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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Model associated with: "Thermodynamic control on the decomposition of organic matter across different electron acceptors"

This model data package is associated with the publication “Thermodynamic control on the decomposition of organic matter across different electron acceptors” submitted to Soil Biology and Biochemistry (Zheng et al., 2023; https://doi.org/10.1016/j.soilbio.2024.109364).In this research, a thermodynamic modeling framework is built to flexibly incorporate both organic matter (OM) molecules and electron acceptors for estimating potential free energy release from various redox reactions and to further predict reaction rates based on Microbial Transition State Theory. The model package includes scripts for thermodynamic modeling and postprocessing. Input Fourier-transform ion cyclotron resonance (FTICR) data are from a previous experimental study (Boye et al., 2018), and model outputs are free energy predictions and stoichiometric coefficients associated with all possible redox reactions.This data package is associated with the project GitHub repository found at MM_bioenergetic_modeling.This data package contains four folders (Input_FTICR, Model, Output, and Output_processing), a file-level metadata (FLMD) csv, and a data dictionary (dd) csv. Please see Zheng_bioenergetic_modeling_flmd.csv for a list of all files contained in this data package and descriptions for each. The Zheng_bioenergetic_modeling_dd.csv file describes the csv column headers. The “Model” folder contains scripts to run energy balance calculations for each electron acceptor. The “Output” folder contains csv files with stoichiometric information from model simulations. And the "Output_processing" folder contains scripts for reaction rate calculations and to generate plots.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Tier 2 Safety Basis Document: Weapons and Complex Integration - Building 225

This Safety Basis Document (SBD) covers operations in the Weapons and Complex Integration (WCI) Building 225 (B225) facility. B225 is located in the southwestern quadrant of Lawrence Livermore National Laboratory (LLNL) and is operated and owned by WCI. This SBD satisfies the requirements of LLNL ES&H Manual Document 3.1, Nonnuclear Safety Basis Program (Ref. 2). B225 is classified as a Low Hazard Facility based on the inventory of radiological materials. Other hazards in B225: chemicals, radiation generating devices, and industrial hazards are managed at the Light Science and Industry (LSI) level. Biological and explosive hazards are not authorized in B225. There are four general Administrative Controls (ACs) identified as the B225 Operational Safety Requirements (OSRs). These administrative controls are deemed sufficient to ensure safe operations with respect to co-located workers and the public. Other safety features and administrative requirements are required by the LLNL ES&H Manual, including those to protect the facility workers and the environment, but these have not been selected as credited controls to protect the co-located workers or the public, which are the target populations of concern for the SBD.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2022

Temperature Controlled Glass Additive Manufacturing

Glass additive manufacturing (AM) is an emerging technology with a wide range of applications in chemistry, biology, optical science, and engineering. A custom laser-based glass 3D printer was developed by a group of engineers at Los Alamos National Laboratory (LANL) and is being optimized to produce hardware for chemical processing equipment, microfluidic systems, as well as optical elements. AM glass using a filament deposition modeling (FDM) approach allows for generation of parts with high optical quality. The quality of the glass can be affected by the generation of defects such as bubbles and vaporization which affect the optical quality of the glass. The defects can also affect the mechanical performance of the glass and lead to sample cracking.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Engineering Anti-Microbial Peptide Production in Fungi and Bioprocess Development (CRADA 502)

Crop Protection, specifically controlling agricultural diseases and pests, is essential for crop production at every agricultural scale. Biologics hold enormous potential in this equation to decrease use of more toxic pesticides. Currently, the widespread use of biologics in crop protection is severely hampered by the lack of available tools for their mass production. To ensure biologics are regulated under EPA Biopesticide regulations, the following must be true: The biopesticide is a naturally occurring substance or structurally similar and functionally identical to a naturally occurring substance with a history of exposure to humans and the environment demonstrating minimal toxicity. Since this pertains to the marketed product it is also essential that fermentation hosts have a history of exposure and safe use by humans This research focuses on developing a novel platform for the production and delivery of the cghSAMP peptide using the filamentous fungus Aspergillus niger. A. niger is a well-established industrial microorganism, widely recognized for its strong protein secretion capabilities, high-yield production of enzymes, and classification as a generally recognized as safe (GRAS) organism. By genetically modifying A. niger to express the cghSAMP peptide transgene, we aim to leverage the fungus's robust fermentation system to produce a high volume of the antimicrobial agent. This engineered system represents a potential breakthrough in sustainable disease management, offering an environmentally friendly method for localized application or large-scale production of a biopesticide designed to mitigate the effects of citrus greening disease. The main objectives of this project were: 1. Developing a high-yield and cost-efficient bioprocess to produce an AMP in a current ABF host or readily onboarded hosts. 2. Scale up the process in stirred tank reactors and produce at least 100 grams of AMP at 1- 5g/L

