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At least 127 records · Page 7

TRACER Lightning Mapping Array Field Campaign Report

Our observational contribution to the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility’s Tracking Aerosol Convection Interactions Experiment (TRACER) was the deployment of additional Lightning Mapping Array sensors to provide enhanced capability to the Houston Lightning Mapping Array (HLMA) during the TRACER intensive operational period. To that end, the Texas Tech University personnel (Professor Bruning and Dr. Brunner, and graduate students Jessica Souza, David Singewald, Stephanie Weiss, and Matthew Miller) deployed two portable LMA antennae at locations G and B shown in the map below. The map also shows the predicted lightning flash detection efficiency in black contours, as well as color-shaded very-high-frequency (VHF) source detection efficiency, which roughly corresponds to the sensitivity to lightning channel detail. Feeds from these sensors were integrated in the HLMA processing in real-time and in post-processing, partially leveraging National Science Foundation support through the TRACER campaign that supported the core HLMA, operated by Timothy Logan.

54 ENVIRONMENTAL SCIENCES↗

From subsidies to stressors: Positively skewed ecological gradients alter biological responses to nutrients in streams

Abstract Subsidy–stress gradients offer a useful framework for understanding ecological responses to perturbation and may help inform ecological metrics in highly modified systems. Historic, region‐wide shifts from bottomland hardwood forest to row crop agriculture can cause positively skewed impact gradients in alluvial plain ecoregions, resulting in tolerant organisms that typically exhibit a subsidy response (increased abundance in response to environmental stressors) shifting to a stress response (declining abundance at higher concentrations). As a result, observed biological tolerance in modified ecosystems may differ from less modified regions, creating significant challenges for detecting biological responses to restoration efforts. Using the agriculturally dominated Mississippi Alluvial Plain (MAP) ecoregion in Mississippi, USA, as a case study, we tested the hypothesis that macroinvertebrate taxa that typically display a subsidy response to nutrient enrichment in less modified ecoregions (i.e., nutrient‐tolerance) shift to a stress response to increasing nutrients in highly modified watersheds with elevated baseline nutrient conditions (i.e., nutrient intolerance). The abundance and diversity of MAP‐specific intolerant taxa identified with threshold indicator taxa analysis were either unresponsive or exhibited a subsidy response to increasing nutrients in less modified ecoregions in Mississippi with less land alteration and lower nutrient concentrations, but declined at higher concentrations, providing evidence for a stress response to elevated nutrients in the MAP. Additionally, MAP‐specific tolerant and intolerant taxa richness responded to increased nutrients predictably and consistently across space and time within the MAP. However, in MAP streams, elevated specific conductance was predicted to dampen the response of tolerant and intolerant taxa richness to increasing nutrient concentrations, highlighting the importance of considering multistressor interactions when interpreting biological data. Lastly, we demonstrate the efficacy of this approach with sediment bacterial communities characterized with amplicon sequencing, which lack sufficient life history characteristics necessary for the development of multimetric indices. Both macroinvertebrate and bacterial communities responded similarly to increasing nutrient concentrations, suggesting DNA‐based approaches may provide an efficient biological assessment tool for monitoring water quality improvements in highly modified watersheds.

DeVilbiss, Stephen E. [U.S. Geological Survey Lowe↗

Indicator Patterns of Forced Change Learned by an Artificial Neural Network

Abstract Many problems in climate science require the identification of signals obscured by both the “noise” of internal climate variability and differences across models. Following previous work, we train an artificial neural network (ANN) to predict the year of a given map of annual‐mean temperature (or precipitation) from forced climate model simulations. This prediction task requires the ANN to learn forced patterns of change amidst a background of climate noise and model differences. We then apply a neural network visualization technique (layerwise relevance propagation) to visualize the spatial patterns that lead the ANN to successfully predict the year. These spatial patterns thus serve as “reliable indicators” of the forced change. The architecture of the ANN is chosen such that these indicators vary in time, thus capturing the evolving nature of regional signals of change. Results are compared to those of more standard approaches like signal‐to‐noise ratios and multilinear regression in order to gain intuition about the reliable indicators identified by the ANN. We then apply an additional visualization tool (backward optimization) to highlight where disagreements in simulated and observed patterns of change are most important for the prediction of the year. This work demonstrates that ANNs and their visualization tools make a powerful pair for extracting climate patterns of forced change.

