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Results for “elemental profiling”

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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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment

The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. Here, we identify two non-coding structural variants in individuals with FOXG1 syndrome-like features, allowing us to delineate a ~ 124 kb commonly affected regulatory region. Using epigenomic profiling and in vivo enhancer assays, we characterize and validate regulatory elements within the commonly affected regulatory region and wider FOXG1 TAD. We see strong activation of previously validated forebrain enhancers, and identify an enhancer cluster and progenitor-specific enhancer region that are strongly activated during forebrain-directed neural progenitor cell differentiation, a process in which FOXG1 is an important regulator. Perturbation of these elements results in varying degrees of reduced FOXG1 transcription in forebrain neural progenitor cells and in population shifts within these cells, while removal of the TAD boundary leads to aberrant expression of the neighbouring PRKD1 gene. Our findings characterize enhancer and architectural elements essential for proper FOXG1 transcription during neurodevelopment, therefore improving variant interpretation in this region.

Hamerlinck, Lisa↗
DOE OSTI2026

The Use of Machine Learning Models for Predicting the Dielectric Strength of Gases

Technological advancements in high voltage systems have pushed sulfur hexafluoride (SF6) to its operational limits. Furthermore, this gas has other drawbacks including a high liquefaction temperature and a high global warming potential. Therefore, there has been an urgent need to find alternative gases with high dielectric strength (DS). In this work, density functional theory (DFT) is used to calculate molecular descriptors that are fed into an artificial neural network (ANN) and a random forest (RF). These machine learning (ML) models are then used to predict the DS for hundreds of molecules. A finite element model (FEM) is also used to calculate the electric field profile of multiple simple electrode geometries as the applied voltage to the system is increased. Results indicate that the random forest model has better generalization to unseen data than the neural network. The highest DS value predicted by the RF was 2.16 relative to the experimental DS of SF6. The results also demonstrate how choosing a gas with a higher DS and a geometry with minimal edges and corners can significantly increase the operating voltage of an electrical system. Due to its superior generalization, the RF represents the most promising path toward an accurate DS predictor once sufficient experimental data are available.

Mileski, Matthew [AFIT]↗
DOE OSTI2025

Directed energy deposition of radially functionally graded nickel based superalloys IN625 and IN738: Microstructure and mechanical properties

This study investigates the microstructure and mechanical properties of radially functionally graded (RFG) materials fabricated from nickel-based superalloys IN625 and IN738 using directed energy deposition (DED). RFG cylindrical deposits with radial gradients of IN625-IN738 and IN738-IN625 were successfully fabricated and confirmed to be crack-free through tailored composition grading, scan strategy and process parameters that minimized thermal gradients and solidification velocities. Microstructural analysis revealed distinct variations across the gradient, characterized by differences in dendrite arm spacing, microsegregation, and the formation of distinct γ' precipitates and carbide/boride phases (MC, M 6 C, M 2 C, and MB 2 ) in as-deposited (AD) conditions, which evolved into M 23 C 6 and M 2 B upon subsequent heat treatment (HT). EBSD showed predominant columnar grains with a [100] texture, while microhardness profiles demonstrated consistent variation across the gradients. Mechanical testing highlighted the synergy of the graded structure, combining IN738's strength with IN625's ductility, resulting in enhanced properties such as a yield strength of 1131 MPa, ultimate tensile strength of 1382 MPa, and elongation of 12 % for HT IN625-IN738 grading. Numerical simulations employing CALPHAD thermodynamic calculations and finite element thermal modeling are used to establish phase evolution and microstructural feature correlation with thermal profiles, aiding in the optimization of process-structure-property relationship.

Additive manufacturing↗
DOE OSTI2025

Molecular Imaging of Microbially Induced Corrosion of Synthetic Archeological Glasses by a Rhizosphere Bacterium

