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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.

Ahrendt, Steven R. [USDOE Joint Genome Institute (↗
DOE OSTI2024

Forward Modeling of Gamma Reaction History Signatures From Anticipated Deuterium-Tritium Filled MagLIF Implosions on Sandia’s Z-Machine

Nuclear reaction history measurements provide a bang time and burn width of Inertial Confinement Fusion (ICF) implosions and are essential for understanding implosion performance to constrain ICF capsule design. When fusion fuel contains Deuterium (D) and Tritium (T) gas, reaction history is informed by measuring the 16.75 MeV gamma rays generated from the D(T,γ) 5 He reaction. Such DT based reaction history measurements have not been made on the Magnetized Laser Inertial Fusion (MagLIF) platform on Sandia’s Z-Machine due to the lack of Tritium being used. The recent development of ICF implosions with tritiated fuel will open the possibility of measuring the gamma reaction history on the Z-Machine. A forward model of the Gamma Reaction History diagnostic on Z (GRH-Z) has been developed using the MCNP6.3 (Monte-Carlo N-Particle) radiation transport code. The model included the Z-Machine geometry of interest to characterize the impact of neutron induced gamma rays on the DT reaction history measurements. In addition, the impulse response functions of the GRH-Z diagnostic to understand the temporal response of the detector, and the minimum yields required to make a reaction history measurement were calculated. This approach also predicted that with T 2 gas doping of MagLIF implosions a reaction history may be made for high performance shots >8e12-2.4e13 depending on the chosen threshold for the detector, with a maximum signal to background ratio of 25%. It was found that for long duration ICF implosions that additional collimation will be needed to prevent the neutron induced gamma rays from modifying the shape of the measured DT reaction history curve.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

2025 Advances in NekRS: Supporting improved performance for nuclear applications

This report presents several 2025 advancements in NekRS, a high-fidelity spectral element CFD code developed at Argonne National Laboratory to support the NEAMS thermal-hydraulics program. The forthcoming v25 release consolidates several of these advances, adding new features for portability across heterogeneous GPU architectures, real-time in situ visualization, improved turbulence modeling, and conjugate heat transfer coupling. Over the past year, NekRS has demonstrated strong scalability and performance on DOE’s leading exascale platforms, including Aurora and Frontier, confirming its readiness for some of the largest and most complex simulations attempted to date. These achievements provide a powerful new platform for high-fidelity data generation, which in turn supports the development and validation of advanced closure models critical for reactor safety and design. Significant algorithmic innovations have also been introduced. A new global runtime h-refinement capability simplifies workflows by reducing mesh preparation burdens and enabling coarse-to-fine restarts. Building on this, a novel multigrid strategy was implemented to accelerate pressure and transport solves at scale, addressing long-standing bottlenecks in exascale CFD. Together, these developments improve both the efficiency and accessibility of high-fidelity simulations for reactor-relevant problems. Collectively, these enhancements represent a major step forward in simulation technology, positioning NekRS as a cornerstone of NEAMS efforts to enable accurate, efficient, and scalable high-fidelity analysis of advanced nuclear systems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Mountain Basin Controls on the Snow-to-Streamflow Signal: An AIC-Weighted Multiple Linear Regression Framework

