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

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗
DOE OSTI2024

Budget-Constrained Sizing of Renewable and Energy Storage Systems for Farm-Scale Ammonia Production Within the Food-Energy-Water Nexus

In the transition toward sustainable agriculture, farms have emerged as eco-friendly pioneers, harnessing clean hybrid wind and solar systems to improve farm performance. A concern in this paradigm is the effective sizing of renewable energy systems to ensure optimal energy use within budget considerations. This research focuses on optimizing renewable energy sizing in small-scale ammonia production to meet specific farm demands and enhance local resilience, emphasizing the interplay between environmental and economic factors. These findings promise increased energy efficiency and sustainability in this innovative agricultural sector. Additionally, our approach considers small-scale ammonia plant needs and the dynamic relationships between ammonia, water, and farm demands. Simulations demonstrate substantial cost savings in farm electricity consumption. Specifically, scenarios with renewable energy integration in the farm can reduce at least 13% electricity cost compared to a grid-dependent system in the 15-year simulation.

ammonia↗
DOE OSTI2025

The Thermococcales as a model system: historical perspectives and emerging tools

Thermococcales are among the most widely studied hyperthermophilic Archaea and have become key models for understanding life at extreme temperatures. Early work in the 1980s culminated in the isolation of novel Thermococcales species from hydrothermal vents that grew rapidly, tolerated extreme heat, and metabolized diverse substrates, making them uniquely amenable for laboratory studies. Their thermostable enzymes and emerging genetic tools facilitated detailed investigations of core processes such as DNA replication, repair, and transcription under conditions that challenge most life forms. These practical advantages, together with the accumulation of tools and protocols, cemented the role of Thermococcales as a model system. Here, we recount how chance discoveries, environmental adaptations, and experimental practicality intersected to establish Thermococcales as a central model for studying archaeal biology and extremophile physiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

UT-GOM2-2 Preliminary Report: Terrebonne Basin Northern Gulf of Mexico, 30 July-28 September 2023

In the summer and fall of 2023, the Gulf of Mexico Deepwater Hydrate Coring Expedition (UT-GOM2-2) drilled, cored, made downhole measurements, and analyzed samples from the seafloor to the base of the gas hydrate stability zone in one location (Site H, WR313) in the Terrebonne basin, deepwater Gulf of Mexico. Analyses of data and samples from the expedition will inform biological, geochemical, and geomechanical models to constrain the role of gas hydrates in the carbon cycle and the potential for gas hydrates as an energy resource. Pressure and conventional cores were collected continuously to a depth of 155.1 meters below the seafloor (mbsf). At deeper depths, cores were taken periodically from hydrate-bearing sands and their bounding muds to a total depth of 861.3 mbsf. 162.6 m of conventional core and 54.8 m of pressure core were obtained. Twelve temperature measurements were made between 27.1 and 144.5 mbsf to determine the geothermal gradient. At the seafloor, more than 4 m of sandy silt of unknown origin was encountered. Beneath this sand, to a depth of ~200 mbsf, the section was composed of interbedded mud and biogenic carbonate ooze. The biogenic ooze correlated to low density and high porosity intervals observed in the previously acquired logging while drilling (LWD) data and as measured. Calcareous nannofossil biostratigraphy constrains the entire record to the Pleistocene (< 0.91 million years) with a pronounced increase in sedimentation rate with depth. Beneath 200 mbsf, the section was predominantly composed of mud with two thicker, hydrate-bearing coarse-grained intervals, which are commonly known as the Blue and Orange sands. The dissolved gas concentration was quantified from pressure cores. In the shallow section, dissolved methane concentration increased below the sulfate-methane transition zone (SMTZ) and reaches saturation (the limit of solubility for methane) at 147 mbsf. Gas expansion was very common in conventional and depressurized pressure (conventionalized) cores below the SMTZ. At deeper depths, the methane concentration within muds bounding the Blue and Orange reservoirs was generally found to be less than saturation. The dissolved and hydrate gas composition is consistent with a microbial source, containing greater than 99.99% methane and only trace concentrations of ethane, propane, and butane. The methane to ethane ratio (C 1 /C 2 ) and the methane to ethane plus propane (C 1 /(C 2 +C 3 )) decrease with depth down to at least 678 mbsf, mainly driven by the increase in ethane with depth. It is unclear if this trend continues through the Orange sand interval. The δ 13 C isotopic signature of methane ranges between -69.9 and -78.5 ‰ Vienna Pee Dee Belemnite (VPDB). Pressure core recovery of all sandy intervals was poor. However, pressure core logs of the Orange sand show intervals of low density and high velocity, which are indicative of high hydrate saturation. One core from within the Orange sand was composed of interbedded graded sandy silt and mud. The sandy silts from this core are composed of mainly quartz and feldspar with some lithics. Most of the recovered pressure core samples are maintained at near in-situ pressure and temperature (within the hydrate stability field) at the University of Texas Pressure Core Center awaiting analysis. In the shallow section, samples will be used to determine the flux of organic carbon through the basin system, find the rate at which that carbon was consumed, and understand the microbial population responsible for these processes. In the deeper section, samples from in and around the hydrate reservoirs will be used to determine the petrophysical properties of the reservoir and bounding seals in these systems.