54 ENVIRONMENTAL SCIENCES↗

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗

A thermochemical database from high-throughput first-principles calculations and its application to analyzing phase evolution in AM-fabricated IN718

A comprehensive thermochemical database is constructed based on high–throughput first-principles phonon calculations of over 3000 atomic structures in limited concentrations in Ni, Fe, and Co alloys involving a total of 26 elements including Al, B, C, Cr, Cu, Hf, La, Mn, Mo, N, Nb, O, P, Re, Ru, S, Si, Ta, Ti, V, W, Y, and Zr, providing thermochemical data largely unavailable from existing experiments. Here, the database can be employed to predict the equilibrium phase compositions and fractions directly from first-principles by minimizing the chemical potential of a multicomponent system with a fixed overall chemical composition and a fixed temperature. It is applied to the additively manufactured nickel-based IN718 superalloy to analyze the phase evolution with temperature. IN718 is known for its great performance in tensile, fatigue, creep, and rupture strength, combined with easy fabrication and corrosion resistance. In particular, we successfully predicted the formation of L1 0 -FeNi, γ’-Ni 3 (Fe,Al), α-Cr, δ-Ni 3 (Nb,Mo), γ”-Ni 3 Nb, and η-Ni 3 Ti at low temperatures (below 680 K), γ’-Ni 3 Al, δ-Ni 3 Nb, γ”-Ni 3 Nb, α-Cr, and γ-Ni(Fe,Cr,Mo) at intermediate temperatures (between 680 and 1140 K), and δ-Ni 3 Nb and γ-Ni(Fe,Cr,Mo) at high temperatures (above 1140 K) in IN718. These predictions are validated by EDS mapping of compositional distributions and corresponding identifications of phase distributions. The database is expected to be a valuable source for future thermodynamic analysis and microstructure prediction of alloys involving the 26 elements.

36 MATERIALS SCIENCE↗

Identifying spatiotemporal patterns in opioid vulnerability: investigating the links between disability, prescription opioids and opioid-related mortality

Background: The opioid crisis remains one of the most daunting and complex public health problems in the United States. This study investigates the national epidemic by analyzing vulnerability profiles of three key factors: opioid-related mortality rates, opioid prescription dispensing rates, and disability rank ordered rates. Methods: This study utilizes county level data, spanning the years 2014 through 2020, on the rates of opioid-related mortality, opioid prescription dispensing, and disability. To successfully estimate and predict trends in these opioid-related factors, we augment the Kalman Filter with a novel spatial component. To define opioid vulnerability profiles, we create heat maps of our filter’s predicted rates across the nation’s counties and identify the hotspots. In this context, hotspots are defined on a year-by-year basis as counties with rates in the top 5% nationally. Results: Our spatial Kalman filter demonstrates strong predictive performance. From 2014 to 2018, these predictions highlight consistent spatiotemporal patterns across all three factors, with Appalachia distinguished as the nation’s most vulnerable region. Starting in 2019 however, the dispensing rate profiles undergo a dramatic and chaotic shift. Conclusions: The initial primary drivers of opioid abuse in the Appalachian region were likely prescription opioids; however, it now appears that abuse is sustained by illegal drugs. Additionally, we find that the disabled subpopulation may be more at risk of opioid-related mortality than the general population. Public health initiatives must extend beyond controlling prescription practices to address the transition to and impact of illicit drug use.

