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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
NASA NTRSDate not supplied

AMMPER: a user-friendly agent-based model that recapitulates simple metabolic responses of yeast to deep-space radiation

For humans venturing to deep space, radiation exposure poses a major health risk. Fundamental research into the biological effects of space radiation are essential for enabling exploration, and the first experimental organisms we send to deep space will be microbial. Yet there are many ways in which microorganisms are likely to experience the effects of high-energy particle radiation (such as Galactic Cosmic Rays) differently from multicellular animals, partly due to the simple fact that microbes are small and unicellular-- less likely to get hit in the first place, and less likely to communicate damage between cells. Computational modeling can aid in designing experiments and predicting the biological effects of radiation, but thus far particle radiation models have not focused on microbes. Here we present the latest developments in AMMPER, the Agent-based Model for Microbial Populations Exposed to Radiation. Originally written in 2021, AMMPER is a Python-based model that incorporates radiation track data from NASA's RITRACKS software and simulates the growth, damage, and death of yeast cells in 3D. It is now freely available as an open-source package on NASA's GitHub repository. Recent improvements include the ability to simulate the dynamics of alamarBlue, a color-changing redox dye commonly used to track metabolic activity in microbial spaceflight experiments. We demonstrate that a simple blue-pink-clear transition model is able to recapitulate key features observed in empirical data from ground studies. AMMPER also includes a new graphical user interface and introductory tutorial to facilitate ease of use by a wider audience. AMMPER can help us to understand how spatially heterogeneous particle radiation damage at the single-cell level can translate to growth differences at the population level, ultimately allowing us to better interpret experiments using microbes as model organisms and how well their results apply to humans.

yeast↗
DOE OSTI2024

Design, Synthesis, and Validation: Genome Scale Optimization of Energy Flux through Compartmentalized Metabolic Networks in a Model Photosynthetic Eukaryotic Microbe (Final Report)

Photosynthetic organisms have recently gained considerable attention for a role in development of renewable energy sources. Genome-enabled systems biology methodology and modeling, coupled with high throughput genome engineering strategies, present opportunities to develop sustainable and economical applications such as fuel production within the next 10 to 15 years. However, optimization of light-driven metabolism for biomass or biofuel production will require significant advances in methodological throughput as well as improvements in detailed systems biology understanding of photosynthetic processes and cellular metabolism. The ability of diatoms to thrive in upwelling-induced, periodically nutrient-rich conditions makes them the base for the world’s shortest and most energy-efficient food webs. Diatom photosynthesis is estimated to account for between 25% and 40% of the 45-50 billion tons of organic carbon fixed annually in the sea.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2020

Modeling Electrolytic Conversion of Metabolic CO2 and Optimizing a Macrofluidic Electrochemical Reactor for Advanced Closed Loop Life Support Systems

The International Space Station (ISS) is currently equipped with a complex, heavy, and power consuming system that recovers approximately 50% of O2 from metabolic CO2. Future long duration missions will require a sustainable and highly efficient system capable of yielding a minimum of 75% O2 recovery. A Macrofluidic Electrochemical Reactor (MFECR) technology development effort is currently underway at NASA Marshall Space Flight Center (MSFC) to significantly increase current O2 recovery efficiency and reduce complexity of the system. This paper presents a comprehensive multi-physic 3D model developed at MSFC on CO2 conversion to O2 and C2H4 at standard conditions via MFECR. The 3D spatial domain of the model is a replica of the actual MFECR’s 3D drawing generated for the MFECR fabrication and operated to recover O2 from CO2 yielding C2H4 as byproduct. Electrochemical (EC) physics that includes EC multicomponent reaction mechanisms, mass transport, and current density distributions is coupled in the model with all the other physics phenomena involved in the process, such as free and porous fluid flow, multicomponent mass transfer, heat transfer, and DC electrical current generation along with Joule heating effect. The authors plan to use experimental results to validate this comprehensive and rigorous model and build a reliable simulator that will not only assist the authors on the MFECR design but also optimize its operation.