A regression-based analysis quantifies how basin characteristics modulate the snow-to-streamflow signal. First, we use the ERA5-Land reanalysis gridded product (European Centre for Medium Range Weather Forecasts reanalysis 5 -Land component) for 4,655 hydrologic unit code - 10 (HUC10) mountain basins across the western United States (US) for water years 1987–2024. Linear regressions are performed for peak snow water equivalent (SWE) and annual streamflow for each mountain basin. Models use ordinary least squares in Python’s statsmodels package. After which, an Akaike Information Criterion (AIC)–weighted ensemble multiple linear regression (MLR) framework with 47 watershed traits is used to predict the linear regression coefficient of determination (r-squared) defining the ability of peak SWE to predict annual streamflow across all mountain basin. Predictor sets are constrained to avoid multicollinearity by excluding models with variance inflation factors (VIF) greater than 5. Mountain basin traits included in the MLR include seasonal climate, topography, vegetation type and structure, and bedrock geology. Accepted models are considered if their AIC is within 2.0 of the model with the minimum AIC, or best model. To compare predictor influence across acceptable models, we computed standardized regression coefficients. To evaluate structural redundancy among models, we constructed binary inclusion vectors for each acceptable model, denoting whether a predictor was present (1) or absent (0). Core predictor variables are defined as occurring in at least 67% of the acceptable models. For this regional analysis, only one model was found acceptable, with higher snow-to-streamflow translation (higher r-squared) occurring in colder mountain basins with higher relative winter precipitation, more snow accumulation and a lower fraction of annual precipitation that falls in the spring and summer. The second component of the data package uses previously published, high-resolution output from an integrated hydrological model of the East River watershed using the U.S. Geological Survey Groundwater and Surface water Flow model (GSFLOW, doi:10.15485/1998576). East River MLR expands upon the approach described above to explore the response of five streamflow metrics—annual streamflow, runoff efficiency, 7-day minimum flow, low-flow duration, and non-perennial stream fraction to snow system indicators including peak SWE, snow-covered area, snow disappearance date, and the fraction of basin area characterized by low-to-no snow, as well as seasonal precipitation and temperature, and annual hydrologic variables representing soil moisture, evapotranspiration (ET), the partitioning of incoming precipitation to evapotranspiration (ET/P), groundwater storage, and groundwater inflow to streams. MLR was done on all water years (P0: 1987-2024) and for each period as determined in the split analysis using pooled regression techniques (P1: 1987-2011 and P2: 2012-2024) to evaluate shifting predictor variable emphasis on streamflow generation. Results indicate that since 2012, peak SWE has lost statistical strength in its prediction of annual streamflow and runoff efficiency, and the indirect influence of spring temperature has emerged as critically important. Low-flow metrics remain largely influenced by soil moisture, vegetation water use and groundwater inflows with summer precipitation becoming a direct influence on minimum summer flow. Together, these data and Python-based analysis tools provide a framework for identifying the key watershed characteristics that control how streamflow responds to snow from year to year. The package also helps quantify uncertainty in statistical models and assess how snow–streamflow relationships vary across regions and over time. This dataset contains comma-separated values files (.csv), text files (.txt), python code files (.py), figure files (.png), and shapefiles (.cpg, .dbf, .prj, .sbn, .sbx, .shp, .xml). Further details on file contents and MLR execution can be found in the readme file and the FLMD files. Work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Ocpp 2.0.1. Interim Kpi Calculator

The project is split into four pieces. The first is a raw OCPP log parser. The second is a file splitter. The third is a message parser. The final piece is the Interim KPI calculator. The OCPP log parser was created from two different formats of raw OCPP 2.0.1 data. Its intended purpose is to extract device IDs and OCPP event messages from nontabular text logs. The parser looks for specific substrings in the logs to identify which of the two "standards" it should select from. The KPI generator does not perform any of its calculations in parallel. Instead, we opt for a naive batching approach. The splitter takes the file generated from the parser and creates many smaller files for each of the device IDs in the dataset. This allows the pandas queries in the log formatter to be iterate over a significantly smaller slice of data, increasing performance significantly. The message parser step takes messages from each of the files (containing distinct device IDs) and breaks the message out into pieces. The final result is a file with different columns specifying different attributes of the JSON message. The file is an aggregation of all different devices. This is the most complex portion of the code. The KPI calculator takes the parsed messages, as a single file, and calculates the KPI from that data. An excel file is produced with four sheets. These contain the metrics for Session Success, Charge Start Success, Charge End Success, and Charge Start Time. It includes the metrics for the different equations in the Interim KPI Implementation Guide as well as a weighted sum of the different equations for each KPI (excluding Charge End Success and Charge Start Time).