60 APPLIED LIFE SCIENCES↗

CO2 Plume Imaging with Accelerated Deep Learning-based Data Assimilation Considering Multiple Realizations: Application to the Illinois Basin-Decatur Carbon Sequestration Project

We propose a fast and efficient deep learning workflow for near real-time data assimilation, forecasting and visualization of CO2 plume evolution in saline aquifer and demonstrate its application at a field site. Unlike the previous work, this study incorporates the impact of spatial heterogeneity using multiple realizations. In the proposed workflow, a neural network model utilizes available monitoring data such as downhole pressure measurements as input and predicts the propagating pressure ‘front’ using the diffusive time of flight (DTOF) map which is considered as representative reservoir image of the flow field. The DTOF is the arrival time of pressure front propagation, which can be computed by the Fast Marching Method rapidly without flow simulations. Reservoir model calibration can be implemented by selecting the training data samples that describe the predicted DTOF map based on observed data. The power and efficacy of our workflow is demonstrated by application to the Illinois Basin-Decatur Project.

CO2 plume imaging↗

Correlated Anion Disorder in Heteroanionic Cubic TiOF 2

Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO 3 -type) TiOF 2 using X-ray pair distribution function (PDF), 19 F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF 2 , characterized by predominant cis-[O 2 F 4 ] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19 F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19 F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF 4 . We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Rapid Identification of Synthetic Routes to Functional Metastable Phases Using X-ray Probed Laser Anneal Mapping (XPLAM) Time-Temperature Quench Maps

Many material systems have known or predicted functional phases that are metastable at standard temperature and pressure. While substantial advances have been made in the high-throughput and combinatorial synthesis of materials with a range of stoichiometries, investigation of thermal processing remains largely the domain of iterative uniform anneals or static gradients. Here we develop X-ray probed laser anneal mapping (XPLAM), a high throughput technique coupling spatially resolved X-ray diffraction with microsecond to millisecond laser gradient anneals to produce temperature–dwell–transformation (TDT) diagrams of the phase as a function of quench time and temperature. In addition to showing regimes where specific metastable phases form preferentially, TDT diagrams provide insight into the submillisecond kinetics of solid–solid phase transitions. This is a unique tool for mapping reaction pathways for metastable phases. As a first demonstration of XPLAM, we study Bi2O3, which has a rich set of polytypes, including the d-phase with an exceptionally high oxygen ion conductivity. We demonstrate the first annealing-driven synthesis of room temperature d-Bi2O3. We expect XPLAM to prove a powerful technique for rapid identification of synthetic routes to metastable phases and to generate the exhaustive data sets required for machine learning-guided exploration of materials processing.

36 MATERIALS SCIENCE↗

An Advanced Machine Learning and Artificial Intelligence System for Demonstrating Radiation Regulatory Compliance in DOE Accelerator Facilities

In this Phase II proposal, Applied Research LLC (ARLLC), Thomas Jefferson National Accelerator Facility (Jefferson Lab), and Old Dominion University (ODU) propose the combination of domain knowledge (beam characteristics, fixed structural shielding, earthen burden (the soil and foliage added to the dome of the experimental halls as additional shielding), etc.), machine learning (ML) and/or artificial intelligence (AI) to correlate a variety of multi-modal onsite signals and the radiation fields seen in accessible areas of the accelerator site and the site boundary. The ML/AI will consider the complex influence of environmental parameters affecting the radon contribution of the measurements, focusing on actual data obtained from Jefferson Lab. In Phase I, the coded beam and location data were fed into a deep learning model to predict doses at several designated locations in Jefferson Lab’s facility. Moreover, a dense radiation map was generated using only a sparse collection of the samples in a facility. In Phase II, we will develop a software prototype containing a radiation prediction algorithm, dense radiation map algorithms, and background noise prediction algorithms, with actual data used to evaluate the prototype. This work will provide a framework for evaluation of radiation measurement results around the site based on learned responses. In addition, the proposed approach allows more granular mapping of radiation levels. Better understanding and communication of these levels is related to the overall approach in keeping doses to personnel ALARA.