Dominguez, Jesus A.↗
DOE OSTI2025

Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance

Central carbon metabolism in model cyanobacteria involves multiple pathways to adapt to energy-light limitations across diel cycles. However, the success in mechanistic modeling for phenotypic prediction of the protein regulators in the metabolic state depends on capturing the vast possibilities emerging from multiple regulatory pathways in complex biological processes. Here, we developed a physics-informed machine learning approach based on energy-landscape concepts to predict regulatory proteins responding to cyclic circadian and unforeseen light perturbations in cyanobacterial metabolic networks. Our approach provides interpretable de novo models for inferring gene expression dynamics from Synechococcus elongatus over diel cycles and using redox proteome analysis to distinguish immediate light-responsive elements from circadian-regulated processes in carbon metabolism pathways. We identified distinct temporal signatures with the analysis of the redox proteome: there was an immediate shift in cysteine redox states accompanied by a limited change in protein abundance under constant illumination and after 2 hours of darkness. This discovery indicates that the generation of reductants coordinates photoinduced electron transport with redox metabolic pathways in two discernable molecular mechanisms: fast redox-based protein modifications occur immediately after the light disturbance, followed by slow transcriptional regulations across networks. This temporal regulation reveals how metabolic networks integrate rapid light responses with programmed circadian rhythms to maintain cellular homeostasis under the light-energy limitations over the diel cycle.

Biomolecular & subcellular processes↗
DOE OSTI2024

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including $\tiny{L}$-glutamine, $\tiny{D}$-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hyporheic‐Zone Processes and Stream Oxygen Dynamics: Insights From a Multiscale Reactive Transport Model

Aquatic ecosystem metabolism encapsulates the daily fixation (gross primary production, GPP d ) and mineralization (ecosystem respiration, ER d ) of organic carbon. In fluvial systems, these are commonly estimated by inverse solutions to field observations using a model that describes oxygen concentrations varying in the water column in response to metabolic fluxes and air‐water gas exchange controlled by a rate coefficient (K 600 ). The most common conceptual model is the single‐station metabolism (SSM) model. The simplicity and flexibility of this conceptualization make it attractive; however, it implicitly assumes that all the processes that consume oxygen in fluvial systems can be lumped into a bulk estimate of respiration with poorly understood consequences for estimates of GPP d , ER d , and K 600 . Here, we focus on the implications of using SSM conceptualization when estimating metabolic fluxes from oxygen dynamics in channels where hyporheic exchange occurs. We use a new multiscale numerical model for reactive transport in streams that represents hyporheic exchange and streambed heterotrophic respiration. Nondimensionalization of this model reveals dimensionless groups that collectively control oxygen dynamics. Numerical experiments offer a mechanistic understanding of the impacts of hyporheic exchange on diel oxygen dynamics revealing that potential biases arise from neglecting mass transfer limitations. Specifically, we found that hyporheic exchange significantly affects diel oxygen dynamics, even for nonreactive streambed sediments. Moreover, while the SSM performs well in many situations, we find conditions where significant bias is produced by hyporheic exchange, even when oxygen data are well‐fitted. These situations pose a major challenge in the interpretation of metabolism assessment estimates.

Gomez‐Velez, Jesus D. [Oak Ridge National Laborato↗
DOE OSTI2024

Systems-Level Modeling for CRISPR-Based Metabolic Engineering

The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. Here, the advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

The response of Dahl salt-sensitive and salt-resistant female rats to a space flight model

Vitamin D metabolism in the Dahl salt-sensitive (S) rat, a model of salt-induced hypertension, differs from that in the Dahl salt-resistant (R) rat. We have tested the hypothesis that differences in vitamin D metabolism would render the Dahl S rat more susceptible than the Dahl R rat to the effects of a space flight model. Dahl female rats were tail suspended (hind limb unloaded) for 28 days, while fed a low salt (3 g/kg sodium chloride) diet. Plasma 25-OHD concentrations of S rats were significantly lower than that of R rats. Plasma 1,25-(OH)2D concentration was 50% lower in unloaded than in loaded S rats, but was unaffected in unloaded R rats. The left soleus muscle weight and breaking strength of the left femur (torsion test) were 50% and 25% lower in unloaded than in loaded S and R rats. The mineral content of the left femur, however, was significantly lower (by 11%) only in unloaded S rats. We conclude that female S rats are more vulnerable than female R rats to decreases in plasma 1,25-(OH)2D concentration and femur mineral content during hind limb unloading, but equally vulnerable to muscle atrophy and reduced breaking strength of the femur.