Quinn, Casey↗
DOE OSTI2025

sourcePy

Pollutant source identification techniques (of which there are many variations) are either locked behind researchers writing their own code for each use case or GUI platforms that are easy to use but inflexible and opaque. The Python package sourcePy brings together many of the pollutant source identification algorithms, giving the user full control out of the box. It aims to create a platform for source identification experiments where the full analysis from beginning to end can be done in Python, with a level of specificity in design that isn't available in the GUI options. sourcePy provides users with a few key features: -A Python interface with HYSPLIT, which can be used to generate trajectories and concentration plumes -Several Python classes which standardize the preparation and processing of data related to source identification experiments -Example scripts and notebooks that allow even new python users to get started with their own experiments quickly -Visualization methods

Arseneau, Isaac [Oak Ridge National Laboratory (OR↗
DOE OSTI2024

Debiasing with Diffusion: Probabilistic Reconstruction of Dark Matter Fields from Galaxies with CAMELS

Abstract Galaxies are biased tracers of the underlying cosmic web, which is dominated by dark matter (DM) components that cannot be directly observed. Galaxy formation simulations can be used to study the relationship between DM density fields and galaxy distributions. However, this relationship can be sensitive to assumptions in cosmology and astrophysical processes embedded in galaxy formation models, which remain uncertain in many aspects. In this work, we develop a diffusion generative model to reconstruct DM fields from galaxies. The diffusion model is trained on the CAMELS simulation suite that contains thousands of state-of-the-art galaxy formation simulations with varying cosmological parameters and subgrid astrophysics. We demonstrate that the diffusion model can predict the unbiased posterior distribution of the underlying DM fields from the given stellar density fields while being able to marginalize over uncertainties in cosmological and astrophysical models. Interestingly, the model generalizes to simulation volumes ≈500 times larger than those it was trained on and across different galaxy formation models. The code for reproducing these results can be found athttps://github.com/victoriaono/variational-diffusion-cdm✎.

Astronomy & Astrophysics↗
DOE OSTI2024

Dark Radiation Constraints on Heavy QCD Axions

The naturalness problem of PQ symmetry motivates study of the heavy QCD axion, with masses m a > 1 MeV generated at scales above the QCD scale, and low values of the PQ symmetry breaking scale, ƒ a . We compute the abundance of such axions in a model-independent way, assuming only that they freeze-out after reheating from inflation, and are not subsequently diluted by new physics. If these axions decay between neutrino decoupling and the last scatter era of the Cosmic Microwave Background (CMB), they dilute the neutrinos and their abundance is constrained by CMB measurements of the energy density in dark radiation, N eff . We accurately compute this bound using a numerical code to evolve the axion momentum distribution, including many key processes and effects previously ignored. We assume that the only relevant axion decays are to final states involving Standard Model particles. We determine regions of (m a , ƒ a ) that will give a signal in N eff at CMB Stage 4 experiments. We similarly compute the N eff bound and CMB Stage 4 signal for heavy axions that can decay to light mirror photons. Finally, we compute the bounds on heavy axions with mass below 1 MeV that decay after the era of CMB last scatter, from their contribution to cold or hot dark matter or N eff at this era.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Uranium measurements in the field using high-resolution cadmium zinc telluride detectors

