Results for “regenerating” — Page 50

DOE OSTI2025

Bottomonium suppression in pNRQCD and open quantum system approach

By employing the potential non-relativistic quantum chromodynamics (pNRQCD) effective field theory within an open quantum system framework, we derive a Lindblad equation governing the evolution of the heavy-quarkonium reduced density matrix, accurate to next-to-leading order (NLO) in the ratio of the state's binding energy to the medium's temperature [1]. The derived NLO Lindblad equation provides a more reliable description of heavy-quarkonium evolution in the quark-gluon plasma at low temperatures compared to the leading-order truncation. For phenomenological applications, we numerically solve this equation using the quantum trajectories algorithm. By averaging over Monte Carlo-sampled quantum jumps, we obtain solutions without truncation in the angular momentum quantum number of the considered states. Our analysis highlights the importance of quantum jumps in the nonequilibrium evolution of bottomonium states within the quark-gluon plasma [2]. Additionally, we demonstrate that the quantum regeneration of singlet states from octet configurations is essential to explain experimental observations of bottomonium suppression. The heavy-quarkonium transport coefficients used in our study align with recent lattice QCD determinations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Co-Processing Catalytic Fast Pyrolysis Oil in an FCC Reactor

Studies of co-processing catalytic fast pyrolysis (CFP) oil with vacuum gas oil (VGO) are conducted in a Davison Circulating Riser (DCR). The CFP oil (CFPO) for this study was produced by upgrading fast-pyrolysis vapors from pine in an ex-situ fixed-bed reactor. CFPOs were co-processed at up to 5 vol% with VGO at 521°C and 2.57 bar. The yields of oil, aqueous phase, tail gas, and coke were measured. The amount of coke was determined from the carbon containing components in the regenerator flue gas. A compositional analysis was conducted with gas chromatography and elemental analyzers. The organic liquids were distilled into gasoline, jet-fuel, diesel, and resid fractions. A biocarbon analysis was conducted on the organic phase and its individual boiling-point fractions. The results show a small decrease in liquid yield and a generally increased gas yield when co-processing CFPO with VGO. For experiments with E-Cat as catalyst, approximately 70% of biocarbon is incorporated into liquid fuels relative to fossil carbon, while more of the biocarbon is contained in tail gas (as carbon dioxide or olefins) and/or coke. The measurements indicate that cracked CFPO components are predominantly included in the jet-fuel and diesel fractions. A techno-economic analysis (TEA) estimated the minimum fuel selling price (MSFP) for fuel-range products derived from FCC co-processing of CFPO at $3 to $4 per gasoline-gallon equivalent (GGE) at a yield of 51 GGE per ton of biomass.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator

Abstract. Tropical forest degradation from logging, fire, and fragmentation not only alters carbon stocks and carbon fluxes, but also impacts physical land surface properties such as albedo and roughness length. Such impacts are poorly quantified to date due to difficulties in accessing and maintaining observational infrastructures, as well as the lack of proper modeling tools for capturing the interactions among biophysical properties, ecosystem demography, canopy structure, and biogeochemical cycling in tropical forests. As a first step to address these limitations, we implemented a selective logging module into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) by mimicking the ecological, biophysical, and biogeochemical processes following a logging event. The model can specify the timing and aerial extent of logging events, splitting the logged forest patch into disturbed and intact patches; determine the survivorship of cohorts in the disturbed patch; and modifying the biomass and necromass (total mass of coarse woody debris and litter) pools following logging. We parameterized the logging module to reproduce a selective logging experiment at the Tapajós National Forest in Brazil and benchmarked model outputs against available field measurements. Our results suggest that the model permits the coexistence of early and late successional functional types and realistically characterizes the seasonality of water and carbon fluxes and stocks, the forest structure and composition, and the ecosystem succession following disturbance. However, the current version of FATES overestimates water stress in the dry season and therefore fails to capture seasonal variation in latent and sensible heat fluxes. Moreover, we observed a bias towards low stem density and leaf area when compared to observations, suggesting that improvements are needed in both carbon allocation and establishment of trees. The effects of logging were assessed by different logging scenarios to represent reduced impact and conventional logging practices, both with high and low logging intensities. The model simulations suggest that in comparison to old-growth forests the logged forests rapidly recover water and energy fluxes in 1 to 3 years. In contrast, the recovery times for carbon stocks, forest structure, and composition are more than 30 years depending on logging practices and intensity. This study lays the foundation to simulate land use change and forest degradation in FATES, which will be an effective tool to directly represent forest management practices and regeneration in the context of Earth system models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.