Microbially induced corrosion (MIC) focuses on the degradation of solid materials, such as glass or metal. Soil microbes are often associated with the corrosion of foreign objects in the rhizosphere. Paenibacillus polymyxa SCE2, a facultative anaerobic bacterium in soil, is of the same genus as bacteria found near nuclear waste disposal sites. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used for imaging surface changes induced by P. polymyxa SCE2 cultured on two synthetic glass coupons to represent natural analogs of materials that were studied in relation to the vitrification of nuclear waste. Multimodal imaging was used to verify bacterial coverage across the glass surface after long-term growth. ToF-SIMS spectral analysis showed detection of glass component ions, such as silicon oxide (m/z – 59.96 SiO 2 – ) and aluminum oxide (m/z – 101.95 Al 2 O 3 – ), and biofilm’s extracellular polymeric substance (EPS) components, such as pentadecanoic acid (m/z – 241.22 C 15 H 29 O 2 – ) and sterol lipids (m/z – 311.16 C 20 H 23 O 3 – ). ToF-SIMS spectral, imaging, and depth profiling analyses showed that the glass rich in silica and other light elements (“granite glass”) had more “corrosion related” peaks than the glass that was less silica-rich and contained more iron (“dike glass”). Furthermore, these surface and interface compositional and spatial differences observed in the mass spectra and imaging were attributed to bacterial metabolism and an electron transfer mechanism influenced by morphological and compositional differences between the two types of glasses. ToF-SIMS is effective in studying microbial effects, bringing new molecular insights into MIC in a broader context of materials degradation.

Amorphous materials↗
DOE OSTI2026

Comparative genomics provides insights into the cold adaptation of endophytic fungi associated with Deschampsia antarctica

Endophytic fungi from Deschampsia antarctica , the southernmost flowering plant, provide insights into the cold adaptation mechanisms of plant-associated fungi in extreme environments. This study presents the genome sequences and comparative analysis of eight fungal isolates from D. antarctica leaves. These Antarctic fungal isolates were analyzed alongside 121 plant-associated fungal genomes to uncover signatures of adaptation and endophytic specialization. Antarctic endophytes show striking patterns, including reduced genome size (∼26.3 Mb on average), streamlined gene content (∼8844 genes), and notably small secretomes (∼288 proteins). Despite this reduced gene repertoire, they maintain a robust set of genes encoding carbohydrate-active enzymes (CAZymes) but lack those for lignin and bacterial cell wall degradation, indicating a symbiotic lifestyle that avoids host damage and predation. One isolate, Alternaria sp. UNIPAMPA017 stood out, with 26% of its genome occupied by transposable elements. Lifestyle, rather than phylogeny, was the main driver of CAZyme and secretome profiles, underscoring ecological convergence. Compared to endophytes from Arabidopsis and Populus, D. antarctica endophytes harbor fewer pectin-degrading enzymes, reflecting their adaptation to the cell wall structure of their monocot host. Together, these fungi reveal a pattern of genomic reduction and functional fine-tuning, hallmarks of life adapted to persist in cold, nutrient-scarce niches.

Ascomycota↗
DOE OSTI2024

Convergent laser beam shapes: Unveiling the dynamics of Laser-induced elastic waves in composite materials

Overcoming the low signal-to-noise ratio (SNR) in laser ultrasonic testing of composite materials remains a significant challenge. Current efforts focus on enhancing SNR by inserting more energy into the material through temporal and/or spatial modulation of the laser beam. However, potential SNR improvements through wave convergence and wave energy manipulation have been overlooked. This paper addresses this gap by demonstrating the convergence of different wave types to a designated point and by showing the feasibility of directing absorbed laser energy into a specific wave type through spatial modulation of the laser beam. To achieve this, mathematical expressions for the convergent laser beams are derived. Various laser beam profiles are then introduced to the thermoelastic equations and solved using the finite element method. The sample under investigation is a transversely isotropic unidirectional carbon fiber reinforced plastic, characterized by anisotropic thermal expansion coefficients and thermal conductivities. Results reveal pronounced convergence of the intended wave type at the center due to laser beam shaping. This study showcases the ability to direct absorbed laser energy toward a specific wave type through spatial modulation of the laser beam and highlights the role of material anisotropy in energy focusing.

composite materials↗
DOE OSTI2025

Effect of seasonal anoxia on geochemical cycling in a stratified pond: Comparison to cooler pond conditions 40 years ago

