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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Assessing the impact of substrate-level enzyme regulations limiting ethanol titer in Clostridium thermocellum using a core kinetic model

Clostridium thermocellum is a promising candidate for consolidated bioprocessing because it can directly ferment cellulose to ethanol. Despite significant efforts, achieved yields and titers fall below industrially relevant targets. This implies that there still exist unknown enzymatic, regulatory, and/or possibly thermodynamic bottlenecks that can throttle back metabolic flow. By (i) elucidating internal metabolic fluxes in wild-type C. thermocellum grown on cellobiose via 13 C-metabolic flux analysis ( 13 C-MFA), (ii) parameterizing a core kinetic model, and (iii) subsequently deploying an ensemble-docking workflow for discovering substrate-level regulations, this paper aims to reveal some of these factors and expand our knowledgebase governing C. thermocellum metabolism. Generated 13 C labeling data were used with 13 C-MFA to generate a wild-type flux distribution for the metabolic network. Notably, flux elucidation through MFA alluded to serine generation via the mercaptopyruvate pathway. Using the elucidated flux distributions in conjunction with batch fermentation process yield data for various mutant strains, we constructed a kinetic model of C. thermocellum core metabolism (i.e. k-ctherm138). Subsequently, we used the parameterized kinetic model to explore the effect of removing substrate-level regulations on ethanol yield and titer. Upon exploring all possible simultaneous (up to four) regulation removals we identified combinations that lead to many-fold model predicted improvement in ethanol titer. In addition, by coupling a systematic method for identifying putative competitive inhibitory mechanisms using K-FIT kinetic parameterization with the ensemble-docking workflow, we flagged 67 putative substrate-level inhibition mechanisms across central carbon metabolism supported by both kinetic formalism and docking analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale

The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and a few genetic perturbations thereof. Unlike stoichiometric models that are mostly invariant to the specific strain, it remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. This important question underpins the applicability range and prediction limits of kinetic reconstructions. To this end, herein we parameterize two separate large-scale kinetic models using K-FIT with genome-wide coverage corresponding to two distinct strains of Saccharomyces cerevisiae: CEN.PK 113-7D strain (model k-sacce306-CENPK), and growth-deficient BY4741 (isogenic to S288c; model k-sacce306-BY4741). The metabolic network for each model contains 306 reactions, 230 metabolites, and 119 substrate-level regulatory interactions. The two models (for CEN.PK and BY4741) recapitulate, within one standard deviation, 77% and 75% of the fitted dataset fluxes, respectively, determined by 13 C metabolic flux analysis for wild-type and eight single-gene knockout mutants of each strain. Strain-specific kinetic parameterization results indicate that key enzymes in the TCA cycle, glycolysis, and arginine and proline metabolism drive the metabolic differences between these two strains of S. cerevisiae. Our results suggest that although kinetic models cannot be readily used across strains as stoichiometric models, they can capture species-specific information through the kinetic parameterization process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis

Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PP i ) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PP i sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PP i synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PP i -generating cycles. In all cases, the metabolic cost of PP i synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PP i could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PP i sources likely account for most PP i production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PP i levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (k app ) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Altogether, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism

Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13 C and 2 H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2 H-labeled nutrient substrates faces limitations due to their high cost and limited availability in comparison to 13 C-tracers. Furthermore, isotope tracer studies in industrially relevant bacteria that metabolize complex substrates such as cellulose, hemicellulose, or lignocellulosic biomass, are challenging given the difficulty in obtaining these as isotopically labeled substrates. In this study, we examine the potential of deuterated water ( 2 H 2 O) as an affordable, substrate-neutral isotope tracer for studying central carbon metabolism. We apply 2 H 2 O labeling to investigate the reversibility of glycolytic reactions across three industrially relevant bacterial species -C. thermocellum, Z. mobilis, and E. coli-harboring distinct glycolytic pathways with unique thermodynamics. We demonstrate that 2 H 2 O labeling recapitulates previous reversibility and thermodynamic findings obtained with established 13 C and 2 H labeled nutrient substrates. Furthermore, we exemplify the utility of this 2 H 2 O labeling approach by applying it to high-substrate C. thermocellum fermentations -a setting in which the use of conventional tracers is impractical-thereby identifying the glycolytic enzyme phosphofructokinase as a major bottleneck during high-substrate fermentations and unveiling critical insights that will steer future engineering efforts to enhance ethanol production in this cellulolytic organism. This study demonstrates the utility of deuterated water as a substrate-agnostic isotope tracer for examining flux and reversibility of central carbon metabolic reactions, which yields biological insights comparable to those obtained using costly 2 H-labeled nutrient substrates.