03 NATURAL GAS↗
DOE OSTI2025

Expedition UT-GOM2-2 Summary

In the summer and fall of 2023, the University of Texas (UT) Deepwater Hydrate Coring Expedition (UT-GOM2-2) drilled, cored, made downhole measurements, and analyzed samples from the seafloor to the base of the gas hydrate stability zone at Site H, in the Walker Ridge Protracted Area Block 313 (Site H, WR313), in the Terrebonne Basin, deepwater Gulf of America (Gulf of Mexico). Analyses of data and samples from the expedition will inform biological, geochemical, and geomechanical models to constrain the role of gas hydrates in the carbon cycle and the potential for gas hydrates as an energy resource.

03 NATURAL GAS↗
DOE OSTI2024

Quantum-enhanced photoprotection in neuroprotein architectures emerges from collective light-matter interactions

Background Superradiance is the phenomenon of many identical quantum systems absorbing and/or emitting photons collectively at a higher rate than any one system can individually. This phenomenon has been studied analytically in idealized distributions of electronic two-level systems (TLSs), each with a ground and excited state, as well as numerically in realistic photosynthetic nanotubes and cytoskeletal architectures. Methods Superradiant effects are studied here in idealized toy model systems and realistic biological mega-networks of tryptophan (Trp) molecules, which are strongly fluorescent amino acids found in many proteins. Each Trp molecule acts as a chromophore absorbing in the ultraviolet spectrum and can be treated approximately as a TLS, with its 1 L a excited singlet state; thus, organized Trp networks can exhibit superradiance. Such networks are found, for example, in microtubules, actin filaments, and amyloid fibrils. Microtubules and actin filaments are spiral-cylindrical protein polymers that play significant biological roles as primary constituents of the eukaryotic cytoskeleton, while amyloid fibrils have been targeted in a variety of neurodegenerative diseases. We treat these proteinaceous Trp networks as open quantum systems, using a non-Hermitian Hamiltonian to describe interactions of the chromophore network with the electromagnetic field. We numerically diagonalize the Hamiltonian to obtain its complex eigenvalues, where the real part is the energy and the imaginary part is its associated enhancement rate. We also consider multiple realizations of increasing static disorder in either the site energies or the decay rates. Results We obtained the energies and enhancement rates for realistic microtubules, actin filament bundles, and amyloid fibrils of differing lengths, and we use these values to calculate the quantum yield, which is the ratio of the number of photons emitted to the number of photons absorbed. We find that all three of these structures exhibit highly superradiant states near the low-energy portion of the spectrum, which enhances the magnitude and robustness of the quantum yield to static disorder and thermal noise. Conclusion The high quantum yield and stable superradiant states in these biological architectures may play a photoprotective rolein vivo, downconverting energetic ultraviolet photons—absorbed from those emitted by reactive free radical species—to longer, safer wavelengths and thereby mitigating biochemical stress and photophysical damage. Contrary to conventional assumptions that quantum effects cannot survive in large biosystems at high temperatures, our results suggest that macropolymeric collectives of TLSs in microtubules, actin filaments, and amyloid fibrils exhibit increasingly observable and robust effects with increasing length, up to the micron scale, due to quantum coherent interactions in the single-photon limit. Superradiant enhancement and high quantum yield exhibited in neuroprotein polymers could thus play a crucial role in information processing in the brain, the development of neurodegenerative diseases such as Alzheimer’s and related dementias, and a wide array of other pathologies characterized by anomalous protein aggregates.