Landick, Robert↗

DOE OSTI2026

The anaerobic fungus Caecomyces churrovis produces H 2 via a non-bifurcating NADH-dependent enzyme complex

ABSTRACT Hydrogenosomes are mitochondria-derived organelles that produce ATP and H 2 to support energy metabolism in anaerobic eukaryotes. H 2 production allows reoxidation of reduced cofactors generated during fermentative metabolism; however, the metabolic mechanisms for H 2 production in anaerobic eukaryotes remains incompletely understood. In particular, it remains unclear whether anaerobic fungi (AF) hydrogenosomes use a ferredoxin-dependent pathway or a distinct mechanism to regenerate NAD(P) + and link electron transfer to H 2 formation. Here, by combining genomic search, proteomic analysis, and enzymology, we reveal the molecular mechanism for H 2 production in the AF strain Caecomyces churrovis . Our enzyme assays on the organelle fraction of C. churrovis revealed the activity of H 2 :NAD + oxidoreductase but not pyruvate:ferredoxin oxidoreductase, which is usually linked to H 2 formation. We identified genes encoding [FeFe] hydrogenase (Hyd) and NADH dehydrogenase subunits E and F (NuoE, NuoF) in C. churrovis , and confirmed their expression in the isolated hydrogenosomal fractions by proteomic analysis. Combining the individually purified enzymes, we found Hyd and NuoEF proteins formed H 2 directly from NADH independently of ferredoxin, functioning as a non-bifurcating NADH-dependent enzyme rather than an electron-bifurcating enzyme. We identified homologs of hydrogenosomal NuoE, NuoF, and Hyd in many other AF, indicating this pathway is commonly shared among the AF. This work demonstrates the existence of a non-bifurcating NADH-dependent enzyme complex in eukaryotes. Moreover, this complex could potentially be exploited as a target for controlling AF H 2 production and altering fungal metabolism. IMPORTANCE H 2 production is a prominent feature of anaerobic energy metabolism, yet our understanding of eukaryotic mechanisms remains limited. Anaerobic fungi (AF) are key decomposers of lignocellulose and contribute to hydrogen flux in anaerobic environments. Although it has been more than 40 years since the H 2 production from AF was first reported, the molecular mechanism for hydrogenosomal H 2 production and redox balance remains unclear. We demonstrate that AF produce H 2 from NADH utilizing a non-bifurcating NADH-dependent enzyme complex rather than an electron-bifurcating, ferredoxin-dependent variant. We show that this enzyme complex is conserved across multiple AF lineages and thus demonstrate the occurrence of a non-bifurcating NADH-dependent enzyme in eukaryotes. This discovery expands our understanding of eukaryotic hydrogenosomal metabolism, reveals a previously unknown strategy for redox balancing, and highlights potential targets for manipulating H 2 production. These insights have broad implications for microbial energy metabolism, anaerobic ecosystems, and bioengineering of H 2 -producing systems.

Zhang, Bo [Department of Chemical Engineering, Uni↗

DOE OSTI2022

Machine learning-assisted elucidation of CD81–CD44 interactions in promoting cancer stemness and extracellular vesicle integrity

Tumor-initiating cells with reprogramming plasticity or stem-progenitor cell properties (stemness) are thought to be essential for cancer development and metastatic regeneration in many cancers; however, elucidation of the underlying molecular network and pathways remains demanding. Combining machine learning and experimental investigation, here we report CD81, a tetraspanin transmembrane protein known to be enriched in extracellular vesicles (EVs), as a newly identified driver of breast cancer stemness and metastasis. Using protein structure modeling and interface prediction-guided mutagenesis, we demonstrate that membrane CD81 interacts with CD44 through their extracellular regions in promoting tumor cell cluster formation and lung metastasis of triple negative breast cancer (TNBC) in human and mouse models. In-depth global and phosphoproteomic analyses of tumor cells deficient with CD81 or CD44 unveils endocytosis-related pathway alterations, leading to further identification of a quality-keeping role of CD44 and CD81 in EV secretion as well as in EV-associated stemness-promoting function. CD81 is coexpressed along with CD44 in human circulating tumor cells (CTCs) and enriched in clustered CTCs that promote cancer stemness and metastasis, supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights machine learning as a powerful tool in facilitating the molecular understanding of new molecular targets in regulating stemness and metastasis of TNBC.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Structural insights into regulation of CNNM-TRPM7 divalent cation uptake by the small GTPase ARL15