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Enriched Background Isotope Study (EBIS): Analysis of 14C-Enriched Carbon Cycle in Soils and Litter at Forested Oak Ridge and AmeriFlux Sites, 2001-2011

These data provide a record of the multi-year, multi-institutional Enriched Background Isotope Studies (EBIS) projects that ran from 2000 through 2011. Elevated levels of 14C enriched CO2 in the air and soil atmosphere as well as leaf, stem, and root tissues were observed on the Oak Ridge Reservations (ORR) during the summer of 1999, and were attributed to local incinerator activities on and/or near the ORR (Trumbore et al. 2002). The isolated enrichment of the background levels of 14C in local forest ecosystem represented a unique opportunity to study unresolved carbon cycling processes such as the contribution of leaf versus root litter contributions to soil carbon accumulation, the rate of vertical transport of carbon into deep soil storage pools, and the differential contribution of physicochemical versus faunal driven processes to soil carbon cycling and sequestration. Leaf litter from the local enriched forest was transplanted to selected sites on the ORR and to selected AmeriFlux study sites to study soil C cycling across a range of soils and climates. The EBIS research projects provide data on C flux from litter sources to mineral soil sinks for United States eastern hardwood forests necessary for testing process hypotheses and judging efficacy of soil C cycling models. Experimental results from this study are being used to parameterize and refine existing carbon dynamics models, the quantification of the long-term fate of ecosystem carbon inputs and as a means to judge the potential for ecosystem carbon sequestration via enhance litter inputs to soil. EBIS observations support conclusions that intra- and inter-annual soil carbon cycling in hardwood forest soils should be characterized as a least a two-compartment system where surface leaf-litter and belowground root turnover represent primary carbon sources for organic-layer and mineral-soil carbon cycles, respectively. EBIS experiments were conducted to complete enriched litterfall maniplations in upland forests on Ultisol and Inceptisol soils of the Oak Ridge Reservation, Oak Ridge, Tennessee. We also collected additional14C-enriched materials for new experimental applications, and applied those materials to multiple AmeriFlux sites over a range of climatic, edaphic and biological conditions. The research provided data for addressing DOE's goal of understanding mechanisms controlling C flux, and for the improvement of models to be applied to policy discussions regarding the safe levels of greenhouse gases for the earth's system. There are 5 data files provided in comma separated (*.csv) format for vegetation, field litter, soil and air [C] and C isotope data from the EBIS studies and associated environmental data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Simulation of high-frequency dissolved oxygen dynamics in a shallow estuary, the Corsica River, Chesapeake Bay

Understanding shallow water biogeochemical dynamics is a challenge in coastal regions, due to the presence of highly variable land-water interface fluxes, tight coupling with sediment processes, tidal dynamics, and diurnal variability in biogeochemical processes. While the deployment of continuous monitoring devices has improved our understanding of high-frequency (12 - 24 hours) variability and spatial heterogeneity in shallow regions, mechanistic modeling of these dynamics has lagged behind conceptual and empirical models. The inherent complexity of shallow water systems is represented in the Corsica River estuary, a small basin within the Chesapeake Bay ecosystem, where abundant monitoring data have been collected from long-term monitoring stations, continuous monitoring sensors, synoptic sensor surveys, and measurements of sediment-water fluxes. A state-of-the-art modeling system, the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), was applied to the Corsica domain with a high-resolution grid and nutrient loads from the most recent version of the Chesapeake Bay watershed model. The Corsica SCHISM model reproduced observed high-frequency variability in dissolved oxygen, as well as seasonal variability in chlorophyll-a and sediment-water fluxes. Time-series signal analyses using Empirical Model Decomposition and spectral analysis revealed that the diurnal and M2 tide frequencies are the dominant high-frequency modes and physical transport contributes a larger share to dissolved oxygen budgets than biogeochemical processes on an hourly time scale. Heterogeneity and patchiness in dissolved oxygen resulting from phytoplankton distributions and geometry-driven eddies amplify the physical transport effect, and on longer time scales oxygen is controlled more by photosynthesis and respiration. Our simulation demonstrates that interactions among physical and biological dynamics generate complex high-frequency variability in water quality and non-linear reposes to nutrient loading and environmental forcing in shallow water systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Foveal vision reduces neural resources in agent-based game learning

