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DOE OSTI2023

Metal hydride composition-derived parameters as machine learning features for material design and H 2 storage

Though hydrogen is a promising energy carrier for a green future, many challenges persist. One is the difficulty in engineering storage solutions, with metal hydrides being a leading contender among solid-state strategies. To facilitate efficient searching of candidate materials, ridge regression, simple decision trees, random forest ensembles, and gradient boosting ensembles were employed to predict the energy of formation, with the random forest ensemble resulting in the lowest test set error. First, two public databases, Materials Project and HydPark, were searched for metal hydrides. Feature engineering was performed before the models were developed, resulting in electronegativity, density, atomic density, d-character, f-character, band gap, hydrogen weight fraction, magnetization, temperature, and pressure being retained. The models were then benchmarked by the lowest test error before a random forest ensemble was used to populate entries missing energy of formation. Furthermore, all were then scored by hydrogen storage capacity and energy of formation suitability. Readily available features including several derived from only the chemical formula which were found to be highly predictive. and so are promising for high-throughput screening of arbitrary novel hydride formulations and blends for thermodynamic feasibility.

25 ENERGY STORAGE↗

DOE OSTI2024

Predicting biomass comminution: Physical experiment, population balance model, and deep learning

An extended population balance model (PBM) and a deep learning-based enhanced deep neural operator (DNO+) model are introduced for predicting particle size distribution (PSD) of comminuted biomass through a large knife mill. Experimental tests using corn stalks with varied moisture contents, mill blade speeds, and discharge screen sizes are conducted to support model development. A novel mechanism in the extended PBM allows for including additional input parameters such as moisture content, which is not possible in the original PBM. The DNO+ model can include influencing factors of different data types such as moisture content and discharge screen size, which significantly extends the engineering applicability of the standard DNO model that only admits feed PSD and outcome PSD. Test results show that both models are remarkably accurate in the calibration or training parameter space and can be used as surrogate models to provide effective guidance for biomass preprocessing design.

09 BIOMASS FUELS↗

DOE OSTI2025

Signatures of Selection for Resistance/Tolerance to Perkinsus olseni in Grooved Carpet Shell Clam ( Ruditapes decussatus ) Using a Population Genomics Approach

ABSTRACT The grooved carpet shell clam ( Ruditapes decussatus ) is a bivalve of high commercial value distributed throughout the European coast. Its production has suffered a decline caused by different factors, especially by the parasite Perkinsus olsenii . Improving production of R . decussatus requires genomic resources to ascertain the genetic factors underlying resistance/tolerance to P. olseni i . In this study, the first reference genome of R . decussatus was assembled through long‐ and short‐read sequencing (1677 contigs; 1.386 Mb) and further scaffolded at chromosome level with Hi‐C (19 superscaffolds; 95.4% of assembly). Repetitive elements were identified (32%) and masked for annotation of 38,276 coding‐ and 13,056 non‐coding genes. This genome was used as a reference to develop a 2bRAD‐Seq 13,438 SNP panel for a genomic screening on six shellfish beds distributed across the Atlantic Ocean and Mediterranean Sea. Beds were selected by perkinsosis prevalence and the infection level was individually evaluated in all the samples. Genetic diversity was significantly higher in the Mediterranean than in the Atlantic region. The main genetic breakage was detected between those regions (F ST = 0.224), being the Mediterranean more heterogeneous than the Atlantic. Several loci under divergent selection (394 outliers; 261 genomic windows) were detected across shellfish beds. Samples were also inspected to detect signals of selection for resistance/tolerance to P. olseni i by using infection‐level and population‐genomics approaches, and 90 common divergent outliers for resistance/tolerance to perkinsosis were identified and used for gene mining. Candidate genes and markers identified provide invaluable information for controlling perkinsosis and for improving production of the grooved carpet shell clam.