Seasonal stratification in temperate lakes deeper than a few meters creates favorable conditions for pronounced vertical redox zones, often resulting in anaerobic hypolimnions and significant geochemical changes. Here, this study examined thermocline formation and trace element behavior in a seasonally stratified pond amid rising air temperatures. Over two years, data were collected from Pond B at the US Department of Energy Savannah River Site in Aiken, South Carolina. Pond B, a man-made monomictic reservoir, received cooling water from a nuclear reactor from 1961 to 1964. Strong thermal stratification forms a distinct thermocline in May and progresses downward until November. Compared to the 1980s, this study shows a delayed onset and extended duration of stratification. The prolonged summer stratification reduces deep water oxygen replenishment, extending hypoxic conditions. Trace and major elements sampled in the water column revealed strong correlations between As, Fe, and Mn profiles, with concentrations increasing by 1–2 orders of magnitude in the anaerobic hypolimnion. This period captured the seasonal transition from winter mixing to summer stratification to fall overturn. Under anoxic conditions, Fe(III) reduces to Fe(II) in the sediment, releasing dissolved iron into the water column. The extended anoxic periods likely promoted arsenic release from sediments. Prolonged anoxia may enhance arsenic mobilization and solubility in the lake. This study illustrates how climate-induced changes in seasonal stratification of contaminated waters can convert contaminant sinks into sources, offering insights into the cycling of arsenic and other dissolved ions in stratified lakes and their implications for water quality management.

Anoxic conditions↗
DOE OSTI2025

Improved robustness of sequentially deposited potassium cesium antimonide photocathodes achieved by increasing the potassium content towards theoretical stoichiometry

Alkali antimonide semiconductor photocathodes are promising candidates for high-brightness electron sources for advanced accelerators, including free-electron lasers (FEL), due to their high quantum efficiency (QE), low emittance, and high temporal resolution. Two challenges with these photocathodes are (1) the lack of a universal deposition recipe to achieve crystal stoichiometries and (2) their high susceptibility to vacuum contamination, which restricts their operation pressure to ultrahigh vacuums and leads to a short lifetime and low extraction charge. To resolve these issues, it is essential to understand the elemental compositions of deposited photocathodes and correlate them to robustness. Here, we report depth profiles for potassium cesium antimonide photocathodes, which were investigated using synchrotron radiation x-ray photoelectron spectroscopy, and the robustness of those photocathodes. We prepared two types of photocathodes with different potassium contents via sequential thermal evaporation. Depth profiles revealed that the photocathodes with a potassium deficit had excess cesium at the surface, while the ratio of potassium and cesium to antimony decreased rapidly within the film. In contrast, the photocathodes with sufficient potassium had close to the theoretical stoichiometry of K 2 CsSb at the surface and maintained that stoichiometry for over half the entire film thickness. Both photocathode types had a similar maximum QE at 532 nm; however, exposure to oxygen revealed that the photocathode with a crystalline stoichiometry of K 2 CsSb maintained QE at one order of magnitude higher pressure compared to its potassium-deficit counterpart. These results highlight the importance of synthesizing potassium cesium antimonide photocathodes with sufficient potassium to achieve the theoretical crystalline stoichiometry for both high QE and improved robustness.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Extracting the electronic structure of light elements in bulk materials through a Compton scattering method in the readily accessible hard x-ray regime

Here, our Compton profile measurements of Ti and TiH 2 using readily available hard X-ray radiation at 27.5 keV, detected by both a Hitachi Vortex silicon-drift detector and a high-resolution superconducting transition-edge sensor array, are found to be in excellent accord with state-of-the-art density functional theory based calculations. The spherically averaged difference between the Compton profiles of TiH 2 and Ti is well described by an inverted parabola, supporting an itinerant behavior of the electron gas screening the protons in the Ti matrix. Our experimental approach, validated by two different detectors, extends the applicability of Compton scattering technique to the readily accessible hard x-ray regime (below 30 keV). Our study suggests possibilities for experiments at low-flux bending magnet synchrotron beamlines and paves the way for the development of tabletop Compton experiments with x-ray tubes.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Validating corrosion models: A comparison of governing equations

Experimental validation of Finite Element Method (FEM) models varying electrochemical governing equations, inclusion of chemical reactions, and time on the resultant damage profile for two galvanic couples is explored. Two anode materials (Magnesium AZ31 and Carbon Steel) in contact with a cathode (Stainless Steel 304 L) were modeled in/exposed to NaCl (1 and 0.1 M respectively for the anode materials) for up to one week. The physics approach, inclusion of chemical reactions, and the boundary conditions required to accurately represent the damage profile in FEM models depended on the galvanic couple materials and, ultimately, the corrosion rate. For high rates of corrosion (i.e., magnesium anode), the Nernst-Planck equation with Electroneutrality was sufficient to describe the damage, while, for low rates of corrosion (i.e., carbon steel anode), the Laplace equation was sufficient. In all cases, the most complete governing equation (Nernst-Planck-Poisson Equation) was not necessary to accurately describe the damage. Precipitation reactions in solution also played a critical role in the predicted damage profile, especially for high corrosion rate systems. Finally, for short time periods (< 6 h), the choice of governing equations does not significantly influence damage profile results. Overall, the choice of physics to reduce error in simulations relies on the boundary conditions, geometry, conductivity of the solution, electrochemical potential differences, and time of exposure. The above results are discussed with regard to accuracy and computational savings.