09 BIOMASS FUELS↗
DOE OSTI2024

KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states

Large-scale kinetic models provide the computational means to dynamically link metabolic reaction fluxes to metabolite concentrations and enzyme levels while also conforming to substrate level regulation. However, the development of broadly applicable frameworks for efficiently and robustly parameterizing models remains a challenge. Challenges arise due to both the heterogeneity, paucity, and difficulty in obtaining flux and/or concentration data but also due to the computational difficulties of the underlying parameter identification problem. Both the computational demands for parameterization, degeneracy of obtained parameter solutions and interpretability of results has so far limited widespread adoption of large-scale kinetic models despite their potential. Herein, we introduce the Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the (non)steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP is benchmarked against previously parameterized large-scale kinetic models demonstrating an at least an order of magnitude faster convergence than the tool K-FIT while at the same time attaining better data fits. Finally, this versatile toolbox accepts different kinetic descriptions, metabolic fluxes, enzyme levels and metabolite concentrations, under either steady-state or instationary conditions to enable robust kinetic model construction and parameterization. KETCHUP supports the SBML format and can be accessed at https://github.com/maranasgroup/KETCHUP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Metabolic flux and resource balance in the oleaginous yeast Rhodotorula toruloides

The yeast Rhodotorula toruloides is a promising bioproduction organism due to its high lipid yields and ability to grow on cheap and abundant substrates. Quantitative, systems-level assessment of its metabolic activity is accordingly merited. Resource-balance analysis (RBA) models capture not only reaction stoichiometry but also enzyme requirements for catalysis, providing valuable tools for understanding metabolic trade-offs and optimizing metabolic engineering strategies. Here, in this work, we present systems-level measurements of R. toruloides metabolic flux based on isotope tracing and metabolic flux analysis. In combination with new proteomic measurements, these flux data are used to parameterize a genome-scale resource balance model rtRBA. We find that S. cerevisiae and R. toruloides grow at nearly indistinguishable rates using similar biosynthetic but dramatically different central metabolic programs. R. toruloides consumes one-fifth as much glucose, which it metabolizes primarily via the pentose phosphate pathway and TCA cycle unlike primarily glycolysis in S. cerevisiae . Overall, across these two divergent yeasts, protein abundances aligned more closely than metabolic flux. Resource balance modeling of these metabolic programs predicts superior theoretical yields but lower productivities in R. toruloides than S. cerevisiae for industrial chemicals, highlighting the value of rapid glucose uptake for productivity but respiratory metabolism for yields.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

OzDES Reverberation Mapping of Active Galactic Nuclei: Final Data Release, Black-Hole Mass Results, & Scaling Relations

Over the last decade, the Australian Dark Energy (OzDES) collaboration has used Reverberation Mapping to measure the masses of high redshift supermassive black holes. Here we present the final review and analysis of this OzDES reverberation mapping campaign. These observations use 6-7 years of photometric and spectroscopic observations of 735 Active Galactic Nuclei (AGN) in the redshift range 0.13-3.85 and bolometric luminosity range 44.3 - 47.5 erg/s. Both photometry and spectra are observed in visible wavelengths, allowing for the physical scale of the AGN broad line region to be estimated from reverberations of the H{̱e̱ṯa̱}̱, MgII and CIV emission lines. We successfully use reverberation mapping to constrain the masses of 62 super-massive black holes, and combine with existing data to fit a power law to the lag-luminosity relation for the H{̱e̱ṯa̱}̱ and MgII lines with a scatter of ~0.25 dex, the tightest yet identified, fit specifically for consistency with high redshift AGN. We fit a similarly constrained relation for CIV, resolving a tension with the low luminosity literature AGN by accounting for selection effects arising from finite survey length. We also examine the impact of emission line width and luminosity (related to accretion rate) in reducing the scatter of these scaling relationships and find no significant improvement over the lag-only approach for any of the three lines. Using these relations, we further estimate the masses and accretion rates of 246 AGN with single epoch methods. We also use these relations to estimate the relative sizes of the H{̱e̱ṯa̱}̱, MgII and CIV emitting regions. In short, we provide a comprehensive benchmark of high redshift AGN reverberation mapping at the close of this most recent generation of surveys, including light curves, time-delays, and a set of significantly improved radius-luminosity relations for use with high-redshift populations.