Sambade, Inés M. [Department of Zoology, Genetics ↗

DOE OSTI2025

Charge Transfer and Recombination Pathways through Fullerene Guests in Porphyrin-Based MOFs

Porphyrin-based metal–organic frameworks (MOFs) offer a unique platform for building porous donor–acceptor networks that exhibit long-lived charge separation and transport upon incorporation of electron acceptor guest species. Here, in this work, porphyrin-based MOFs, PCN-222(H 2 ) and PCN-222(Zn), synthesized as nanoparticle suspensions, are successfully infiltrated with fullerene acceptor molecules, C 60 or PC 61 BM, in both polar and nonpolar solvent environments. The location and relative binding strength of these guest species are evaluated through a combination of N 2 physisorption measurements, photoluminescence quenching, and UV–vis absorption titration experiments. Semiempirical tight binding calculations are used to screen potential locations of the fullerene guest within the MOF pores, and hybrid density functional theory (DFT)-computed interaction energies confirm the energetically favorable positions. The fundamental photophysics of these donor–acceptor host–guest combinations are probed using ultrafast transient absorption spectroscopy. Sub-picosecond electron transfer involving initial exciplex population is observed, with slow charge recombination lifetimes on the order of τ ~1 ns for all systems in both dimethylformamide and 1,4-dioxane. Charge recombination occurs through population of fullerene and/or framework porphyrin triplet states depending on the porphyrin metalation status. The photophysics of the fullerene-loaded MOFs are discussed in the context of relevant porphyrin–fullerene donor–acceptor molecules to highlight the unique role of the framework environment in dictating photoinduced electron transfer and decay pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Flat-Band-Enabled Triplet Excitonic Insulator in a Diatomic Kagome Lattice

The excitonic insulator (EI) state is a strongly correlated many-body ground state, arising from an instability in the band structure of narrow-gap semiconductors towards exciton formation. Here we show that the flat valence and conduction bands of a Yin-Yang Kagome lattice, as exemplified in a superatomic graphene lattice, conspire to enable an interesting state of triplet EI, based on first-principles Density Functional Theory (DFT) calculations combined with many-body GW and Bethe-Salpeter Equation (BSE). As an intrinsic property of topological flat bands, highly localized electron and hole wavefunctions significantly reduce the screening and enhance the exchange interaction, leading to an unusually high triplet exciton binding energy (~1.2 eV) exceeding the GW band gap by ~0.2 eV and a huge singlet-triplet splitting of ~0.4 eV. Here, the flat-bands-enabled triplet EI state also points to the possibility of complete population inversion between the two topological flat bands for the realization of excited quantum spin Hall effect. Our findings enrich once again the intriguing physics of flat bands, which has drawn broad interest.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Data for "Efficient Mutagenesis and Genotyping of Maize Inbreds Using Biolistics, Multiplex CRISPR/Cas9 Editing, and Indel-Selective PCR"

gene editing↗

DOE OSTI2024

Existing evidence on the effects of climate variability and climate change on ungulates in North America: a systematic map

