuits 2 and 3 was a plasma distillation process, which initially separates rare earth elements (REEs) from other elements. This is followed by selective electrowinning in various ionic liquids. The selection was made on the basis of thermodynamic modeling and experimental data previously published by a project partner. The combination offers an innovative approach to integrated refining and RE metal production. For Circuit 4, an extensive literature review was conducted for the processing of the CMs. The ultimate decision was to utilize a combined plasma and ionic liquid process as well to produce individual high-purity concentrates of Zn, Ni, Co, Mn, and Mg. A separate flowsheet for Li and Sr was recommended, which would yield carbonates of these elements. Due to the lack of suitable experimental data at this time, a process recommendation could not be provided but several methods have been proposed for consideration. Lastly, a techno-economic analysis (TEA) was conducted to assess the effectiveness of the proposed process for further investigation. The TEA results revealed a capital expense (CapEx) of $737 million and an annual operational expense (OpEx) of $220 million. Due to the selected elements, the hypothetical heap leach pad can produce 1 metric tonne per day of REO equivalent, but a conscious decision was made to only treat targeted REEs, resulting in the production of 0.4 metric tonne of REM. An estimated annual revenue of $90.87 million was projected based on standard market pricing information provided by the funding agency. During the TEA, ten different modules were evaluated for costing purposes. The precipitation circuit was identified as the largest single operational expense, followed by the Mg/Mn process due to the amount of treated metal. In terms of capital expenditures, the heap leach process incurred the highest cost, followed by the Mg/Mn process. The scalability of the plasma process is a crucial consideration since the reactors cannot be scaled beyond the largest demonstrated size due to their reliance on surface area of the slag and vapor phase. The purity estimate for the REEs are generally 98%±2% to produce a metal. The purity level being lower than the project objective was due to the lack of specific experimental data needed to tighten the tolerance of the estimates. Based on literature and previous experience, the CMs are estimated as follows; Ga (95%+, metal), Sr (95%+, carbonate), Li (95%+, carbonate), Ni (98%±2%, metal), Zn (95%+, metal sponge), Ge (95%+, metal), Co (98%±2%, metal), and Mn (98%±2%, metal).

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2025

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗
DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results. Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions. PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗
DOE OSTI2018

Optimizing de novo genome assembly from PCR-amplified metagenomes

Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods: Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. Results: . Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. This enrichment scales with the number of PCR cycles performed, and is presumably due to preferential amplification of short inserts. Standard assembly pipelines are confounded by this type of coverage unevenness, so we evaluated other assembly options to mitigate these issues. We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥ 10kb by 10 to 100-fold for low input metagenomes. Conclusions: PCR-amplified metagenomes have enabled scientists to explore communities traditionally challenging to describe, including some with extremely low biomass or from which DNA is particularly difficult to extract. Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes.

Roux, Simon↗