A new generation of cadmium zinc telluride (CZT) detectors has become available and is being evaluated by the International Atomic Energy Agency (IAEA) for safeguards verifications in the field. The new CZT detector, model M400, is a room temperature spectrometer manufactured by H3D, Inc. The M400 demonstrates superior energy resolution, effective isotope identification capabilities, and convenient usability features when tested in a controlled laboratory environment. These characteristics define the M400 as a potential platform for IAEA field detection applications, which could become suitable for nuclear material characterization (e.g., enrichment verification) and nuclear safeguards missions. The capabilities of gamma spectrometry codes including Fixed energy, Response function Analysis with Multiple efficiencies (FRAM) from Los Alamos National Laboratory, CZT for Uranium (CZTU) from Lawrence Livermore National Laboratory, and Gamma Detector Response and Analysis Software (GADRAS) from Sandia National Laboratories were adapted for M400 spectra, and the performance of the codes has been validated. This was reported in a prior work. To further validate the performance of the high-energy resolution CZT detector and the isotopic analysis codes, a field measurement campaign consisting of uranium hexafluoride (UF 6 ) cylinder measurements was conducted at a fuel fabrication facility. A total of 34 Type 30B cylinders containing UF6 were measured using three different M400 CZT detectors. Each detector was outfitted with a custom rectangular collimator and shield made out T-Flex®, a tungsten-impregnated polymer. Measurements were performed at three different locations of the cylinder, ensuring that the measurement geometry satisfied the infinite thickness criterion. The spectra from the M400 CZT were analyzed using the code General Enrichment Meter (GEM). For analyzing the gamma-ray spectra from UF 6 cylinder, the GEM code is the appropriate tool since it relies only on the gamma-ray emissions from 235 U and not from other isotopes. Results from the spectral analysis were compared with the known abundance of 235 U in the cylinders, as well as with the International Target Values 2020 (ITV2020). The suitability of the different underlying techniques used by the various codes for UF 6 analysis is discussed. The challenges of measuring UF 6 contained in cylinders and mitigation strategies are highlighted.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Laser wavelength dependence of particle acceleration mechanisms in high intensity laser–solid density plasma interactions

We investigate the generation of relativistic electrons and the subsequent ion acceleration due to target-normal sheath acceleration when ultra-intense (⁠ I > 10 18 W/cm 2 ⁠) short pulse (⁠ τ L < 10ps⁠) lasers are incident onto solid density targets as laser wavelength is varied. Scaling laws for the hot electron temperature, T hot ⁠, and the maximum ion energy, E max ⁠, are recast as a function of laser wavelength. These predictions are compared to results from particle-in-cell computer simulations in a variety of geometries, including cases where realistic plasma density profiles as determined by a radiation hydrodynamics code are used. It is found that the wavelength dependence observed in simulation is less pronounced than what is predicted from the well-established scaling laws. An assessment of how switching to longer laser wavelengths, specifically 2 μm Tm:YLF technology, would impact current high energy density science applications and diagnostics is made.

Electromagnetism↗
DOE OSTI2024

Design and modeling of indirectly driven magnetized implosions on the NIF

The use of magnetic fields to improve the performance of hohlraum-driven implosions on the National Ignition Facility (NIF) is discussed. The focus is on magnetically insulated inertial confinement fusion, where the primary field effect is to reduce electron-thermal and alpha-particle loss from the compressed hotspot (magnetic pressure is of secondary importance). We summarize the requirements to achieve this state. The design of recent NIF magnetized hohlraum experiments is presented. These are close to earlier shots in the three-shock, high-adiabat (BigFoot) campaign, subject to the constraints that magnetized NIF targets must be fielded at room-temperature, and use ≲1 MJ of laser energy to avoid the risk of optics damage from stimulated Brillouin scattering. We present results from the original magnetized hohlraum platform, as well as a later variant that gives a higher hotspot temperature. In both platforms, imposed fields (at the capsule center) of up to 28 T increase the fusion yield and hotspot temperature. Integrated radiation-magneto-hydrodynamic modeling with the Lasnex code of these shots is shown, where laser power multipliers and a saturation clamp on cross-beam energy transfer are developed to match the time of peak capsule emission and the P2 Legendre moment of the hotspot x-ray image. The resulting fusion yield and ion temperature agree decently with the measured relative effects of the field, although the absolute simulated yields are higher than the data by 2.0−2.7×. The tuned parameters and yield discrepancy are comparable for experiments with and without an imposed field, indicating the model adequately captures the field effects. Self-generated and imposed fields are added sequentially to simulations of one BigFoot NIF shot to understand how they alter target dynamics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Effect of controlled magnetic island bifurcation on electron diffusion