43 PARTICLE ACCELERATORS↗

Median bed-material sediment particle size across rivers in the contiguous US

Abstract. Bed-material sediment particle size data, particularly the median sediment particle size (D50), are critical for understanding and modeling riverine sediment transport. However, sediment particle size observations are primarily available at individual sites. Large-scale modeling and assessment of riverine sediment transport are limited by the lack of continuous regional maps of bed-material sediment particle size. We hence present a map of D50 over the contiguous US in a vector format that corresponds to approximately 2.7 million river segments (i.e., flowlines) in the National Hydrography Dataset Plus (NHDPlus) dataset. We develop the map in four steps: (1) collect and process the observed D50 data from 2577 U.S. Geological Survey stations or U.S. Army Corps of Engineers sampling locations; (2) collocate these data with the NHDPlus flowlines based on their geographic locations, resulting in 1691 flowlines with collocated D50 values; (3) develop a predictive model using the eXtreme Gradient Boosting (XGBoost) machine learning method based on the observed D50 data and the corresponding climate, hydrology, geology, and other attributes retrieved from the NHDPlus dataset; and (4) estimate the D50 values for flowlines without observations using the XGBoost predictive model. We expect this map to be useful for various purposes, such as research in large-scale river sediment transport using model- and data-driven approaches, teaching environmental and earth system sciences, planning and managing floodplain zones, etc. The map is available at https://doi.org/10.5281/zenodo.4921987 (Li et al., 2021a).

54 ENVIRONMENTAL SCIENCES↗

Investigating the Effects of Mixing Dynamics on Twin-Screw Granule Quality Attributes via the Development of a Physics-Based Process Map

Twin-screw granulation (TSG) is an emerging continuous wet granulation technique that has not been widely applied in the industry due to a poor mechanistic understanding of the process. This study focuses on improving this mechanistic understanding by analyzing the effects of the mixing dynamics on the granule quality attributes (PSD, content uniformity, and microstructure). Mixing is an important dynamic process that simultaneously occurs along with the granulation rate mechanisms during the wet granulation process. An improved mechanistic understanding was achieved by identifying and quantifying the physically relevant intermediate parameters that affect the mixing dynamics in TSG, and then their effects on the granule attributes were analyzed by investigating their effects on the granulation rate mechanisms. The fill level, granule liquid saturation, extent of nucleation, and powder wettability were found to be the key physically relevant intermediate parameters that affect the mixing inside the twin-screw granulator. An improved geometrical model for the fill level was developed and validated against existing experimental data. Finally, a process map was developed to depict the effects of mixing on the temporal and spatial evolution of the materials inside the twin-screw granulator. This process map illustrates the mechanism of nucleation and the growth of the granules based on the fundamental material properties of the primary powders (solubility and wettability), liquid binders (viscosity), and mixing dynamics present in the system. Furthermore, it was shown that the process map can be used to predict the granule product quality based on the granule growth mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

59 BASIC BIOLOGICAL SCIENCES↗

AI-Enabled Robots for Automated Nondestructive Evaluation and Repair of Power Plant Boilers. Final Report