Carbon steel↗
DOE OSTI2024

Alloying effects on deformation induced microstructure evolution in copper

In this work, we investigated the effects of alloying elements on plastic deformation and microstructure evolution in polycrystalline copper (Cu) and Cu alloyed with 1 wt. % lead (Cu-1 %Pb). These materials were selected due to the size mismatch between Cu and Pb, with the latter forming precipitates at grain boundaries. Multi-modal characterization techniques, including neutron diffraction, electron backscatter diffraction (EBSD), and transmission electron microscopy (TEM), along with finite element simulations were employed to study the deformation behavior across multiple length scales. While both Cu and Cu-1%Pb exhibited similar macroscale response and final deformation textures, both dislocation line profile analysis and TEM revealed increased dislocation density in deformed Cu-1%Pb specimens. The presence of lead precipitates also significantly affected local plastic deformation during compression, with their influence diminishing with increasing strain. These results demonstrate the complex relationships between alloying elements, plastic deformation, microstructural evolution, and material behavior under load. The insights gained from this multi-scale and multi-technique approach contribute to the fundamental understanding of microstructural evolution in immiscible alloys and are valuable for tailoring the properties of structural materials for specific engineering applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Estimation Methodology to Evaluate Hypothetical Downwind Impacts from Fusion Plants

The continuing move toward establishing fusion systems for power generation and the associated research to that end is prompting examination of the potential health and safety impacts of such plants to the environment and human health. As many fusion facilities will have tritium inventories on site as part of the fusion fuel, evaluating the potential for downwind impacts from fusion facilities or power plants resulting from accident or routine emissions is a general requirement for assessing location and impacts to workers and the public. As part of siting considerations and permitting, the fusion facilities would be evaluated for potential for downwind concentration and dose impacts. For accident assessment scenarios, the downwind impacts are usually modeled as an instantaneous (or near-instantaneous) release of material transported following the wind. A range of meteorological conditions are usually assessed to determine a bounding case which results in a dose exceeding a specified threshold (e.g., 95 th or 99 th percentile; DOE 2015). This report provides initial estimates of the downwind dose impacts from a potential tritium release at a fusion power plant-relevant facility and identifies potential distances required to limit impacts to nearby population. This effort is meant to provide a bounding analysis and theoretical understanding of impacts of tritium releases for facilities subject to various environmental and atmospheric conditions. Using a Gaussian dispersion model to simulate a brief plume, downwind concentration and dose is projected for tritium oxide. Releases are assumed to consist entirely of tritium oxide due to the increased dose impacts from the oxide form relative to the elemental form of tritium. We also briefly identify how climatological conditions could potentially be used to support risk profile determination.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Modeling the effect of wind speed and direction shear on utility‐scale wind turbine power production

Abstract Wind speed and direction variations across the rotor affect power production. As utility‐scale turbines extend higher into the atmospheric boundary layer (ABL) with larger rotor diameters and hub heights, they increasingly encounter more complex wind speed and direction variations. We assess three models for power production that account for wind speed and direction shear. Two are based on actuator disc representations, and the third is a blade element representation. We also evaluate the predictions from a standard power curve model that has no knowledge of wind shear. The predictions from each model, driven by wind profile measurements from a profiling LiDAR, are compared to concurrent power measurements from an adjacent utility‐scale wind turbine. In the field measurements of the utility‐scale turbine, discrete combinations of speed and direction shear induce changes in power production of −19% to +34% relative to the turbine power curve for a given hub height wind speed. Positive speed shear generally corresponds to over‐performance and increasing magnitudes of direction shear to greater under‐performance, relative to the power curve. Overall, the blade element model produces both higher correlation and lower error relative to the other models, but its quantitative accuracy depends on induction and controller sub‐models. To further assess the influence of complex, non‐monotonic wind profiles, we also drive the models with best‐fit power law wind speed profiles and linear wind direction profiles. These idealized inputs produce qualitative and quantitative differences in power predictions from each model, demonstrating that time‐varying, non‐monotonic wind shear affects wind power production.