Physics↗
DOE OSTI2026

The Q 10 of in situ microbial soil respiration varies with mean annual temperature, precipitation, pH, and plant cover: a meta-analysis and spatial prediction of Q 10

The temperature sensitivity of soil microbial respiration, commonly quantified using the Q 10 coefficient, is a key parameter in carbon cycle models. Uncovering how environmental factors affect in situ Q 10 values can therefore provide critical insight into potential shifts in global carbon stocks under climate change. We collected data from previously published field experiments that measured soil microbial respiration across a range of temperatures. We hypothesized that the Q 10 coefficient of in situ soil microbial respiration would vary based on environmental factors including mean annual temperature (MAT), mean annual precipitation (MAP), plant cover type, pH, soil C:N, and latitude. Linear regression revealed that Q 10 correlates negatively with MAT and MAP and positively with pH and absolute latitude. Additionally, average Q 10 varied significantly across different plant cover types; it was highest in mountain grasslands and lowest in tropical moist forests. Variation in microbial Q 10 across environmental factors may arise from underlying mechanisms such as enzyme kinetics, substrate availability and complexity, and microbial adaptation. To capture patterns in Q 10 more comprehensively, we developed a multiple linear regression model of Q 10 based on the most individually significant environmental drivers and applied it to public datasets to generate a global map of predicted Q 10 . Q 10 was higher in high-latitude and high-altitude regions, where large permafrost carbon stores are vulnerable to thawing and decomposition. We also compared fits between the Q 10 equation and a model produced from macromolecular rate theory (MMRT). We found that the MMRT model had the superior fit and may be better suited to model temperature sensitivity of complex biological reactions. Overall, our results emphasize that relationships between microbial Q 10 and environmental variables should be accounted for in climate models. Incorporating these variations in the Q 10 parameter, rather than using a fixed value, will help predict whether CO 2 emissions will be buffered or exacerbated by soil microbial respiration under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Rapid Design and Engineering of Smart and Secure Microbiological Systems (Final Report)

The design and application of successfully engineered biosystems requires an understanding of how engineered microbes will interact with other organisms – either as one-on-one competitors or in the context of microbial consortia. Engineering microorganisms from first principles for non-laboratory, environmental applications is inherently challenging because: (1) engineered systems tend to quickly revert back to their wild-type behaviors; and (2) these systems typically pay a price in reduced fitness, making them uncompetitive against invasive contaminating species (i.e., metabolic burden). For this project, we used a synthetic biology-based strategy to investigate the organization, control, stabilization, and destabilization of natural and engineered microbes. This approach enabled development of (1) single-strain systems capable of detecting and responding to target organisms in the environment; (2) a pipeline for refining and engineering biological constructs in new, non-model host organisms; and (3) improved systems for rapidly designing, engineering, and assaying new biological modules. This coupled approach to safeguard system design is predictable and portable across bacterial species and is focused on microbes that are part of the beneficial plant microbiome. A long-term goal beyond the proposed research is to enable the rational engineering of microbial communities based on first principles of biological design that mimic the smart performance of microorganisms observed in natural systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗
DOE OSTI2026

A standardized workflow for kinetic metabolic model curation and dissemination

Kinetic metabolic models provide invaluable insights into cellular metabolism, supporting applications in synthetic biology, metabolic engineering, and systems biology. However, reproducibility and utility of these models hinge on clear and rigorous documentation, standardized annotation, and accessible visualization. This paper presents a workflow for building, annotating, visualizing, and sharing kinetic metabolic models. Our method integrates community standards and open-source tools to ensure reproducibility, interoperability, and user accessibility. This procedure enables researchers to produce reusable and well-documented kinetic models, advancing their role as powerful tools in metabolic research.