Boiler failure could cause loss of life and safety issues, cost hundreds of thousands of dollars in equipment repairs, property damage and production losses, and drive up the cost of electric power. Boiler maintenance is challenging and risky for inspectors working on scaffolding in confined hazardous spaces inside of a boiler and sometimes the space is hard to access. The operation is also time-consuming due to the large area of vertical structures for inspection and the tremendous effort needed for scaffolding. Recently, the use of robotics (e.g., drones and crawlers) in power plants for maintenance is growing rapidly. However, the existing robotics solutions show two notable technological gaps: no live repair capability, and no Artificial Intelligence (AI) for smart autonomy. The objective of this project is to develop an integrated autonomous robotic platform that is equipped with compact non-destructive evaluation (NDE) sensors to perform live inspection, operates onboard repair devices to perform live repair, and uses AI for intelligent data fusion and predictive analysis for automated and smart spatiotemporal inspection, analysis and repair of the furnace walls in coal-fired boilers. The approach to achieve the objective includes developing NDE sensors with signal processing techniques, designing and evaluating repair devices for robots based on fusion and solid-state technologies, and an autonomous robotic platform that can attach to and navigate on boiler furnace walls using magnetic drive tracks. The robot is also powered by AI to automate data gathering (e.g., 3D mapping and damage localization) and predictive analysis. This project has advanced the state-of-the-art by providing technological breakthroughs including compact NDE and repair tools for robots, AI capabilities for smart autonomy, and a robotic platform for automated boiler maintenance. This project has great potential to result in significant benefits including limiting or eliminating the need to send operators to assess difficult-to-access or hazardous areas, enabling automated live inspection and repair, avoiding time consuming scaffolding (especially for partial maintenance during unplanned outage), collecting comprehensive and well-organized data smartly, and avoiding or limiting the need for onsite or remote piloting technicians. The impacts can be tremendous in terms of the time and cost savings, reducing the risk for human operators, and increasing boiler reliability, usability, and efficiency. In addition, by developing the new technologies on the autonomous inspection and repair robot, by involving multiple undergraduate and graduate students working together with the faculty members on this project, and by generating knowledge and building up collaborations with industrial partners, this effort will significantly update the education capabilities, support long-term fundamental research, and maintain the leadership of Colorado School of Mines and Michigan State University in energy fields.

20 FOSSIL-FUELED POWER PLANTS↗

Extending evolutionary forecasts across bacterial species

Improving evolutionary forecasting requires progressing from studying repeated evolution of a single genotype under identical conditions to formulating broad principles. These principles should enable predictions of how similar species will adapt to similar selective pressures. Evolve-and-resequence experiments with multiple species allow testing forecasts on different biological levels and elucidating the causes for failed predictions. Here, we show that forecasts for adaptation to static culture conditions can be extended to multiple species by testing previous predictions for Pseudomonas syringae and Pseudomonas savastanoi. In addition to sequence divergence, these species differ in their repertoire of biofilm regulatory genes and structural components. Consistent with predictions, both species repeatedly produced biofilm mutants with a wrinkly spreader phenotype. Predominantly, mutations occurred in the wsp operon, with less frequent promoter mutations near uncharacterized diguanylate cyclases. However, mutational patterns differed on the gene level, which was explained by a lack of conservation in relative fitness of mutants between more divergent species. The same mutation was the most frequent for both species suggesting that conserved mutation hotspots can increase parallel evolution. This study shows that evolutionary forecasts can be extended across species, but that differences in the genotype–phenotype–fitness map and mutational biases limit predictability on a detailed molecular level.

59 BASIC BIOLOGICAL SCIENCES↗

Startup Test Plan and Predictions for Highly Enriched Uranium to Low-Enriched Uranium Fuel Conversion at the University of Missouri Research Reactor

Nonpower reactors licensed by the U.S. Nuclear Regulatory Commission require a startup test plan as part of any facility modification to verify operability prior to resumption of operations. In order to support conversion of the University of Missouri Research Reactor from the use of highly enriched uranium to low-enriched uranium (LEU) fuel, a startup test plan has been devised to measure certain reactor physics parameters for the initial all-fresh LEU core licensing documentation that will be submitted. These parameters include the approach to critical, primary coolant void coefficient of reactivity, flux trap void coefficient of reactivity, determination of flux trap sample reactivity worth, radial and axial thermal neutron flux mapping, control blade worth calibration, primary and pool coolant temperature coefficient of reactivity, and flux mapping of experimental positions. Here, predictions for these parameters made using the Monte Carlo N-Particle Version 5 (MCNP5) radiation transport code are reported. These predictions will support the startup tests by providing a baseline set of expectations and additional insight into the performance of the LEU core.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