Magnetic islands strongly influence cross-field electron transport in magnetized plasmas. In particular, bifurcations of the island topology modify the number and location of O-points, X-points, and separatrix boundaries, thereby altering diffusion pathways. In recent DIII-D experiments, external magnetic perturbations were used to rotate and periodically bifurcate the island on the q = 2 surface, causing a switchback between a q = 2/1-dominated structure and a narrower q = 4/2-dominated structure. To investigate how this topological change affects electron transport, we employ the field line tracing code TRIP3D with an implemented collisional operator. Thermal, tracer electrons launched from O-points, X-points, and outside separatrix boundaries reveal distinct diffusion regimes, including classical, subdiffusive, and superdiffusive behavior, depending on both the dominant island mode and launch location. These results suggest that island bifurcation can alter electron diffusion across rational surfaces, with direct implications for particle confinement. While the present work emphasizes diffusion as a general framework, the findings provide insight into the conditions under which electron trapping into an island or stochastization of the island's separatrix can enable additional mechanisms, such as the generation of energetic electrons.

DIII-D↗
DOE OSTI2026

Pulsed-Neutron Experiments at the Inherently Safe Subcritical Assembly

The pulsed neutron technique is a powerful, dynamic method to assay the reactivity of a multiplying system. This work presents the novel application of the pulsed neutron technique to the Inherently Safe Subcritical Assembly, an experimental configuration accepted by the International Criticality Safety Benchmark Evaluation Project Handbook. The experiments were replicated with COG11.3, a continuous-energy Monte Carlo code. The pulsed neutron data were analyzed using the Sjöstrand and Gozani area-ratio methods and by extracting the prompt neutron decay constant. Subsequent static k-eigenvalue and 𝛼-eigenvalue simulations were also performed for the same configurations. Neutron detector dead-time effects from the experiments were corrected using the Backwards Extrapolation Method and shown to have a negligible impact on the estimated reactivities. The results highlight that capturing time-dependent effects like delayed neutron precursor buildup are essential to accurately reproduce experimental results. They also highlight the importance of shielding the detectors from generator source neutrons in deeply subcritical configurations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

PV Generation and Load Forecasting for Adjuntas PR Community Microgrids

Existing frameworks to forecast time-series photovoltaic (PV) output power and consumer load for microgrid operations and controls assume a near-continuous availability of real-time input features from the field assets such as PV inverters, energy meters, and weather station. These incoming data points are used to periodically retrain models and update forecast snapshots over a moving horizon window, be it one hour-ahead, one-day ahead, or one-week ahead. However, such frameworks are not resilient to disruptions in data availability caused by losses in communications between the field sensors and data loggers. Hence, there is a need for programs that assume no availability of real-time microgrid asset data and still make reliable forecasts that can be used for decision-making. Such programs would be apt to function in extreme weather events such as hurricanes and would use lightweight recursive time-series models to independently forecast solar irradiance and ambient temperature, then compute PV power from those forecasts, as well as independently forecast consumer load. The codebase performs forecasting for the scenario of when the microgrid does not have a reliable access to forecasts or real-time observations of solar irradiance (I) and ambient temperature (AT) and load (Load) to be able to adequately forecast, in real-time, the PV power production or a business' load. In this case, using historical values of PV power and load, a univariate forecasting of generation and consumption are respectively made. The use-case in particular has two sub-scenarios: one, a normal 7-day ahead forecast where the unavailability of real-time data is assumed due to infrastructure issues such as loss of communication or sensor maintenance or service downtimes. Whereas a hurricane-caused unavailability of real-time data requires a second model trained specifically on historical hurricane days to be able to capture the extreme day behavior of generation in particular, and load if applicable. A gradient boosted regression tree comprises an ensemble of additive models that map between the input of historical values (be it irradiance, temperature, or load) and their corresponding output forecasts of a given horizon such that the individual learner predictions are summed up over the total number of such learners in the ensemble to produce an aggregate forecast. A weighting mechanism is applied to the training data in each iteration, where actual and forecast values are compared to penalize incorrect forecasts by increasing the weight and reducing it to reward correct forecasts. The code's benefits are that it: (a) accounts for a contingency where communication loss renders newly measured real-time data unavailable for model tuning and snapshot updates; (b) presents blind forecasting that recursively determines the next time-step value in a horizon using the forecast of the same attribute from a prior step; and (c) employs lightweight models that, once trained, can reliably generalize for different horizons, which make them suitable for enhancing the resilience of field microgrids prone to extreme events that encounter disruptions to data availability.