NASA Program Biomedical Research and Countermeasur↗
NASA NTRS1992

Modeling the effects of hypoxia on ATP turnover in exercising muscle

Most models of metabolic control concentrate on the regulation of ATP production and largely ignore the regulation of ATP demand. We describe a model, based on the results of Hogan et al. (J. Appl. Physiol. 73: 728-736, 1992), that incorporates the effects of ATP demand. The model is developed from the premise that a unique set of intracellular conditions can be measured at each level of ATP turnover and that this relationship is best described by energetic state. Current concepts suggest that cells are capable of maintaining oxygen consumption in the face of declines in the concentration of oxygen through compensatory changes in cellular metabolites. We show that these compensatory changes can cause significant declines in ATP demand and result in a decline in oxygen consumption and ATP turnover. Furthermore we find that hypoxia does not directly affect the rate of anaerobic ATP synthesis and associated lactate production. Rather, lactate production appears to be related to energetic state, whatever the PO2. The model is used to describe the interaction between ATP demand and ATP supply in determining final ATP turnover.

Non-NASA Center↗
NASA NTRSDate not supplied

Modeling Electrolytic O2 Recovery from Metabolic CO2 for Advanced Closed Loop Life Support Systems in Extraterrestrial Human Missions

The International Space Station (ISS) is currently equipped with a complex, heavy, and power consuming system that recovers approximately 50% of O2 from metabolic CO2. Future long duration human missions to the Moon and Mars will necessitate a sustainable and highly efficient metabolic oxygen recovery system capable of yielding a minimum of 75% O2 recovery. A Macrofluidic Electrochemical Reactor (MFECR) technology development effort is currently underway at NASA Marshall Space Flight Center (MSFC) to significantly increase current metabolic O2 recovery efficiency, expand mission sustainability, and reduce complexity of the system. The novel design combines CO2 conversion to O2 along with C2H4 as byproduct and water electrolysis (currently conducted in two separate units) into a single compact unit that runs at standard conditions and is theoretically capable of generating O2 with a theoretical maximum metabolic CO2 conversion of 73% while consuming less than metabolic water. This paper presents a comprehensive multi-physic 3D model developed at MSFC on CO2 conversion to O2 and C2H4 at standard conditions via MFECR. The 3D spatial domain of the model is a replica of the actual MFECR’s 3D drawing generated for the MFECR fabrication and operated to recover O2 from CO2 yielding C2H4 as byproduct. Electrochemical (EC) physics that includes EC multicomponent reaction mechanisms, mass transport, and electrical current density distributions is coupled in the model with all the other physics phenomena involved in the MFECR’s process, such as two-phase flow, free and porous fluid regimes, multicomponent mass transfer, heat transfer, and DC electrical current generation along with Joule heating effect. The EC reaction sections of the MFECR consists of two porous gas diffusion electrodes (GDE) and an electrolyte serpentine channel sandwiched in the middle. The CO2 feeds the cathode serpentine channel and part of the O2 product is fed back to the anode serpentine chamber. An alkaline solution feeds the electrolyte serpentine chamber wetting the GDEs of both, the anode and cathode allowing the OH- ionic transport between them. The EC reactions in the cathode’s GDE yield C2H4 from CO2 and H2 from water while the EC reaction in the anode’s GDE yields O2. The authors will present in this paper the validation of the model using experimental data and the utilization of the validated model in building a reliable simulator that will not only assist the authors on the MFECR design but also the optimization of its operation in the ISS and future spatial human missions.

Jesus A Dominguez↗
NASA NTRS2004

High Salt Intake Promotes Urinary Loss of Vitamin D Metabolites by Dahl Salt-Sensitive Rats in a Space Flight Model

Vitamin D metabolism in the Dahl salt-sensitive (S) rat, a model of salt-induced hypertension, differs from that in the Dahl salt-resistant (R) rat. We have demonstrated that female S rats are more vulnerable than female R rats to decreases in plasma 25-hydroxyvitamin D (25-OHD) and 1,25-dihydroxyvitamin D (1,25-(OH)2D) concentrations during hind limb unloading (a space flight model). We report here on the response of the vitamin D endocrine system of S and R rats to hind limb unloading during high salt intake. Dahl female rats (9.7-week-old) were tail-suspended (hind limb unloaded) for 28 days, while fed a diet containing twice the salt in standard rat chow (2 % sodium chloride). Control rats were fed the same diet, but were not hind limb unloaded. Vitamin D metabolites were analyzed by HPLC and radioimmunoassay kits from Diasorin.