Efficient processing of information is crucial for the optimization of neural resources in both biological and artificial visual systems. In this paper, we study the efficiency that may be obtained via the use of a fovea. Using biologically-motivated agents, we study visual information processing, learning, and decision making in a controlled artificial environment, namely the Atari Pong video game. We compare the resources necessary to play Pong between agents with and without a fovea. Our study shows that a fovea can significantly reduce the neural resources, in the form of number of neurons, number of synapses, and number of computations, while at the same time maintaining performance at playing Pong. To our knowledge, this is the first study in which an agent must simultaneously optimize its visual system, along with its decision making and action generation capabilities. That is, the visual system is integral to a complete agent.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Ablating nanoscale pores in crystalline quartz using laser-induced micro-plasmas in tri-layer structures

We demonstrate a novel approach for achieving rapid, consistent, and controllable micro-pore fabrication in single-crystalline quartz. These micro-pores are essential for applications in biology, i.e., studying ion channels in general and mechano-sensitive channels (MSC) in particular. The fabrication process consists of direct material ablation using pulsed UV light from a 193 nm excimer laser. These pulses ablate single-crystalline quartz chips by burning a laser-induced plasma in a tri-layer structure. Controllable plasma confinement and thus pore size is achieved by sandwiching a thin layer of a selected organic solution between the quartz chip and different substrates. This solution causes the confined micro-plasma to generate special ablation conditions, to create uniformly sized and shaped nanopores.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Algae Biofilm Produced from Anaerobic Digester Wastewater Demonstrated as Biofertilizer for Dwarf Wheat

Aims: To correlate yield of dwarf wheat fertilized with algae biofilm produced using anaerobic digester effluent (digestate) from a municipal water resource recovery facility as nutrient source and compare with yield using non-algae biofilm based fertilizers and a negative control. Study Design: Greenhouse testing for measurement of biomass yields and statistical analysis of wheat yield data results. Place and Duration of Study: Department of Biological Engineering Algae Processing and Products Facility greenhouse between March and June, 2024. Methodology: Yield of a dwarf cultivar of red spring wheat was measured as a function of four treatments including three fertilizers and a negative control: (1) algae biofilm cultivated on anaerobic digester effluent, (2) positive control of Osmocote commercial slow release fertilizer, (3) anaerobic digester biosolids, and (4) negative control with no fertilizer addition. Results: Average yield values (gm) for the four treatments were: (1) 1.25, (2) 0.99, (3) 0.72, and (4) 0.52, respectively. Algae biofilm fertilizer performed significantly better than Osmocote with P = .002, anaerobic digester biosolids with P = .05, and no fertilizer addition with P = .05. Struvite, a slow release fertilizer, was observed to be associated with the algae biofilm as a precipitate of the high concentrations of nutrients within the anaerobic digester water. Struvite (MgNH4PO46H2O) releases plant available nitrogen and phosphorus over time and is biologically precipitated due to the increase in solution pH as a result of photosynthesis by the algae biofilm. Conclusion: Algae biofilm cultivated on anaerobic digester wastewater can serve as a biofertilizer for recycling nutrients within the biosphere for sustainable nutrient management.

09 BIOMASS FUELS↗
DOE OSTI2020

Machine learning predicts new anti-CRISPR proteins

The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Photocaged functional nucleic acids for spatiotemporal imaging in biology

Imaging of species in living organisms with high spatiotemporal resolution is essential for understanding biological processes. While functional nucleic acids (FNAs), such as catalytic nucleic acids and aptamers, have emerged as effective sensors for a wide range of molecules, photocaged control of these FNAs has played a key role in translating them into bioimaging agents with high spatiotemporal control. In this paper, we summarize methods and results of photocaged FNAs based on photolabile modifications, photoisomerization, and photothermal activation. Future directions, including strategies to improve the performance of these photocaged FNAs, are also described.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Controlled mechanochemical coupling of anti-junctions in DNA origami arrays