Cook, Margaret [Univ. of Washington, Seattle, WA (↗
DOE OSTI2026

Crop models: integrating systems from the molecular to global for agricultural productivity and sustainability

Mathematical models that simulate crop growth in response to environmental conditions and management practices are essential tools for exploring agriculture-based strategies to address food security and environmental sustainability challenges. Early applications of crop models focused on supporting farmers in making management decisions. Applications have since expanded to estimating future impacts on local and global food production from changing climates. Emerging applications of crop models aim to leverage how these models integrate plant processes across biological scales to identify engineering or breeding strategies that account for environmentally-responsive dynamics at field scales and for exploring solutions to improve sustainability. In this review, we highlight recent studies across these four broad application areas and highlight potential future directions for the crop modeling field.

Piao, Ximin [Univ. of Illinois at Urbana-Champaign↗
DOE OSTI2026

Computationally efficient Bayesian estimation of graphical networks for omics data

Graphical networks are useful, widely-used modeling approaches to represent complex biological processes with biological measurements generated by platforms such as mass spectrometry. Bayesian analyses of graphical networks for omics data have several advantages over their frequentist counterparts, such as the inclusion of prior knowledge in the estimation of models. However, Bayesian approaches to date have only been feasible for data with a couple hundred biomolecules due to prohibitive computational time, but omics data often contains tens of thousands of biomolecules. Here, we present and illustrate a more computationally efficient approach named BPlane (Bayesian PseudoLikelihood-based Algorithm for Network Estimation) to extend Bayesian modeling capabilities for larger-sized datasets, such as most untargeted proteomics data. Via simulation, we demonstrate that BPlane produces substantial computational savings over a current state-of-the-art Bayesian algorithm while maintaining competitive edge detection accuracy. On a SARS-CoV2 proteomics data with 7000 proteins, the competing algorithm takes three times as long to complete the first iteration as BPlane takes to converge after over 100 iterations.

EM algorithm↗
DOE OSTI2026

Data from a four-day long microcosm experiment addressing the destabilization of artificial mineral-associated organic matter by model root exudates embedded in a soil matrix from the Rocky Mountain Biological Laboratory (Gothic, CO, USA), 2019

This dataset provides data collected during a four-day long laboratory soil microcosm experiment testing the efficacy of root exudate-driven mineral-associated organic matter destabilization. This dataset contains four data files in comma-separate values (*.csv). The files provide the metadata and the experimental results on microbial respiration, MAOM-derived respiration, and sequential mineral-extractions. This data was used to produce the figures in Bölscher et al., 2026. The results of the experiment can be found in the open access article Bölscher et al., 2026 (https://doi.org/10.1016/j.soilbio.2026.110276). Abstract: Mineral-associated organic matter (MAOM) is often considered stable, but root exudates can destabilize MAOM via various pathways. Theory and model system studies suggest that direct MAOM destabilization by strong ligands, like oxalic acid, or reducing agents, like catechol, is more effective than indirect, microbial-mediated MAOM destabilization, stimulated by less reactive compounds like glucose. Here, we demonstrate that the presence of a soil matrix alters the efficacy of exudate-driven MAOM destabilization pathways. Glucose and catechol destabilized significantly greater amounts of MAOM from ferrihydrite and aluminum hydroxide (Al (OH)3) embedded in a soil matrix than oxalic acid. Our findings indicate that indirect, microbial-mediated MAOM destabilization may play a larger role than direct MAOM destabilization in soil environments.

Destabilization↗
DOE OSTI2024

Machine Learning Driven Sensitivity Analysis of E3SM Land Model Parameters for Wetland Methane Emissions

Methane (CH 4 ) is globally the second most critical greenhouse gas after carbon dioxide, contributing to 16%–25% of the observed atmospheric warming. Wetlands are the primary natural source of methane emissions globally. However, wetland methane emission estimates from biogeochemistry models contain considerable uncertainty. One of the main sources of this uncertainty arises from the numerous uncertain model parameters within various physical, biological, and chemical processes that influence methane production, oxidation, and transport. Sensitivity Analysis (SA) can help identify critical parameters for methane emission and achieve reduced biases and uncertainties in future projections. This study performs SA for 19 selected parameters responsible for critical biogeochemical processes in the methane module of the Energy Exascale Earth System Model (E3SM) land model (ELM). The impact of these parameters on various CH 4 fluxes is examined at 14 FLUXNET- CH 4 sites with diverse vegetation types. Given the extensive number of model simulations needed for global variance-based SA, we employ a machine learning (ML) algorithm to emulate the complex behavior of ELM methane biogeochemistry. We found that parameters linked to CH 4 production and diffusion generally present the highest sensitivities despite apparent seasonal variation. Comparing simulated emissions from perturbed parameter sets against FLUXNET-CH 4 observations revealed that better performances can be achieved at each site compared to the default parameter values. This presents a scope for further improving simulated emissions using parameter calibration with advanced optimization techniques.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