Cystathionine-β-synthase (CBS)-pair domain divalent metal cation transport mediators (CNNMs) are an evolutionarily conserved family of magnesium transporters. They promote efflux of Mg 2+ ions on their own and influx of divalent cations when expressed with the transient receptor potential ion channel subfamily M member 7 (TRPM7). Recently, ADP-ribosylation factor-like GTPase 15 (ARL15) has been identified as CNNM-binding partner and an inhibitor of divalent cation influx by TRPM7. Here, we characterize ARL15 as a GTP and CNNM-binding protein and demonstrate that ARL15 also inhibits CNNM2 Mg 2+ efflux. The crystal structure of a complex between ARL15 and CNNM2 CBS-pair domain reveals the molecular basis for binding and allowed the identification of mutations that specifically block binding. A binding deficient ARL15 mutant, R95A, failed to inhibit CNNM and TRPM7 transport of Mg 2+ and Zn 2+ ions. Structural analysis and binding experiments with phosphatase of regenerating liver 2 (PRL2 or PTP4A2) showed that ARL15 and PRLs compete for binding CNNM to coordinate regulation of ion transport by CNNM and TRPM7.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Harnessing photoenzymatic reactions for unnatural biosynthesis in microorganisms

Photoenzymatic catalysis enables new-to-nature transformations, but its scalability is limited by high enzyme loading, costly cofactors, and radical-induced instability. Here we report the integration of light-driven photoenzymatic reactions into the cellular metabolism of Escherichia coli, bridging flavin-based photobiocatalysis with biosynthesis. Using synthetic biology strategies, we engineered microbial cells to continuously produce olefin substrates and ene-reductase photoenzyme while regenerating cofactors directly from glucose. By externally supplying radical precursors or by introducing synthetic pathways for their in situ production, we enabled fermentation-based microbial photobiosynthesis, achieving high titers and demonstrating its feasibility for scale-up in bioreactor. This approach extends photobiocatalysis from in vitro applications to in vivo semi-biosynthesis and complete biosynthesis, revealing its full potential for integrating light-driven reactions into cellular metabolism.

Bioproducts↗

DOE OSTI2020

Sorbents for the oxidation and removal of mercury

A promoted activated carbon sorbent is described that is highly effective for the removal of mercury from flue gas streams. The sorbent comprises a new modified carbon form containing reactive forms of halogen and halides. Optional components may be added to increase reactivity and mercury capacity. These may be added directly with the sorbent, or to the flue gas to enhance sorbent performance and/or mercury capture. Mercury removal efficiencies obtained exceed conventional methods. The sorbent can be regenerated and reused. Sorbent treatment and preparation methods are also described. New methods for in-flight preparation, introduction, and control of the active sorbent into the mercury contaminated gas stream are described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Sorbents for the oxidation and removal of mercury

A promoted activated carbon sorbent is described that is highly effective for the removal of mercury from flue gas streams. The sorbent comprises a new modified carbon form containing reactive forms of halogen and halides. Optional components may be added to increase reactivity and mercury capacity. These may be added directly with the sorbent, or to the flue gas to enhance sorbent performance and/or mercury capture. Mercury removal efficiencies obtained exceed conventional methods. The sorbent can be regenerated and reused. Sorbent treatment and preparation methods are also described. New methods for in-flight preparation, introduction, and control of the active sorbent into the mercury contaminated gas stream are described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Amino acids react with carbon dioxide (CO2) and form nanofibers and nanoflowers

A method for capturing CO2 comprising dissolving at least one pure amino acid (AA) in water without the use of a catalyst for establishing protonation of an amino group of the amino acid, adding at least one base solution to the amino acid and water solution to deprotonate the protonated amino group of the amino acid and forming an amino acid-XOH—H2O wherein X is sodium or potassium, and subjecting CO2 to the amino acid-XOH—H2O to form new nanomaterials is provided. A regenerable nanofiber is disclosed comprising a NaHCO3 nanofiber, a KHCO3 nanofiber, or an amino acid nanofiber made from subjecting a CO2 gas to an amino acid aqueous solvent. Preferably, the amino acid aqueous solvent is one or more of a Gly-NaOH—H2O, an Ala-NaOH—H2O, a Phe-NaOH—H2O, a Gly-KOH—H2O, an Ala-KOH—H2O, and a Phe-KOH—H2O.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Sorbents for the oxidation and removal of mercury

A promoted activated carbon sorbent is described that is highly effective for the removal of mercury from flue gas streams. The sorbent comprises a new modified carbon form containing reactive forms of halogen and halides. Optional components may be added to increase reactivity and mercury capacity. These may be added directly with the sorbent, or to the flue gas to enhance sorbent performance and/or mercury capture. Mercury removal efficiencies obtained exceed conventional methods. The sorbent can be regenerated and reused. Sorbent treatment and preparation methods are also described. New methods for in-flight preparation, introduction, and control of the active sorbent into the mercury contaminated gas stream are described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Methods for stabilizing biological and soft materials for atom probe tomography

