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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 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Machine learning molecular dynamics simulations toward exploration of high-temperature properties of nuclear fuel materials: case study of thorium dioxide

Predicting materials properties of nuclear fuel compounds is a challenging task in materials science. Their thermodynamical behaviors around and above the operational temperature are essential for the design of nuclear reactors. However, they are not easy to measure, because the target temperature range is too high to perform various standard experiments safely and accurately. Moreover, theoretical methods such as first-principles calculations also suffer from the computational limitations in calculating thermodynamical properties due to their high calculation-costs and complicated electronic structures stemming from f-orbital occupations of valence electrons in actinide elements. Here, we demonstrate, for the first time, machine-learning molecular-dynamics to theoretically explore high-temperature thermodynamical properties of a nuclear fuel material, thorium dioxide. The target compound satisfies first-principles calculation accuracy because f-electron occupation coincidentally diminishes and the scheme meets sampling sufficiency because it works at the computational cost of classical molecular-dynamics levels. We prepare a set of training data using first-principles molecular dynamics with small number of atoms, which cannot directly evaluate thermodynamical properties but captures essential atomistic dynamics at the high temperature range. Then, we construct a machine-learning molecular-dynamics potential and carry out large-scale molecular-dynamics calculations. Consequently, we successfully access two kinds of thermodynamic phase transitions, namely the melting and the anomalous λ transition induced by large diffusions of oxygen atoms. Furthermore, we quantitatively reproduce various experimental data in the best agreement manner by selecting a density functional scheme known as SCAN. Our results suggest that the present scale-up simulation-scheme using machine-learning techniques opens up a new pathway on theoretical studies of not only nuclear fuel compounds, but also a variety of similar materials that contain both heavy and light elements, like thorium dioxide.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Mg vacancy and impurity-limited MgO single crystal thermal conductivity

Magnesium oxide (MgO) exhibits one of the highest thermal conductivities among oxides and is widely used as a dielectric material and substrate in semiconductor devices, in refractory applications, and as a promising filler in thermal interface materials for electronics. Its high thermal conductivity may be sensitive to impurity and defects, yet this influence is still uncertain. Here, in this study, the impact of the common impurities, i.e., Al, Ca, Ti, V, Fe, Si, B, Nb, Zr, Na, and K, as well as Mg and O vacancies on phonon scattering and thermal conductivity of MgO is studied using a fully first-principles T-matrix framework. It is found that B, Nb, and Zr impurities, along with Mg vacancies, lead to exceptionally strong reductions in thermal conductivity. By contrast, O vacancies and other impurities have modest to minimal impacts. Leveraging the T-matrix results, we reassess the perturbative, mass-only formalism whose use is pervasive in the literature and show that neglecting bond disorder does not necessarily lead to underestimation: for all transition-metal impurities studied, bond perturbations partially cancel mass disorder, causing the traditional perturbative model to overestimate scattering. We propose a simple modified perturbative expression that incorporates both mass and bond disorder and closely reproduces the T-matrix trends. Our predicted low-temperature trends by including phonon-impurity and phonon-boundary scattering match reasonably well with experiments. This work provides an in-depth study of impurity- and vacancy-limited thermal conductivity of MgO and suggests that reported “high-purity” MgO values have likely not yet reached the intrinsic upper limit, which may be substantially higher.

36 - MATERIALS SCIENCE↗
DOE OSTI2021

Development and validation of a gamma-ray detection response model for neutron-diagnosed subcritical experiments

In a neutron-diagnosed subcritical experiment, a highly sensitive and fast detector is required to accurately determine the true fission γ-ray emission rate from an object composed of special nuclear material under interrogation, in addition to a proper detector response model for use in forward modeling. We present the development of a detector response model that is based in GEANT4 and uses post-processing techniques to include photomultiplier tube time and pulse height response effects. We also define a set of detector performance evaluation metrics that emphasized our experimental objectives. A suite of time and pulse height response measurements for several diverse detector assemblies are described. These assemblies were simulated with this response model and benchmarked against the laboratory measurements. This response model reproduces the pulse height curve shapes and performance hierarchy of the measured detectors well. Additionally, the simulated time response curves exhibit reasonable agreement with counterpart measurements. These measurements and simulation results together suggest that a large volume EJ-299-49 plastic scintillator that is mated to an ultraviolet transmitting plastic light guide and relies on total internal reflection for light transport to the photocathode will provide significantly faster timing, increase pulse height by a factor of 3, and require 25% less γ rays to meet experimental needs, compared to the candidate detector design developed prior to the availability of this response model. Application of this response model and associated performance metrics in the context of large-scale design sensitivity studies is also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

