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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Multiscale Modeling and Experimental Insights into High-Temperature Soil Biodegradation Dynamics of Semi-Crystalline Poly(Lactic Acid) Nonwoven Fabrics

This study investigates the biodegradation of semi-crystalline poly(lactic acid) (PLA) nonwovens (NWs) in soil at 58 °C using both experimental and mathematical modeling approaches. The model utilizes a system of parabolic diffusion-reaction partial differential equations (PDEs) to elucidate chemical transformations over time and in space. It accounts for phenomena such as the diffusion of water and lactic acid monomers through the polymer matrix and into the surrounding soil, along with their microbial breakdown. It also accounts for the initial PLA crystallinity and predicts its evolution in time. The model is solved numerically for a single filament, and the results were used to shed light on PLA NW transformations observed in soil over a 180-day incubation period. Various characterization techniques, including scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and Raman spectroscopy, were employed to assess morphological changes, crystallinity, and molecular changes in the NWs throughout the experiment. By comparing the experimental data with the model predictions, the hydrolysis rate coefficient was found to be 3.37 × 10 -7 s -1 , while the rate of microbial degradation of lactic acid monomers was faster, of the order of 9.63 × 10 -7 s -1 . The findings highlight the significant role of crystallinity in the biodegradation process. The PLA degradation ceases when no amorphous material remains, and the crystallinity reaches 0.8, as observed in the experiments by day 120. Furthermore, this research contributes to a deeper understanding of PLA biodegradation dynamics and offers insights for effectively managing biodegradable materials in environmental settings.

Diffusion−reaction modeling↗
DOE OSTI2023

Shewanella oneidensis MR-1 respires CdSe quantum dots for photocatalytic hydrogen evolution

Living bio-nano systems for artificial photosynthesis are of growing interest. Typically, these systems use photoinduced charge transfer to provide electrons for microbial metabolic processes, yielding a biosynthetic solar fuel. Here, we demonstrate an entirely different approach to constructing a living bio-nano system, in which electrogenic bacteria respire semiconductor nanoparticles to support nanoparticle photocatalysis. Semiconductor nanocrystals are highly active and robust photocatalysts for hydrogen (H 2 ) evolution, but their use is hindered by the oxidative side of the reaction. In this system, Shewanella oneidensis MR-1 provides electrons to a CdSe nanocrystalline photocatalyst, enabling visible light-driven H 2 production. Unlike microbial electrolysis cells, this system requires no external potential. Illuminating this system at 530 nm yields continuous H 2 generation for 168 h, which can be lengthened further by replenishing bacterial nutrients.

Science & Technology - Other Topics↗
DOE OSTI2020

Modeling Functional Organic Chemistry in Arctic Rivers: An Idealized Siberian System

Rivers of the Arctic will become ever more important for the global climate, since they carry a majority of continental dissolved organic carbon flux into the rapidly changing polar ocean. Aqueous organics comprise a wide array of functional groups, several of which are likely to impact coastal and open water biophysical properties. Light attenuation, interfacial films, aerosol formation, gas release and momentum exchange can all be cited. We performed Lagrangian kinetic modeling for the evolution of riverine organic chemistry as the molecules in question make their way from the highlands to Arctic outlets. Classes as diverse as the proteins, sugars, lipids, re-condensates, humics, bio-tracers and small volatiles are all included. Our reduced framework constitutes an idealized northward flow driving a major hydrological discharge rate and primarily representing the Russian Lena. Mountainous, high solute and tundra sources are all simulated, and they meet up at several points between soil and delta process reactors. Turnover rates are parameterized beginning with extrapolated coastal values imposed along a limited tributary network, with connections between different terrestrial sub-ecologies. Temporal variation of our total dissolved matter most closely resembles the observations when we focus on the restricted removal and low initial carbon loads, suggesting relatively slow transformation along the water course. Thus, channel combinations and mixing must play a dominant role. Nevertheless, microbial and photochemical losses help determine the final concentrations for most species. Chemical evolution is distinct for the various functionalities, with special contributions from pre- and post-reactivity in soil and delta waters. Several functions are combined linearly to represent the collective chromophoric dissolved matter, characterized here by its absorption. Tributaries carry the signature of lignin phenols to segregate tundra versus taiga sources, and special attention is paid to the early then marine behaviors of low molecular weight volatiles. Heteropolycondensates comprise the largest percentage of reactive carbon in our simulations due to recombination/accumulation, and they tend to be preeminent at the mouth. Outlet concentrations of individual structures such as amino acids and absorbers lie above threshold values for biophysical influence, on the monolayer and light attenuation. The extent of coastal spreading is examined through targeted regional box modeling, relying on salinity and color for calibration. In some cases, plumes reach the scale of peripheral arctic seas, and amplification is expected during upcoming decades. Conclusions are mapped from the Lena to other boreal discharges, and future research questions are outlined regarding the bonding type versus mass release as permafrost degrades. Dynamic aqueous organic coupling is recommended for polar system models, from headwaters to coastal diluent.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Rewiring Aromatic Compound Consumption: Chromosomal Amplification and Evolution of a Foreign Pathway in Acinetobacter baylyi ADP1