Sundararajan, Aditya [Oak Ridge National Laborator↗
DOE OSTI2025

Laboratory time series moisture manipulative experiment from sediment across San Antonio, Texas: time series aerobic respiration and geochemistry

This dataset supports a broader study examining the effects of wetting and drying on hyporheic zone respiration. The dataset provides data generated from a laboratory moisture manipulation experiment. The contents include time series aerobic respiration and moisture; dissolved oxygen; sediment geochemistry data; and field metadata (including qualitative information on instream and river corridor characteristics). Samples were collected as part of the WHONDRS Allison Veach collaboration (AV1). The data package associated with the AV1 study is available at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/2529428. AV1 sampling occurred across 7 perennial and 7 intermittent streams in San Antonio, Texas. Each stream/site was visited both in summer during base flow (July-September 2023) and winter during peak flow (January-February 2024). This study uses subsamples from a subset of AV1 samples. The original field samples were labeled as AV1_###. Subsequent subsamples for this study were labeled as EV_###. The labels from the field samples and the EV subsamples can be mapped directly based on the digits following the prefix and underscore (i.e., EV_001 is a subsample from AV1_001). See the critical details section below for more details on sample naming. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) field protocol; and a (6) a subfolder with sediment sample data from the incubation experiment. The sample data subfolder contains (1) effect size; (2) iron (II); (3) gravimetric moisture; (4) respiration rates; (5) raw dissolved oxygen values and plots; (6) specific conductance; (7) pH; (8) temperature; (9) a summary containing mean, median, and standard deviation values of each data type for each treatment (wet and dry); and (10) methods codes. All files are .csv or.pdf.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Vimercati, Lara↗
DOE OSTI2026

From chromatin to crop: epigenetic innovations in bioenergy systems

Energy crops encompass a diverse array of plant species cultivated primarily as a source of biomass for energy generation and biofuel production. As such, they play a pivotal role in the transition to sustainable energy systems. However, their productivity is often limited by environmental stresses, nutrient availability, and the need for optimized yield. While traditional breeding and genetic engineering have driven improvements, challenges such as narrow genetic diversity, long development cycles, trait instability, and unexpected gene interactions remain. Epigenetics offers a largely untapped opportunity to overcome these constraints by regulating gene expression through mechanisms that are dynamic, finely tuned, and responsive to environmental and developmental cues. Epigenetic modifications including DNA methylation, histone post-translational changes, and small non-coding RNAs influence nearly all aspects of plant development and physiology, including traits central to bioenergy crops. While these mechanisms are well characterized in model species such as Arabidopsis thaliana, they remain underexplored in many purpose-grown energy crops. This review summarizes the current state of knowledge of epigenetic regulation in bioenergy species, explores how these mechanisms can be leveraged to enhance crop resilience and productivity, and identifies gaps in our understanding. By characterizing epigenetic mechanisms and harnessing epigenetic variation, we can expand the toolkit for developing resilient, high-yielding bioenergy crops to meet future environmental and energy demands.

09 BIOMASS FUELS↗
DOE OSTI2025

Quantum Simulation of Molecular Dynamics Processes─A Benchmark Study Using a Classical Simulator and Present-Day Quantum Hardware

Here, we explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this issue, we designed a shallower quantum circuit for preparing a Gaussian-like initial wave packet, which improves the performance of real hardware. Next, quantum circuits are implemented to apply the kinetic and potential energy operators for the evolution of a wave function over time. The results of our modeling on classical emulators of quantum hardware agree perfectly with the results obtained using the traditional (classical) methods. This serves as a benchmark and demonstrates that the quantum algorithms and Qiskit codes we developed are accurate. However, the results obtained on the actual quantum hardware available today, such as IBM’s superconducting qubits and IonQ’s trapped ions, indicate large discrepancies due to hardware limitations. This work highlights both the potential and challenges of using quantum computers to solve fundamental quantum molecular dynamics problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