Abstract Allostery is a hallmark of cellular function and important in every biological system. Still, we are only starting to mimic it in the laboratory. Here, we introduce an approach to study aspects of allostery in artificial systems. We use a DNA origami domino array structure which–upon binding of trigger DNA strands–undergoes a stepwise allosteric conformational change. Using two FRET probes placed at specific positions in the DNA origami, we zoom in into single steps of this reaction cascade. Most of the steps are strongly coupled temporally and occur simultaneously. Introduction of activation energy barriers between different intermediate states alters this coupling and induces a time delay. We then apply these approaches to release a cargo DNA strand at a predefined step in the reaction cascade to demonstrate the applicability of this concept in tunable cascades of mechanochemical coupling with both spatial and temporal control.

Science & Technology - Other Topics↗
DOE OSTI2026

Closing the loop on plastics: Biological and hybrid routes for converting plastic waste to polyhydroxyalkanoates

Polyhydroxyalkanoate (PHA) production from plastic-derived substrates offers a promising route to mitigate plastic pollution while reducing dependence on conventional PHA feedstocks. Plastic waste represents an abundant carbon source for microbial fermentation, but efficient conversion remains limited by incomplete deconstruction, inhibitory intermediates, low carbon recovery, and challenges in process integration. Plastic-derived streams contain diverse compounds, including fatty acids, hydrocarbons, fatty alcohols, aldehydes, esters, and aromatic compounds generated during depolymerization. These intermediates can be metabolized by selected microorganisms, particularly Pseudomonas species with versatile fatty-acid and hydrocarbon pathways, as well as Cupriavidus necator and mixed microbial cultures. Unlike reviews that address plastic upcycling or PHA biosynthesis separately, this review focuses on the deconstruction–fermentation interface that governs plastic-to-PHA conversion. It consolidates current progress in plastic deconstruction, substrate conditioning, microbial metabolism, fermentation control, polymer recovery, and techno-economic and life-cycle considerations. Here, by emphasizing substrate composition, biological compatibility, plastic‑carbon recovery, and final polymer quality, the review identifies priorities for scalable and environmentally sustainable PHA production from plastic-derived substrates.

42 ENGINEERING↗
DOE OSTI2020

Dynamic Construction, Perception, and Remodeling of Plant Cell Walls

Plant cell walls are dynamic structures that are synthesized by plants to provide durable coverings for the delicate cells they encase. They are made of polysaccharides, proteins, and other biomolecules and have evolved to withstand large amounts of physical force and to resist external attack by herbivores and pathogens but can in many cases expand, contract, and undergo controlled degradation and reconstruction to facilitate developmental transitions and regulate plant physiology and reproduction. Recent advances in genetics, microscopy, biochemistry, structural biology, and physical characterization methods have revealed a diverse set of mechanisms by which plant cells dynamically monitor and regulate the composition and architecture of their cell walls, but much remains to be discovered about how the nanoscale assembly of these remarkable structures underpins the majestic forms and vital ecological functions achieved by plants.

biofuels (including algae and biomass), bio-inspir↗
DOE OSTI2020

In Situ Chemical Monitoring and Imaging of Contents within Microfluidic Devices Having a Porous Membrane Wall Using Liquid Microjunction Surface Sampling Probe Mass Spectrometry

The ability to observe dynamic chemical processes (e.g., signaling, transport, etc.) in vivo or in situ using nondestructive chemical imaging opens a new door to understanding the complex dynamics of developing biological systems. With the advent of “biology-on-a-chip” devices has come the ability to monitor dynamic chemical processes in a controlled environment, using these engineered habitats to capture key features of natural systems while allowing visual observation of system development. Having the capability to spatially and temporally map the chemical signals within these devices may yield new insights into the forces that drive biosystem development. Here, a porous membrane sealed microfluidic device was designed to allow normal microfluidic operation while enabling continuous, location specific sampling and chemical characterization by liquid microjunction surface sampling probe mass spectrometry (LMJ-SSP MS). LMJ-SSP was used to extract fluids with nL-to-μL/min flow rates directly from selected areas of the microfluidic device without negatively impacting the device function. These extracts were subsequently characterized using MS. This technique was used to acquire MS images of the entirety of several multi-input microfluidic devices having different degrees of fluid mixing. LMJ-SSP MS imaging visualized the spatial distribution of chemical components within the microfluidic channels and could visualize chemical reactions occurring in the device. These microfluidic devices with a porous membrane wall are wholly compatible with the construction of biology-on-a-chip devices. This ultimately would enable correlation of biosystem physical structure with an evolving chemical environment