High Values of the Arctic Amplification in the Early Decades of the 21st Century: Causes of Discrepancy by CMIP6 Models Between Observation and Simulation

Arctic Amplification (AA) in the first decade of the 21st century has reached values between 4 and 5, with a subsequent decrease to current values of about 3.6, while the value was from 2 to 3 during the twentieth century. The ensemble mean of the CMIP6 models has difficulty in reproducing the recently observed high values of the AA. In this report, we identify the main reason for this difficulty to be the CMIP6 models overestimate of the mean global temperature trend since about 1990. The largest values of the AA are observed in winter and spring. A sharp AA peak in 1987 spring was caused by a peak in the Arctic temperature trend occurring at the same time as a dip in the trend of mean global temperature. The winter AA has increased almost monotonically since 1990. Dividing the AA between the Arctic land and ocean areas shows that the ocean area makes a larger contribution to the AA. Our future projection of the AA suggests an increasing AA for about the next decade, followed by a slow decrease to about 3.5 in the 2050s.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Limitations of Bin and Bulk Microphysics in Reproducing the Observed Spatial Structure of Light Precipitation

Abstract Coarse-gridded atmospheric models often account for subgrid-scale variability by specifying probability distribution functions (PDFs) of process rate inputs such as cloud and rainwater mixing ratios ( q c and q r , respectively). PDF parameters can be obtained from numerous sources: in situ observations, ground- or space-based remote sensing, or fine-scale modeling such as large-eddy simulation (LES). LES is appealing to constrain PDFs because it generates large sample sizes, can simulate a variety of cloud regimes/case studies, and is not subject to the ambiguities of observations. However, despite the appeal of using model output for parameterization development, it has not been demonstrated that LES satisfactorily reproduces the observed spatial structure of microphysical fields. In this study, the structure of observed and modeled microphysical fields are compared by applying bifractal analysis, an approach that quantifies variability across spatial scales, to simulations of a drizzling stratocumulus field that span a range of domain sizes, drop concentrations (a proxy for mesoscale organization), and microphysics schemes (bulk and bin). Simulated q c closely matches observed estimates of bifractal parameters that measure smoothness and intermittency. There are major discrepancies between observed and simulated q r properties, though, with bulk simulated q r consistently displaying the bifractal properties of observed clouds (smooth, minimally intermittent) rather than rain while bin simulations produce q r that is appropriately intermittent but too smooth. These results suggest fundamental limitations of bulk and bin schemes to realistically represent higher-order statistics of the observed rain structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Description of the LASSO Data Bundles Product

The U. S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) user facility began a pilot project in May 2015 to design a routine, high-resolution modeling capability to complement ARM’s extensive suite of measurements. This modeling capability has evolved into the Large-Eddy Simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) datastream. The datastream, broadly termed data bundles, contains high-resolution model output, input files, observations for evaluation, and skill scores for the simulations. The initial focus of LASSO is on shallow convection at the ARM Southern Great Plains (SGP) atmospheric observatory. The availability of LES simulations with concurrent observations serves many purposes. LES helps bridge the scale gap between DOE ARM observations and models, and the use of routine LES adds value to observations. It provides a self-consistent representation of the atmosphere and a dynamical context for the observations. Further, it elucidates unobservable processes and properties. LASSO generates a simulation library for researchers that enables statistical approaches beyond a single-case mentality. It also provides tools necessary for modelers to reproduce the LES and conduct their own sensitivity experiments. The LASSO library of data bundles is designed to facilitate a wide range of research. For an observationalist, LASSO can help inform instrument remote-sensing retrievals, conduct observation system simulation experiments (OSSEs), and test implications of radar scan strategies or flight paths. For a theoretician, LASSO can help calculate estimates of fluxes and co-variability of values, and test relationships without having to run the model personally. For a modeler, LASSO can help one know ahead of time which days have good forcing, have co-registered observations at high-resolution scales, and have simulation inputs and corresponding outputs to test parameterizations. Further details on the overall LASSO project are available at https://www.arm.gov/capabilities/modeling/lasso.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

High Values of the Arctic Amplification in Early Decades of the 21st Century: Causes of Discrepancy by CMIP6 Models Between Observation and Simulation