Rational engineering strategies that seek to harness the remarkable diversity of microbial metabolism can be limited by incomplete biological knowledge. As described here, a novel approach to address this challenge involved replacing a native pathway for degrading lignin-derived aromatic compounds via ortho cleavage of protocatechuate in Acinetobacter baylyi ADP1 with a foreign meta-cleavage pathway that uses different enzymes, metabolites, and redox carriers. This alteration may improve lignin valorization and coordinate catabolism with bioproduction strategies. When a 14-kbp region of foreign DNA was inserted in the chromosome, the heterologous genes failed to confer growth on target substrates. Regional gene dosage was increased using a synthetic DNA fragment to promote recombination, and higher copy number enabled growth. During adaptive laboratory evolution, compensatory mutations arose that permit growth with one copy of the foreign genes. This complex metabolic remodeling was accomplished without assumptions about the impediments that initially prevented growth. To understand the changes that emerged, a novel transformation assay identified a combination of mutations sufficient for the new phenotype. Three unexpected changes were revealed: loss of one foreign enzyme, loss of one native enzyme, and loss of a two-component transcriptional regulatory system. This study establishes that large multicopy tandem arrays of poorly adapted pathway genes can confer new functions and improve understanding of metabolism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Epistasis and evolution: recent advances and an outlook for prediction

As organisms evolve, the effects of mutations change as a result of epistatic interactions with other mutations accumulated along the line of descent. This can lead to shifts in adaptability or robustness that ultimately shape subsequent evolution. Here, we review recent advances in measuring, modeling, and predicting epistasis along evolutionary trajectories, both in microbial cells and single proteins. We focus on simple patterns of global epistasis that emerge in this data, in which the effects of mutations can be predicted by a small number of variables. The emergence of these patterns offers promise for efforts to model epistasis and predict evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Growth rate as a link between microbial diversity and soil biogeochemistry

The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining ‘omics and stable isotope probing enable sensitive measurements of growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake, and ecosystem productivity. Finally, measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The microbial rare biosphere: current concepts, methods and ecological principles

ABSTRACT Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the ‘rare biosphere’, across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

Pascoal, Francisco↗
DOE OSTI2019

Directed in vitro evolution of bacterial expansin BsEXLX1 for higher cellulose binding and its consequences for plant cell wall-loosening activities

Expansins are cell wall-loosening proteins found in all land plants and many microbial species. Despite homologous structures, bacterial expansins have much weaker cellulose binding and wall-loosening activity than plant expansins. We hypothesized stronger cellulose binding would result in greater wall-loosening activity and used in vitro evolution of Bacillus subtilis BsEXLX1 to test this hypothesis. Mutants with stronger binding generally had greater wall-loosening activity, but the relationship was nonlinear and plateaued at ~ 40% higher than wild-type. Mutant E191K exhibited stronger cellulose binding but failed to induce creep, evidently due to protein mistargeting. These findings reveal the complexity of interactions between plant cell walls and wall-modifying proteins, a prime consideration when engineering proteins for applications in biofuel production and plant pathogen resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sulfur isotopes from the Paleoproterozoic Francevillian Basin record multigenerational pyrite formation, not depositional conditions

Bulk-rock sulfur isotope data from pyrite in the ~2.1 billion-year sedimentary rocks of the Francevillian Basin, Gabon, have underpinned ideas about initial oxygenation of Earth’s surface environments and eukaryote evolution. In this paper, we show, using micro-scale analytical methods, that the bulk sulfur isotope record represents progressive diagenetic modification. Our findings indicate no significant change in microbial sulfur cycling processes and seawater sulfate composition throughout that initial phase of atmosphere-ocean oxygenation of Paleoproterozoic time. This offers an alternative view of Earth system evolution during the transition from an anoxic to an oxic state and highlights the need for a judicious reappraisal of conceptual models using sulfur isotope data as primary depositional signals linked to global-scale biogeochemical processes.

58 GEOSCIENCES↗
DOE OSTI2026

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture

Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization or endophytism. Our findings reveal that while some Trichoderma species show traits of biosafety concern, its vast ecophysiological diversity enables the development of safe, targeted bioeffectors.