Abstract Background Climate is an important driver of ungulate life-histories, population dynamics, and migratory behaviors. Climate conditions can directly impact ungulates via changes in the costs of thermoregulation and locomotion, or indirectly, via changes in habitat and forage availability, predation, and species interactions. Many studies have documented the effects of climate variability and climate change on North America’s ungulates, recording impacts to population demographics, physiology, foraging behavior, migratory patterns, and more. However, ungulate responses are not uniform and vary by species and geography. Here, we present a systematic map describing the abundance and distribution of evidence on the effects of climate variability and climate change on native ungulates in North America. Methods We searched for all evidence documenting or projecting how climate variability and climate change affect the 15 ungulate species native to the U.S., Canada, Mexico, and Greenland. We searched Web of Science, Scopus, and the websites of 62 wildlife management agencies to identify relevant academic and grey literature. We screened English-language documents for inclusion at both the title and abstract and full-text levels. Data from all articles that passed full-text review were extracted and coded in a database. We identified knowledge clusters and gaps related to the species, locations, climate variables, and outcome variables measured in the literature. Review findings We identified a total of 674 relevant articles published from 1947 until September 2020. Caribou ( Rangifer tarandus ), elk ( Cervus canadensis ), and white-tailed deer ( Odocoileus virginianus ) were the most frequently studied species. Geographically, more research has been conducted in the western U.S. and western Canada, though a notable concentration of research is also located in the Great Lakes region. Nearly 75% more articles examined the effects of precipitation on ungulates compared to temperature, with variables related to snow being the most commonly measured climate variables. Most studies examined the effects of climate on ungulate population demographics, habitat and forage, and physiology and condition, with far fewer examining the effects on disturbances, migratory behavior, and seasonal range and corridor habitat. Conclusions The effects of climate change, and its interactions with stressors such as land-use change, predation, and disease, is of increasing concern to wildlife managers. With its broad scope, this systematic map can help ungulate managers identify relevant climate impacts and prepare for future changes to the populations they manage. Decisions regarding population control measures, supplemental feeding, translocation, and the application of habitat treatments are just some of the management decisions that can be informed by an improved understanding of climate impacts. This systematic map also identified several gaps in the literature that would benefit from additional research, including climate effects on ungulate migratory patterns, on species that are relatively understudied yet known to be sensitive to changes in climate, such as pronghorn ( Antilocapra americana ) and mountain goats ( Oreamnos americanus ), and on ungulates in the eastern U.S. and Mexico.

Malpeli, Katherine C. (ORCID:000000030780918X)↗

DOE OSTI2020

Strain Improvements that Keep Algae Ponds Growing Strong

A challenge for algal biofuel development is finding strains of algae best suited for producing copious amounts of oil quickly and under industrial-scale conditions. Furthermore, maintaining pond health is also challenging—deteriorating health in a small fraction of algal cells within a pond can quickly lead to the death of the entire pond’s population. To overcome these challenges, Los Alamos National Laboratory (LANL) scientist Christina Steadman and team designed a process to optimize algal physiology and metabolism in cultures by interrogating specific characteristics of the algae cells. This process uses flow cytometry methods and solves two problems: the LANL team can quickly detect potential pond problems, and use this process to streamline the screening of potential algae candidates for biofuel production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Light-induced electron pairing in a bilayer structure

We demonstrate the existence of doubly charged exciton states in strongly screened bilayers of transition metal dichalcogenide layers. These complexes are important because they are preformed electron pairs that can, in principle, undergo Bose–Einstein condensation, in which case they would also form a new type of superconductor, consisting of stable bosons with net charge. Our measurements include 1) continuous control of the doping density with both positive and negative carriers, showing the expected population dependencies on the free carrier density, and 2) measurement of the dependence on magnetic field, showing that this new bound state is a spin triplet. These results imply that it is promising to look for superconductivity in this system.

2D material↗

DOE OSTI2023

Moment tensor event identification for collapses

SUMMARY We introduce a seismic identification method for collapse events using moment tensors (MTs). We start by computing full (six-element) MT solutions for 43 identified collapse events from around the world, and statistically characterizing the population on the MT hypersphere. We then test a large data set of over 1000 full MTs for the western U.S. against the distribution of collapses using a MT-based identification method similarly as used for testing explosions. Known collapses and explosions are readily identified, along with other anomalous events in the Geysers and central California coast. Misidentification rates are determined for various screening angles with optimal misidentification rates between earthquakes and collapses on the order of 3 per cent. The method is demonstrated to be very effective at identifying non-earthquake sources with a 97–98 per cent accuracy. It is likely to be transportable to other regions, and can be used for event identification anywhere full MT solutions are routinely calculated.