Energy & Fuels↗
DOE OSTI2024

Design, Fabrication and Testing of Surveillance Test Articles for MSR Materials Degradation Management

This report details the design, fabrication, and testing of surveillance test articles aimed at assessing material damage in reactor-relevant environments for effective degradation management. Two types of surveillance test articles with reduced sizes were developed based on design algorithms and finite element modeling: welded design and interlocking design. A furnace heating setup was adopted to apply multiple thermal cyclic loading profiles on the test articles with a temperature range of 500°C - 700°C, while the strain response was monitored using a digital image correlation technique. The testing results demonstrated the successful capturing of expected strain range for welded design while machining tolerance should be improved to engage strain coupling in the interlocking design. Mid-term (500 hours) and long-term (1500 hours) cyclic tests were conducted on welded test articles. A constant strain range of ~0.6% was observed at the specimen with testing under 500 hours, while a gradual decrease of strain at specimen was observed after 500 hours. Non-destructive evaluation through X-ray computed tomography confirmed the microcracks in the welds at specimen-driver joints after cyclic test that caused the strain change. Creep testing of the specimen after long-term cyclic test revealed a short creep life than expected. A multi-profile cyclic test was also conducted on a test article and demonstrated consistent strain response under different temperature ramp rates. The report also briefly discussed the challenges and future research efforts to advance test article development for material surveillance.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Prototype Modeling for a Light-Trapping Planar-Cavity Enclosed Particle Solar Receiver

Concentrating solar thermal (CST) systems present a promising avenue for affordable and reliable energy production. Solar receivers are key components that determine the efficiency and longevity of these systems. Particle-based solar receivers have emerged as a compelling alternative to traditional technologies, offering several advantages that address limitations in current CST systems. This is especially true as next-generation CST technologies target applications including electricity generation, thermochemical processes, and industrial process heat, many of which necessitate higher operating temperatures than current commercial molten salt systems. Molten-salt thermal energy storage (TES) systems, commonly used in CSP, face challenges related to freezing and corrosion. Particle-based TES systems, in contrast, do not experience these issues, as particles are stable at high temperatures, exceeding 1000 degrees Celsius. This capability allows for a wider range of applications, including those requiring higher temperatures for industrial processes and efficient electricity generation. A novel innovation in particle-based solar receiver technology is the light-trapping planar cavity receiver (LTPCR) configuration developed by NREL. The LTPCR design consists of small cavity-like structures using opaque planar surfaces, enabling efficient capture and absorption of solar energy. A high incident flux concentration at the cavity aperture is absorbed on the receiver walls, and subsequently transferred to particles on the inside of cavities. The particles flow through the system, forming a fluidized bed inside of the receiver panels, effectively capturing the absorbed solar heat. Air is used as a fluidizing medium in this process to enhance particle heat transfer and mixing. The effectiveness of this design lies in its ability to manage solar flux conditions and ensure high solar-to-thermal receiver efficiency. A 100-kW prototype is currently being tested at the King Saud University in Saudi Arabia to assess the receiver performance. A range of modeling analyses for the optical, thermal, and mechanical effects were conducted to assess the performance of the receiver under on-sun conditions. The solar flux resulting from the KSU heliostat field was modeled using NREL SolTrace software and produced up to 600 kW/m2 at the receiver aperture. The solar flux absorbed on the receiver walls was then used within a computational fluid dynamics (CFD) model to predict wall temperature distributions along with radiation and convection loss. A two-phase CFD model was developed for the fluidized bed of silica sand inside the receiver panels to predict local wall-to-particle heat transfer coefficients, particle temperature distributions, and outlet temperature of the particles. We have also conducted analyses to understand the thermomechanical behavior of these innovative enclosed light-trapping solar receivers optimized for particle heating. We used finite element analysis (FEA) to predict the receiver's performance using temperature distributions obtained from CFD and based on the resulting stress profiles, evaluated creep-fatigue damage with a goal of achieving a 30-year service life. Analysis showed a significant impact of the particle-to-wall heat transfer coefficients (HTCs) on receiver performance, with higher HTCs resulting in reduced stress and increased lifespan. For instance, when using Inconel 740H, increasing the HTC from 800 W/m2 K to 1400 W/m2 K increased the creep life from 4,000 hours to over 100,000 hours. This highlights the importance of understanding and optimizing heat transfer in the design of high-efficiency receivers.