Steindorff, Andrei S. [USDOE Joint Genome Institut↗
DOE OSTI2018

Oil Biodegradation in Deep Marine Basins

Nine important hydrocarbon (oil) basins where offshore petroleum leases have been licensed are compared. These nine basins (Gulf of Mexico, Eastern Mediterranean’s Nile Deep-Sea Fan, Central Mediterranean and the Sirte Basin, North Sea, Caspian Sea, Angola, Trinidad and Tobago, Great Australian Bight, and Brazil’s Amazonian Deep-Sea Basin) are geographically separated and are impacted by very different water masses. The geochemical parameters of these basins are quite distinct, for example, salinities ranging from 39 psu in the Eastern Mediterranean to 12 psu in the Caspian. Additionally, parameters like temperatures of the bottom water are also very distinct, with the temperature in the deep water of the Eastern Mediterranean being between 12 °C and 14 °C and the temperature of the deep water in the North Sea being -2 °C. Each basin represents a unique ecosystem in which distinct microbes may thrive. These distinct environmental parameters may act to constrain the extent of hydrocarbon degradation in these basins. Another potential constraint on hydrocarbon degradation is the extent of natural hydrocarbon seeps in the area. Though many basins have similar if not 16S rRNA identical strains of oil-degrading bacteria, Colwellia psychrerythraea from different basins showed that a mixture of natural selection and neutral evolution has contributed to the divergence of these. Most if not all deep ocean basin microbial communities are dominated by Thaumarchaeota below 200 m. These microaerophilic, ammonium oxidizer, psychrophiles are very adapted to an oligotrophic lifestyle, and though many in this group will degrade oil, they are rapidly outcompeted by other bacteria in oil or high hydrocarbon intrusions, thus the virtual “canary in the coal mine.” Cometabolic biodegradation of oil is well documented but could be an important natural attenuation mechanism for oil in deep marine basins with episodic methane seeps. Microbial community structure can also predict concentrations of oil in deep basins. Many other synergistic effects require more research in environmental systems biology in deep marine basins.

Hazen, Terry C.↗
DOE OSTI2019

Biodesign Research to Advance the Principles and Applications of Biosystems Design

Over the course of civilization, humans have increasingly expanded their freedom to live a better life. In comparison with the primitive society, our modern society has many more choices of life-supporting resources, such as year-round food supply, permanent shelters, diverse energy sources, and effective preventive and curing medicine. However, our society is currently still heavily relying on the resources provided by Mother Nature, which cannot meet the future global needs in terms of both quantity and quality under the pressure of population growth, natural resource reduction, and environmental deterioration. For example, the food sources originating from plants, animals, or microbes do not have the nutrition balance for optimal human health. Climate change and environmental deterioration threaten the food security. Increasingly, infectious diseases (e.g., HIV/AIDS), genetic diseases (e.g., cancer), and improper lifestyle-related disorders (e.g., obesity) become more prevalent and remain challenging to be prevented, controlled, and cured. Conventional medical technologies and modern medicine development are also meeting the ceiling. Antibiotic resistance is threatening the health of humans, animals, and environment. As the human lifespan continues to increase, aging-related diseases, disorders, and poor life quality are becoming global challenges. Plants, animals, and microbes in nature have evolved as part of our Earth ecosystem, not for benefiting humans. Even though humans have put forth tremendous efforts to domesticate plants, animals, and microbes based on random/induced mutations, hybridization, and limited genetic modifications via biological engineering, the improved food and industrial crop plants, animals, and microbial strains are still far from optimized for meeting the human needs. In other words, natural evolution and domestication in plants, animals, and microbes are tinkering processes and therefore cannot meet the ever-exploding population on the one hand and the unending appetite for living better quality life on the other. One promising strategy for solving these global challenges is to employ revolutionary biosystems design (also called biodesign), which is defined as predictable modification of existing organisms or creation of new organisms using rational engineering or automated design based on the theory and principles of biosystems design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering

Conversion of CO 2 to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO 2 , has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. Further, the metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ..delta..phcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Laboratory evolution reveals the metabolic and regulatory basis of ethylene glycol metabolism by Pseudomonas putida KT2440

Pollution from ethylene glycol, and plastics containing this monomer, represent a significant environmental problem. The investigation of its microbial metabolism therefore provides insights into the environmental fate of this pollutant, but also enables its utilization as a carbon source for microbial biotechnology. Here, we reveal the genomic and metabolic basis of ethylene glycol metabolism in Pseudomonas putida KT2440. Although this strain cannot grow on ethylene glycol as sole carbon source, it can be used to generate growth-enhancing reducing equivalents upon co-feeding with acetate. Mutants that utilize ethylene glycol as sole carbon source were isolated through adaptive laboratory evolution. Genomic analysis of these mutants revealed a central role of the transcriptional regulator GclR, which represses the glyoxylate carboligase pathway as part of a larger metabolic context of purine and allantoin metabolism. Secondary mutations in a transcriptional regulator encoded by PP_2046 and a porin encoded by PP_2662 further improved growth on ethylene glycol in evolved strains, likely by balancing fluxes through the initial oxidations of ethylene glycol to glyoxylate. With this knowledge we reverse engineered an ethylene glycol utilizing strain and thus, revealed the metabolic and regulatory basis that are essential for efficient ethylene glycol metabolism in P. putida KT2440.