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Dual arginine recognition of LRRK2 phosphorylated Rab GTPases

Parkinson’s-disease-associated LRRK2 is a multidomain Ser/Thr kinase that phosphorylates a subset of Rab GTPases to control their effector functions. Rab GTPases are the prime regulators of membrane trafficking in eukaryotic cells. Rabs exert their biological effects by recruitment of effector proteins to subcellular compartments via their Rab-binding domain (RBD). Effectors are modular and typically contain additional domains that regulate various aspects of vesicle formation, trafficking, fusion, and organelle dynamics. The RBD of effectors is typically an α-helical coiled coil that recognizes the GTP conformation of the switch 1 and switch 2 motifs of Rabs. LRRK2 phosphorylates Rab8a at T72 (pT72) of its switch 2 α-helix. This post-translational modification enables recruitment of RILPL2, an effector that regulates ciliogenesis in model cell lines. A newly identified RBD motif of RILPL2, termed the X-cap, has been shown to recognize the phosphate via direct interactions between an arginine residue (R132) and pT72 of Rab8a. Here, we show that a second distal arginine (R130) is also essential for phospho-Rab binding by RILPL2. Through structural, biophysical, and cellular studies, we find that R130 stabilizes the primary R132:pT72 salt bridge through favorable enthalpic contributions to the binding affinity. These findings may have implications for the mechanism by which LRRK2 activation leads to assembly of phospho-Rab complexes and subsequent control of their membrane trafficking functions in cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Controllable skyrmion chirality in ferroelectrics

Chirality, an intrinsic handedness, is one of the most intriguing fundamental phenomena in nature. Materials composed of chiral molecules find broad applications in areas ranging from nonlinear optics and spintronics to biology and pharmaceuticals. However, chirality is usually an invariable inherent property of a given material that cannot be easily changed at will. Here, we demonstrate that ferroelectric nanodots support skyrmions the chirality of which can be controlled and switched. We devise protocols for realizing control and efficient manipulations of the different types of skyrmions. Our findings open the route for controlled chirality with potential applications in ferroelectric-based information technologies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Ion Gating in Nanopore Electrode Arrays with Hierarchically Organized pH-Responsive Block Copolymer Membranes

Inspired by biological ion channels, artificial nanopore-based architectures have been developed for smart ion/molecular transport control with potential applications to iontronics and energy conversion. Advances in nanofabrication technology enable simple, versatile construction methods, and post-fabrication functionalization delivers nanochannels with unique ion transport-control attributes. Here, we characterize a pH-responsive, charge-selective dual-gating block copolymer (BCP) membrane composed of polystyrene-b-poly(4-vinylpyridine) (PS 48400 -b-P4VP 21300 ), capable of self-organizing into highly ordered nanocylindrical domains. Because the PS-b-P4VP membrane exhibits pH-dependent structural transitions, it is suitable for designing intelligent pH-gated biomimetic channels, for example, exhibiting on–off transport switching at pH values near the pK a of P4VP with excellent anion permselectivity at pH < pK a . Introducing the BCP membrane onto nanopore electrode arrays (BCP@NEAs) allows the BCP to serve as a pH-responsive gate controlling ion transfer into the NEA nanopores. Such selectively transported and confined ions are detected by using a 100 nm gap dual-ring nanoelectrode structure capable of enhancing current output by efficient redox cycling with an amplification factor >10 2 . In addition, BCP@NEAs exhibit extraordinary pH-gated ion selectivity, resulting in a 3380-fold current difference between anion and cation probes at pH 3.0. Furthermore, this hierarchically organized BCP-gated NEA system can serve as a template for the development of other stimulus-responsive ion gates, for example, those based on temperature and ligand gating, thus exploiting the intrinsic advantages of NEAs, such as enhanced sensitivity based on redox cycling, which may lead to technological applications such as engineered biosensors and iontronic devices.

36 MATERIALS SCIENCE↗