14 SOLAR ENERGY↗
DOE OSTI2024

Element Formation in Radiation-hydrodynamics Simulations of Kilonovae

Abstract Understanding the details of r -process nucleosynthesis in binary neutron star merger (BNSM) ejecta is key to interpreting kilonova observations and identifying the role of BNSMs in the origin of heavy elements. We present a self-consistent, two-dimensional, ray-by-ray radiation-hydrodynamic evolution of BNSM ejecta with an online nuclear network (NN) up to a timescale of days. For the first time, an initial numerical relativity ejecta profile composed of the dynamical component and spiral-wave and disk winds is evolved including detailed r -process reactions and nuclear heating effects. A simple model for the jet energy deposition is also included. Our simulation highlights that the common approach of relating in postprocessing the final nucleosynthesis yields to the initial thermodynamic profile of the ejecta can lead to inaccurate predictions. Moreover, we find that neglecting the details of the radiation-hydrodynamic evolution of the ejecta in nuclear calculations can introduce deviations of up to 1 order of magnitude in the final abundances of several elements, including very light and second r -process peak elements. The presence of a jet affects element production only in the innermost part of the polar ejecta, and it does not alter the global nucleosynthesis results. Overall, our analysis shows that employing an online NN improves the reliability of nucleosynthesis and kilonova light-curve predictions.

Magistrelli, Fabio (ORCID:0009000509767851)↗
DOE OSTI2025

Orbit-averaging and deposition accuracy for runaway electron beams in hybrid kinetic-MHD simulations of the runaway plateau

We develop a new procedure that combines the kinetic orbit runaway electron code (KORC) and the NIMROD extended-magnetohydrodynamic code to simulate runaway electrons (REs) in the post-disruption plateau. KORC integrates guiding-center orbits, with a barycentric-based binary search strategy providing initial guesses for the Newton–Raphson logical-to-physical coordinate inversion, ensuring reliable particle-to-mesh mapping in NIMROD, whose fields remain static for the present study. Samples are drawn in accord with experimental parallel current profiles of RE beams during the plateau phase. Deposition in NIMROD is verified through comparison with a Python-based finite-element code that ensures periodicity in the poloidal direction and continuity at the magnetic axis. Accurate representation of near-axis fields requires finer mesh resolution to prevent under- and overshoots in current density from orbit inaccuracies. Yet, at a fixed particle count, increasing mesh resolution amplifies statistical noise in the deposited fields. An orbit-averaging method accumulates partial current deposits over multiple kinetic steps and reduces the statistical noise with little added computational cost. By coupling kinetic routines from KORC directly into the NIMROD codebase, these developments lay essential groundwork for future self-consistent KORC–NIMROD coupling.

Algorithms and data structure↗
DOE OSTI2026

The landscape of regulatory element evolution in a C4 perennial grass

Gene regulatory evolution is a well-known source of phenotypic diversity and adaptive evolution. Although cis-regulatory elements (CREs) play a vital role in gene expression evolution, the molecular evolution of CREs remains mostly unknown due to the difficulty in identifying and characterizing these functional elements. Comparative genomic analyses of noncoding DNA can be leveraged to identify conserved noncoding sequences (CNS), many of which may harbor functional CREs conserved by purifying selection. However, purely computational inference of CREs from putative CNS can be erroneous due to the complex genomic architecture in plants. One promising experimental approach to identify CREs is by profiling accessible chromatin regions (ACRs) that are often associated with the location of CREs. In this study, we use comparative genomics along with the profiling of ACRs to study the molecular evolution of putative functional noncoding regulatory regions in Panicoid grasses. We identified sets of CNS that varied in relationship to the degree of evolutionary divergence among the studied taxa, including identifying core-Panicoid-CNS. We augmented this analysis by profiling ACRs in Panicum hallii ecotypes using ATAC-seq. ACRs had low SNP density at the summit, harbored a high frequency of core-Panicoid-CNS, and were enriched with expression QTL. These data help to annotate the P. hallii genome for putative functional elements and suggest that a large proportion of these ACRs are evolving under purifying selection. Turnover in CNS and ACR between ecotypes of P. hallii identifies a small set of putatively divergent CREs that may underlie differences in gene regulation between genotypes from inland and coastal habitats. In summary, we profiled ACRs in Panicoid grasses and integrated this data with our putative CNS prediction framework, which provides unique insight into patterns of polymorphism and divergence in CREs in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