09 BIOMASS FUELS↗
DOE OSTI2023

Biochemical Process Modeling and Simulation (BPMS)

The Biochemical Process Modeling and Simulation project aims to reduce the cost and time of research by applying theory, modeling, and simulation to the most relevant bottlenecks in the biochemical process. We use molecular modeling, quantum mechanics, metabolic modeling, fluid dynamics, and reaction-diffusion methods in close collaboration with pretreatment, hydrolysis, upgrading, and TEA. The project's outcomes are increased yields and efficiency of the biochemical process, added value to products, and reduced price of fuels by specifically targeting catalytic efficiency, reactor design, enzyme efficiency, and microbial design. We work closely with experimental projects to identify problems and iterate with experiments to find and refine solutions. By working with experimentalists, we decide on problems that can be solved with simulation that could otherwise not be solved or would take too long with experiment alone to reach BETO's targets. Over the years, we have produced solutions that have resulted in determining the most likely fatty-acid derivative for passive transport out of bacteria that upgrade biomass, and we have also designed enzyme mutations for enhanced lignin upgrading. Metabolic models have been developed to tune the activity of 2,3 butanediol production for the 2030 target. A computational method to deliver understanding of how complex omics data can be interpreted in the metabolic pathways of organisms used in the Agile Biofoundry. We have found methods to overcome specific barriers and continue to develop those methods. Our reactor studies have guided the design of both the microbes and reactors for aerobic and micro-aerobic production at all scales and have been instrumental in improving the accuracy of techno-economic analysis models. This project is essential in the process of selecting the final processes for 2030 SAF production targets. More specifically, recently, we have: 1) Predicted the strength of the basic structural interactions in commodity plastics to provide guidance for plastics upcycling strategies. 2) Developed computational tool to improve the characterization of lignin-derived compounds 3) Developed new methodologies to enable Machine Learning-based Directed Evolution for protein engineering. 4) Developed Machine Learning methods to predict protein promiscuity and mutations to further improve microbial and enzymatic driven processes and demonstrated the utility of ML approaches to engineering proteins from sparse experimental datasets. 5) Developed new methods to enable high-fidelity simulation of aerobic fermentation at industrial scale and resolving mismatch of time scales through subcycling/operator splitting 7) Identified the difficulty in preventing local high-oxygen conditions in industrial bubble columns, which leads to less-desirable acetoin production, suggesting future research directions in alternative reactor configurations (e.g loop reactors, shallow-channel reactors).

BIOMASS FUELS↗
DOE OSTI2026

Innovations in underground hydrogen storage with multiphysics simulations, optimization, and monitoring: A review

Underground Hydrogen Storage (UHS) is a promising solution for large-scale energy storage and a critical component in advancing low-carbon energy system. Ensuring the safety and efficiency of UHS necessitates a comprehensive understanding of multiphysical interactions driven by cyclic pore fluid pressure fluctuations and coupled physicochemical processes. Here, this review examines the key geomechanical responses in UHS, including rock property variations under cyclic loading, fracture evolution and propagation, reservoir stress sensitivity, and fault stability. It also explores the impact of geochemical and microbial reactions on geomechanical characteristics. We provide an in-depth analysis of Thermal-Hydraulic-Mechanical-Chemical (THMC) coupled numerical simulations, highlighting their potential for future multi-scale modeling. Limitations of current machine learning (ML) approaches in addressing UHS challenges are highlighted, emphasizing the need for innovative ML-based methodologies. Operational strategies for hydrogen injection and production are reviewed, focusing on safety, efficiency, and economic viability. The necessity for multi-objective optimization (MOO) to balance storage efficiency, risk mitigation, and cost-effectiveness is also discussed. Current monitoring technologies are evaluated to ensure safe and efficient UHS operations. Finally, this review identifies critical knowledge gaps and underscores the importance of advancing geomechanical understanding under multiphysics-coupling. We highlight the need for ML-driven multiphysics theories, enhanced modeling techniques, and robust optimization strategies to improve UHS performance. This study serves as a comprehensive reference for future research and the large-scale implementation of UHS systems.

25 ENERGY STORAGE↗