A Unidirectional Two-Compartment Neuron Circuit with On-chip STDP learning

Most neuromorphic chips implement the single-compartment point neuron model where synapse circuits connect directly to a leaky integrate and fire (LIF) soma circuit. However, when using a biologically plausible soma circuit (e.g., Hodgkin-Huxley neuron model), an interface circuitry, such as a current conveyor circuit, is needed to transmit synaptic current to the soma circuit. This is especially true for ultra-low power neuron circuits, where membrane capacitance is on the order of 20 fF. This need for an interface circuit arises because the parasitic capacitance and leakage current caused by fabrication mismatch and second-order effects of the output transistors in the synapse circuits can disturb the spiking dynamics of the soma circuit if connected without an interface. Using an interface circuit to isolate the soma’s membrane capacitor from synapses resolves this issue. We propose to use a unidirectional resistor (a transconductance circuit) to connect the synapse and soma circuits instead of conventional current conveyor circuits. Using a biologically plausible spike pattern detection model, we show that the on-chip spike-timing-dependent plasticity (STDP) learning performance of the proposed unidirectional two-compartment neuron circuit is similar to a single-compartment circuit (with a current conveyor as an interface) and additionally, it is more power-efficient and biologically plausible. The chip is fabricated in the Taiwan Semiconductor Manufacturing Company (TSMC) 250 nm technology node and comprises a single neuron circuit.

Gautam, Ashish [ORNL]↗
DOE OSTI2025

QM Investigation of Rare Earth Ion Interactions with First Hydration Shell Waters and Protein-Based Coordination Models

Here, conventional methods for extracting rare earth metals (REMs) from mined mineral ores are inefficient, expensive, and environmentally damaging. Recent discovery of lanmodulin (LanM), a protein that coordinates REMs with high-affinity and selectivity over competing ions, provides inspiration for new REM refinement methods. Here, we used quantum mechanical (QM) methods to investigate trivalent lanthanide cation (Ln 3+ ) interactions with coordination systems representing bulk solvent water and protein binding sites. Energy decomposition analysis (EDA) showed differences in the energetic components of Ln 3+ interaction with representatives of solvent (water, H 2 O) and protein binding sites (acetate, CH 3 COO – ), highlighting the importance of accurate description of electrostatics and polarization in computational modeling of REM interactions with biological and bioinspired molecules. Relative binding free energies were obtained for Ln 3+ with coordination complexes originating from binding sites in PDB structures of a lanthanum binding peptide (PDB entry 7CCO) and LanM, with explicit consideration of the first hydration shell waters, according to quasi-chemical theory (QCT). Beyond the first shell, the bulk solvent environment was represented with an implicit continuum model. Ln 3+ interactions with (H 2 O) 9 and both binding site models became more favorable, moving down the periodic series. This trend was more pronounced with the protein binding site models than with water, resulting in affinity increasing with periodic number, except for the last REM, Lu 3+ , which bound less favorably than the preceding element, Yb 3+ . Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. Conversely, the previously reported experimental data for LanM show a preference for the earlier lanthanides; this is likely due to longer-range interactions and cooperative effects, which are not represented by the reduced models. Using the truncated 7CCO binding site model, the magnitude and trend of the experimental Ln 3+ relative binding free energies for the whole 7CCO peptide were reproduced. In contrast to the previously reported experimental data for LanM, the peptide preferentially binds the earlier lanthanides. This difference likely arises due to longer-range interactions and cooperative effects not represented by the peptide. Further investigation of Ln 3+ interactions with whole proteins using polarizable molecular mechanics models with explicit solvent is warranted to understand the influence of longer-ranged interactions, cooperativity, and bulk solvent. Nevertheless, the present work provides new insights into Ln 3+ interactions with biomolecules and presents an effective computational platform for designing specific single-site REM binding peptides more efficiently.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Chromatin structures from integrated AI and polymer physics model

The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.

Biochemistry & Molecular Biology↗