Techniques are disclosed for stabilizing soft specimen traditionally considered too fragile for APT instruments. These specimens include biological samples, polymers and other fragile materials. For this purpose, a protective structure is disclosed that surrounds the sides of the specimen by supporting walls while only exposing the very end or terminus of the specimen to the electrostatic field of the APT instrument. The protective structure may take the form of a nanoscale conical grinder which continually machines the specimen to regenerate the terminus of the specimen in-situ. Alternately, the protective structure may take the form of a nanopipette in which the specimen is first frozen before undergoing field evaporation together with the tip of the nanopipette. Heretofore only routinely possible for rigid and hard materials, the design thus extends APT analysis to produce three-dimensional atomic-scale maps of soft specimens.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Pyrolysis Vapor and Bio-Oil Preconditioning via Ex Situ Hydrodeoxygenation and Alkylation Using a Heteropolyacid Catalyst

Ex situ catalytic preconditioning of biomass pyrolysis vapors (partial deoxygenation) has the potential for both reducing the oxygen content and beneficially influencing the oxygen speciation of condense bio-oils for enhancement of downstream condensed phase upgrading processes. Here, condensed phase upgrading processes may refer to both coprocessing and hydroprocessing with vacuum gas-oil (VGO). Reduction of oxygen content to produce bio-oils with greater hydrophobicity can enhance VGO-solubility while tailoring of oxygen speciation by removal of reactive carbonyls (e.g., acetic acid) can lessen catalytic deactivation via coking reactions. 1,2 Furthermore, enhanced VGO-solubility and reduced coking leads to greater biogenic carbon incorporation in end-products from condensed phase upgrading processes. By leveraging the hydrodeoxygenation and alkylation activity of a titania-supported molybdenum-heteropolyacid (Mo-HPA/TiO2) catalyst, pyrolysis vapors and resulting condensed bio-oils were effectively preconditioned for downstream upgrading. 3 Data regarding the use of Mo-HPA/TiO2 for pyrolysis vapor preconditioning will be presented on, including method of employment, catalyst characterization, and impacts on bio-oil in relation to downstream condensed phase upgrading processes. Our approach is to: Compare Mo-HPA/TiO2 product distribution to HZSM-5; Investigate Mo-HPA/TiO2 regeneration and characterize changes in acid site character; Assess product differences in terms of enhanced VGO-solubility.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

Capture and release of acid gasses using tunable organic solvents with aminopyridine

A class of water lean, organic solvents that can bind with various acid gasses to form acid gas bound molecules having a high degree of intramolecular hydrogen bonding which enables their use as regenerable solvents for acid gas capture. Unlike the other devices described in the prior art, the present invention takes advantage of shortened distances between the portions of the molecule that form hydrogen bonds within the structures when loaded with an acid gas so as to create a molecule with a higher internal bonding affinity and a reduced proclivity for agglomeration with other molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Capture and release of acid gasses using tunable organic solvents with aminopyridine

A class of water lean, organic solvents that can bind with various acid gasses to form acid gas bound molecules having a high degree of intramolecular hydrogen bonding which enables their use as regenerable solvents for acid gas capture. Unlike the other devices described in the prior art, the present invention takes advantage of shortened distances between the portions of the molecule that form hydrogen bonds within the structures when loaded with an acid gas so as to create a molecule with a higher internal bonding affinity and a reduced proclivity for agglomeration with other molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Membrane-Based Air Dehumidification Using Organic Ionic Liquid Desiccant

Membrane Ionic Liquid Desiccant Air Dehumidification (MILDAD) is a promising alternative to conventional dehumidification systems that employ mechanical compressors and refrigerant-based cooling with evaporator and condensing coils. However, its application has been limited due to high manufacturing and installation cost, durability issues, concerns with corrosion due to leakage and salt carry over into the downstream air and onto surfaces. This paper reviews substantial progress made with new systems based on combining advanced ionic membranes that are pressure resistant, thin walled with high water permeability, and non-porous with synthetic organic, non-crystalline ionic liquid desiccants. Alternative design configurations are discussed comparing cross flow shell-and-tube membrane contactors employing ionic membrane tubes through which ionic liquid desiccant air flows. Performance data for MILDAD prototypes is provided. Dehumidification of the incoming supply airstream and regeneration into exhausted building air is demonstrated. The latent effectiveness of the MILDAD system will be discussed along with some future steps to improve performance of the system.

Bahar, Bamdad↗

DOE OSTI2021

Sorbents for the oxidation and removal of mercury

A promoted activated carbon sorbent is described that is highly effective for the removal of mercury from flue gas streams. The sorbent comprises a new modified carbon form containing reactive forms of halogen and halides. Optional components may be added to increase reactivity and mercury capacity. These may be added directly with the sorbent, or to the flue gas to enhance sorbent performance and/or mercury capture. Mercury removal efficiencies obtained exceed conventional methods. The sorbent can be regenerated and reused. Sorbent treatment and preparation methods are also described. New methods for in-flight preparation, introduction, and control of the active sorbent into the mercury contaminated gas stream are described.

Olson, Edwin S.↗