58 GEOSCIENCES↗

DOE OSTI2023

Examination of an Electrified Bar Rack Fish Guidance Device for Hydropower Turbines

The potential of hydropower turbines to cause injury or mortality to fish is a concern. To reduce this risk, engineers have begun to develop a conically arranged, cantilevered electrified bar rack (Center Sender). This device is proposed to be mounted within the intake of a turbine, guiding downstream-passing fish towards the center of the turbine where blade velocities are lower and blades are thicker, likely reducing the potential for fish to be injured. A simplified version was installed in a flume for testing with Rainbow trout (Oncorhynchus mykiss) while examining several parameters such as electrification, bar spacing, bar angle, and water velocity. The most effective settings were observed to be a water velocity of 1.0 m s -1 with all bars installed at an angle of 40° with electrification on. Other combinations were still effective but had varying results. A minimal proportion (2.3%) of fish passed at lower velocities with bars electrified and mounted at 20°, suggesting that while it functions well as a guidance device in high-velocity conditions, it performs better as a barrier at lower velocities. The study suggests that the Center Sender has promising potential for reducing the harmful effects of hydropower turbines on fish populations by guiding them away from stressors. Further research is needed, but current results encourage its potential use in hydropower operations.

13 HYDRO ENERGY↗

DOE OSTI2022

Analyzing Relationships Between Economic and Neighborhood-Related Social Determinants of Health and Intensive Care Unit Length of Stay for Critically Ill Children With Medical Complexity Presenting With Severe Sepsis

Objectives: Of the Social Determinants of Health (SDoH), we evaluated socioeconomic and neighborhood-related factors which may affect children with medical complexity (CMC) admitted to a Pediatric Intensive Care Unit (PICU) in Shelby County, Tennessee with severe sepsis and their association with PICU length of stay (LOS). We hypothesized that census tract-level socioeconomic and neighborhood factors were associated with prolonged PICU LOS in CMC admitted with severe sepsis in the underserved community. Methods: This single-center retrospective observational study included CMC living in Shelby County, Tennessee admitted to the ICU with severe sepsis over an 18-month period. Severe sepsis CMC patients were identified using an existing algorithm incorporated into the electronic medical record at a freestanding children's hospital. SDoH information was collected and analyzed using patient records and publicly available census-tract level data, with ICU length of stay as the primary outcome. Results: 83 encounters representing 73 patients were included in the analysis. The median PICU LOS was 9.04 days (IQR 3.99–20.35). The population was 53% male with a median age of 4.1 years (IQR 1.96–12.02). There were 57 Black/African American patients (68.7%) and 85.5% had public insurance. Based on census tract-level data, about half (49.4%) of the CMC severe sepsis population lived in census tracts classified as suffering from high social vulnerability. There were no statistically significant relationships between any socioeconomic and neighborhood level factors and PICU LOS. Conclusion: Pediatric CMC severe sepsis patients admitted to the PICU do not have prolonged lengths of ICU stay related to socioeconomic and neighborhood-level SDoH at our center. A larger sample with the use of individual-level screening would need to be evaluated for associations between social determinants of health and PICU outcomes of these patients.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Graph-Based Modeling for the Detection and Tracking of Sarin-Surrogate-Induced Neurotoxicity Using a Human-Relevant, In-Vitro Brain Model

Organophosphorus (OP) nerve agents are a chemical threat to the United States, to the civilian population (e.g., pesticides) and historically weaponized (e.g., sarin) as chemical warfare agents. The unprecedented, accelerated process from “bench-to-bedside” during the SARSCov2 pandemic has made it clear that technology and tools need to be readily available for immediate response. Advances in human organ tissue mimetic systems are a promising technology to evaluate the human-relevant response in vitro for basic and applied research and drug screening. In particular, current brain microphysiological systems (MPS) have the capability to monitor and detect changes in engineered human neural circuit activity. However, current data analytics approaches for these systems lack the granularity to functionally detect and distinguish the different mechanisms that occur in the brain following neurotoxicity, injury, and disease. The goal of this project was to advance the computational analytical capabilities of the brain MPS to detect functional changes in neural circuit structure at different stages of Sarin surrogate-induced neurotoxicity. We developed graph-based models to (1) identify the composition of the neural circuit structure; (2) detect and monitor how this structure changes following sarin-induced neurotoxicity; and (3) evaluate the analytical pipeline using known/promising oxime reactivators. Through experiments on the bMPS where in vitro neuronal cultures were exposed to a sarin surrogate, we demonstrated the capabilities of our computational pipeline to identify different responses in the functional networks of brain cells exposed to low and high concentrations of the nerve agent. We identified a biphasic response of human neural network activity following exposure to a sarin-surrogate that had not been reported in the literature before. The graph-based models and software developed in this project can be used for future studies that leverage the brain MPS technology, such as treatment efficacy assessment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Subsampling and DNA pooling can increase gains through genomic selection in switchgrass

Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross-validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence-based GS when sequencing resources were restricted (2,000 DNA samples per 5-yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5-yr cycle). This study highlights multiple routes for reduced sequencing costs in GS.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

How directed evolution reshapes the energy landscape in an enzyme to boost catalysis

Two steps forward—now look back Whether designed computationally or uncovered in activity screening, enzymes repurposed for biocatalysis rarely start at the peak of proficiency. However, directed evolution can in some cases increase catalytic efficiency of a poor enzyme by many orders of magnitude. Otten et al. used a suite of biochemical techniques to investigate the origins of rate enhancement in a previously evolved model enzyme. Two conformational states are present in the initial, computationally designed enzyme, but only one is active. Shifting the population toward the active state is one factor in increasing catalytic efficiency during evolution. Single mutations do not greatly increase activity, but the synergistic combination of just two out of 17 substitutions can provide most of the rate enhancement seen in the final, evolved enzyme. Science , this issue p. 1442

Science & Technology - Other Topics↗

DOE OSTI2021

Early growth response 2 (EGR2) is a novel regulator of the senescence programme

Abstract Senescence, a state of stable growth arrest, plays an important role in ageing and age‐related diseases in vivo. Although the INK4/ARF locus is known to be essential for senescence programmes, the key regulators driving p16 and ARF transcription remain largely underexplored. Using siRNA screening for modulators of the p16/pRB and ARF/p53/p21 pathways in deeply senescent human mammary epithelial cells (DS HMECs) and fibroblasts (DS HMFs), we identified EGR2 as a novel regulator of senescence. EGR2 expression is up‐regulated during senescence, and its ablation by siRNA in DS HMECs and HMFs transiently reverses the senescent phenotype. We demonstrate that EGR2 activates the ARF and p16 promoters and directly binds to both the ARF and p16 promoters. Loss of EGR2 down‐regulates p16 levels and increases the pool of p16− p21− ‘reversed’ cells in the population. Moreover, EGR2 overexpression is sufficient to induce senescence. Our data suggest that EGR2 is a direct transcriptional activator of the p16/pRB and ARF/p53/p21 pathways in senescence and a novel marker of senescence.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Erbium-implanted materials for quantum communication applications

Erbium-doped materials can serve as spin-photon interfaces with optical transitions in the telecom C band, making them an exciting class of materials for long-distance quantum communication. However, the spin and optical coherence times of Er 3+ ions are limited by currently available host materials, motivating the development of new Er 3+ -containing materials. Here we demonstrate the use of ion implantation to efficiently screen prospective host candidates, and show that disorder introduced by ion implantation can be mitigated through post-implantation thermal processing to achieve inhomogeneous linewidths comparable to bulk linewidths in as-grown samples. We present optical spectroscopy data for each host material, which allows us to determine the level structure of each site, allowing us to compare the environments of Er 3+ introduced via implantation and via doping during growth. Here, we demonstrate that implantation can generate a range of local environments for Er 3+ , including those observed in bulk-doped materials, and that the populations of these sites can be controlled with thermal processing.

74 ATOMIC AND MOLECULAR PHYSICS↗