McDougall, Hugh [Queensland U.]↗
DOE OSTI2025

Halide Vapor Phase Epitaxy of Ge from an Elemental Source

Halide vapor phase epitaxy shows promise for low-cost photovoltaic device manufacturing because of its high growth rates and lower cost elemental precursors but previously has not been used to deposit epitaxial Ge. Here, we demonstrate Ge deposition by generating GeCl 2 in situ from solid Ge and HCl in a N 2 ambient. To achieve Ge growth, we inject AsH 3 and PH 3 as sources of active hydrogen to the growth surface to create a driving force for growth. We do not observe Ge growth unless a supply of hydrogen is added, consistent with thermodynamic calculations. Furthermore, we show the hydrogen source must crack readily on the substrate surface to enable growth; relatively stable sources such as H 2 do not cause growth. Unintentional group V doping is one drawback of using AsH 3 and PH 3 to drive the Ge reaction. We observed As or P concentrations in the Ge films ranging from 4 x 10 17 to 1 x 10 18 atoms/cm 3 , concentrations that can drastically influence device characteristics. However, we note there are numerous other "helper molecule" options that can provide active hydrogen without doping or etching the material. This work provides a path forward for Ge deposition for optoelectronic devices from an elemental source.

14 SOLAR ENERGY↗
DOE OSTI2026

Comparability of Liquid Chromatography Tandem Mass Spectrometry Analysis of Dissolved Organic Matter across Laboratories

Non-targeted liquid chromatography tandem highresolution mass spectrometry (LC−MS/MS) is increasingly applied for the structure-resolved chemical analysis of dissolved organic matter (DOM). With new developments in MS instrumentation and analysis software, the approach has gained substantial momentum over the past decade. However, achieving high-quality analytical data that is reproducible and comparable across laboratories can be a bottleneck in non-targeted metabolomics and organic matter chemical analysis, especially for data reuse in repository-scale analyses. Understanding the capabilities as well as challenges of comparing LC−MS/MS data from different laboratories is necessary for inferring global trends from public data sets. To illuminate instrumentation factors that drive differences and variability, we used a standardized data analysis pipeline, including classical (CMN) and featurebased molecular networking (FBMN), to analyze data from a ring trial by 24 laboratories on identical sample sets of algal and DOM extracts that were mixed in predefined concentrations and spiked with standards. Our results showed that data sets from similar mass spectrometer types with unified instrument parameters were qualitatively comparable, resolving the same general trends and shared mass spectral features. Interlaboratory comparability was best for high-intensity features, while low-intensity features showed greater detection variability. Our analysis also highlights challenges when comparing data from instruments with different acquisition rates or operating with less standardized methods. Lastly, we provide recommendations for data integration, public data sharing, standardization, and best practices for standardized LC−MS/MS data acquisition, which will be critical for long-term time series and intercomparability of DOM chemical analyses.

DOM↗
DOE OSTI2026

Hypophosphite Is a Naturally Occurring Selective Inhibitor of Syntrophic Methanogenesis

Microbial methanogenesis is a major contributor to global warming, and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still underexplored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with the exchange of syntrophic electron carriers (H 2 or formate) in methanogenic systems presents an additional target for methane control. Here, we show that hypophosphite (H 2 PO 2 − ), an inorganic formate analogue, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively nontoxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation, and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate the carbon cycle in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive strategy for methane control in syntrophic methanogenic ecosystems.

chemical inhibitor↗
DOE OSTI2020

Uranium recovery from seawater using amidoxime-based braided polymers synthesized from acrylic fibers