Thierry-Palmer, M.↗
NASA NTRS1974

Modifications to the steady-state 41-node thermoregulatory model including validation of the respiratory and diffusional water loss equations

After the simplified version of the 41-Node Stolwijk Metabolic Man Model was implemented on the Sigma 3 and UNIVAC 1110 computers in batch mode, it became desirable to make certain revisions. First, the availability of time-sharing terminals makes it possible to provide the capability and flexibility of conversational interaction between user and model. Secondly, recent physiological studies show the need to revise certain parameter values contained in the model. Thirdly, it was desired to make quantitative and accurate predictions of evaporative water loss for humans in an orbiting space station. The result of the first phase of this effort are reported.

Source record↗
NASA NTRS1994

Metabolic Cages for a Space Flight Model in the Rat

A variety of space flight models are available to mimic the physiologic changes seen in the rat during weightlessness. The model reported by Wronski and Morey-Holton has been widely used by many investigators, in musculoskeletal physiologic studies especially, resulting in accumulation of an extensive database that enables scientists to mimic space flight effects in the 1-g environment of Earth. However, information on nutrition or gastrointestinal and renal function in this space flight model is limited by the difficulty in acquiring uncontaminated metabolic specimens for analysis. In the Holton system, a traction tape harness is applied to the tail, and the rat's hindquarters are elevated by attaching the harness to a pulley system. Weight-bearing hind limbs are unloaded, and there is a headward fluid shift. The tail-suspended rats are able to move freely about their cages on their forelimbs and tolerate this procedure with minimal signs of stress. The cage used in Holton's model is basically a clear acrylic box set on a plastic grid floor with the pulley and tail harness system attached to the open top of the cage. Food is available from a square food cup recessed into a corner of the floor. In this system, urine, feces, and spilled food fall through the grid floor onto absorbent paper beneath the cage and cannot be separated and recovered quantitatively for analysis in metabolic balance studies. Commercially available metabolic cages are generally cylindrical and have been used with a centrally located suspension apparatus in other space flight models. The large living area, three times as large as most metabolic cages, and the free range of motion unique to Holton's model, essential for musculoskeletal investigations, were sacrificed. Holton's cages can accommodate animals ranging in weight from 70 to 600 g. Although an alternative construction of Holton's cage has been reported, it does not permit collection of separate urine and fecal samples. We describe the modifications to Holton's food delivery system, cage base, and the addition of a separator system for the collection of urine and fecal samples for metabolic and nutrition studies in the tail suspension model.

Harper, Jennifer S.↗
DOE OSTI2025

A physiologically based pharmacokinetic (PBPK) model to align dosimetry of the isobutyl metabolic series in rats and humans

Here, we developed a physiologically based pharmacokinetic (PBPK) model in rats and humans for the isobutyl metabolic series including isobutyl acetate, isobutanol, isobutyraldehyde, and isobutyric acid. Chemical manufactures routinely use these compounds as solvents, for chemical synthesis, as potential biofuels, de-icing fluids, and additives for food and/or fragrance in consumer products. Human exposure to isobutyl compounds can occur through inhalation or oral routes. We previously developed a PBPK model for the propyl metabolic series and utilized it as a framework to create the isobutyl PBPK model due to the chemical similarities between the two series. To support model development, we measured in vitro metabolism of isobutyl acetate in rat and human blood and liver S9 fractions. Compared to rats, humans demonstrated faster isobutyl acetate hydrolysis in liver S9 fractions, while the hydrolysis rates in blood were similar between the two species. We used concentrations of isobutyl compounds measured in air and blood from rats exposed to isobutyl acetate and isobutanol as well as other published data to further parameterize the model. Following exposure to either isobutyl acetate or isobutanol, we observed isobutanol concentrations highest among the isobutyl compounds in the blood of rats. Overall, the model accurately predicts measured time course concentrations of isobutyl acetate, isobutanol, and isobutyric acid in available data in rats and humans. Sensitivity analyses identified alveolar ventilation rates, isobutyl metabolism rates, and cardiac output as the most sensitive parameters affecting concentrations of isobutyl compounds in blood. The isobutyl PBPK model enables comparisons of internal dose metrics across various isobutyl compound exposures and species and allows for calculation of equivalent external exposures that result in the same dose metric. Regulators can employ this PBPK model to predict and align internal dose metrics of isobutyl compounds for risk assessment purposes.

2-methyl-1-propanol↗