Global demand for nuclear energy is expected to rise in the coming decades. To meet these growing needs, new uranium resources must be explored. One of the potential alternatives to traditional uranium mining is oceanic uranium. The capture and recovery of uranium from the ocean has been under investigation for some time, with many recent studies focused on amidoxime based adsorbents. These adsorbents while able to achieve high uranium recovery capacities are, nevertheless, expensive to produce and adsorb a significant amount of hard to remove vanadium. The purpose of this study is to evaluate the adsorption performance of amidoxime based polymer braids synthesized from acrylic fibers which are designed to significantly cut polymer synthesis and conditioning costs. Adsorption experiments were performed in a recirculating raceway flume system at environmental conditions, approximately 10.8 oC, with 40-micron prefiltered seawater over 28 days for small and large sized LCW polymer braids. For both braid sizes, the adsorption of vanadium was far lower on the LCW materials than on Oak Ridge National Laboratory’s amidoxime based AF1 and AI8 small braids, with the LCW small braids outperforming both materials with respect to uranium adsorption under similar conditions. Adsorption modeling was used to simulate the performance at higher temperatures based on 20oC experiments previously performed with similar materials. Simulation results indicated that the small LCW braids would have a less significant advantage with respect to uranium adsorption over both AF1 and AI8 at 20oC and adsorb slightly less uranium than AF1 at 31oC. Vanadium adsorption by LCW small braids was less than one third of vanadium adsorption by either AF1 or AI8 for all temperatures. This behavior indicates that the LCW materials are able to achieve comparable uranium adsorption to other amidoxime adsorbents previously developed, while being cheaper to produce and adsorbing significantly less vanadium.

Wiechert, Alexander I.↗
DOE OSTI2020

Continuous-Flow Centrifugal Solid/Liquid Separation for the Recovery of Rare-Earth Elements Containing Particles from Phosphoric Acid Sludge

Phosphoric acid sludge contains acid (~54% P 2 O 5 ) and solid precipitates including rare earth elements (REEs) at concentrations of ~2200 ppm. Low-cost recovery of valuable P 2 O 5 and simultaneous solid separation could be an economically feasible approach to recovering REEs while increasing the production of phosphoric acid. The sludge, however, is a complicated stream that cannot be separated by traditional technologies because of high viscosity and a large solid content (30–40%). Guided by a force balance model, an efficient solid/liquid separation method is demonstrated, using a continuous-flow centrifugal contactor. Additionally, the shear regime is bypassed by introducing the sludge directly into the rotor where a centrifugal force is exerted on the fluid, inducing phase separation. Solid particles are trapped in the contactor. High liquid recovery is demonstrated and the effects of process parameters on solid capture are investigated. Three contactors in series yield 94% recovery of solids containing 1500–2895 ppm of REEs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Rate-Based Absorption Modeling for Postcombustion CO 2 Capture with Additively Manufactured Structured Packing

Carbon capture using amine-based solvents in an absorption process is a leading candidate for reducing greenhouse gas emissions in industrial flue gas streams. To reduce operating costs and associated parasitic energy of these processes, process intensification utilizing additively manufactured structured packing has emerged as a new technology to manage exothermic reactions during absorption while improving CO 2 capture. A rate-based model framework has been developed for these novel packings that incorporates the mass and heat transfer phenomena for amine-based absorption of CO 2 . The rate-based model framework is first benchmarked using available solubility data and pilot plant data for aqueous monoethanolamine. The model validation shows accurate prediction of both CO 2 equilibrium partial pressures and ion speciation for solubility data as well as CO 2 capture, temperature profile, and solvent composition for pilot plant data in the absorption column. The model framework is then applied toward predicting the CO 2 capture performance of additively manufactured structured packing. Simulations agree with experimental data in predicting the CO 2 capture and the capture performance increase due to cooling within the structured packing device. Finally, advantages of this rate-based model framework are the utilization of correlations that may predict mass transfer and heat transfer coefficients of the packing based on the geometric properties of the device and the implementation of the model framework in open-source programming.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Corrosion Prevention of Additively Manufactured Aluminum Packing Devices Developed for Process Intensification of CO 2 Capture by Aqueous Amines

Corrosion of additively manufactured (i.e., 3D printed) aluminum packing devices, developed to enhance heat and mass transfer in CO 2 absorption columns using amine-CO 2 scrubbing solutions, is investigated in this paper. The aluminum structures printed by selective laser melting with Al-10Si-0.3Mg feed powder are susceptible to corrosion in aqueous monoethanolamine, both fresh and used CO 2 -saturated solutions. The efficacy of corrosion-protective surface layers of aqueous polyether–ketone–ketone (PEKK) dip coating to provide amine corrosion resistance to the 3D printed aluminum structure is also evaluated. PEKK nanothick layers were coated on the corrugated surface of a 3D printed structure, identical to that of the intensified device, yielding 27 times higher corrosion resistance than the uncoated Al alloy surface. Finally, a systematic long-term electrochemical corrosion analysis revealed that a multilayer PEKK dip coating protocol enables protection of the 3D printed Al alloy surface in various CO 2 –monoethanolamine solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