Arctic Amplification (AA) in the first decade of the 21st century has reached values between 4 and 5, with a subsequent decrease to current values of about 3.6, while the value was from 2 to 3 during the twentieth century. The ensemble mean of the CMIP6 models has difficulty in reproducing the recently observed high values of the AA. In this report, we identify the main reason for this difficulty to be the CMIP6 models overestimate of the mean global temperature trend since about 1990. The largest values of the AA are observed in winter and spring. A sharp AA peak in 1987 spring was caused by a peak in the Arctic temperature trend occurring at the same time as a dip in the trend of mean global temperature. The winter AA has increased almost monotonically since 1990. Dividing the AA between the Arctic land and ocean areas shows that the ocean area makes a larger contribution to the AA. Our future projection of the AA suggests an increasing AA for about the next decade, followed by a slow decrease to about 3.5 in the 2050s.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Differential Measurement of Circumstellar Extinction for AA Tau’s 2011 Dimming Event

AA Tau is a classical T Tauri star with a highly inclined, warped circumstellar disk. For decades, AA Tau exhibited photometric and spectroscopic variabilities that were successfully modeled as occultations of the primary star by circumstellar material. In 2011, AA Tau entered an extended faint state, presumably due to enhanced levels of circumstellar dust. We use two sets of contemporaneous optical–near-IR (NIR) spectra of AA Tau, obtained in 2008 and 2014 December, to directly measure the wavelength-dependent extinction associated with the dust enhancement driving AA Tau’s 2011 optical fade. Taken alone, AA Tau’s apparent optical–NIR increased extinction curve cannot be fit well with standard extinction laws. At optical wavelengths, AA Tau’s dimming event is consistent with predictions of common extinction models for an increase of A {sub V} = 2, but no such model reproduces AA Tau’s color–color excess at NIR wavelengths. We show that veiling emission accounts for the apparent anomalous NIR extinction: after including this veiling flux, AA Tau’s dimming event is consistent with a standard A {sub V} = 2 extinction law across the full optical–NIR range. We also report an increase in AA Tau’s mid-IR flux since its 2011 fade and suggest that an increase in the height of AA Tau’s inner disk is the most likely explanation for both the IR brightening and the additional extinction along the line of sight. In addition to informing our understanding of AA Tau, this analysis demonstrates that caution should be exercised when inferring extinction (and stellar parameters) from the NIR color–color excess of young stars with measurable NIR veiling fluxes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

A comparative analysis of YOLOv8 and U-Net image segmentation approaches for transmission electron micrographs of polycrystalline thin films

Metallic thin films offer a platform to experimentally study the dynamics of microstructural evolution, but the required transmission electron microscopy (TEM)-based imaging generates complex images that are challenging to segment and quantify. This work provides a comparative analysis of a new YOLOv8 model and an established U-Net model for bright-field TEM images of polycrystals, employing a framework leveraging physical observables to evaluate performance against two hand-traced benchmark datasets. This methodology obviates the comparison of large, diversely structured, and manually labeled datasets that are required to assess performance on a per-image/per-pixel basis. It is found that the YOLOv8 model, adapted for real-time instance segmentation, has up to 43× faster inferencing (NVIDIA GeForce RTX 4090) compared to U-Net and reconstructs hand-traced grain size distributions (GSDs) with excellent fidelity, finding mean diameter within 3% for grains near an optimal magnification; for grains that deviate from the optimal pixel-diameter, the size of small- (large)-diameter grains is systematically over- (under)-estimated. This is partially mitigated by including scale-aware augmentations during training. Moreover, when the bias is corrected post-inference by a rigid shift in distribution, the YOLOv8 model reproduces ground truth GSDs with exceptional fidelity, with statistical tests indicating <5% probability that the distributions are distinct. Based on ground truth data, calibration curves pertaining to this shift can be constructed for a given model. This issue is not present in the U-Net model’s results, indicating that for quantitative measurements where the true size of objects is of interest, special procedures must be implemented for YOLO-based models.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Electronegative metal dopants improve switching variability in Al 2 ⁢O 3 resistive switching devices

Resistive random-access memories are promising for nonvolatile memory and brain-inspired computing applications. High variability and low yield of these devices are key drawbacks hindering reliable training of physical neural networks. In this paper, we show that doping an oxide electrolyte, Al 2 ⁢O 3 , with electronegative metals makes resistive switching significantly more reproducible, surpassing the reproducibility requirements for obtaining reliable hardware neuromorphic circuits. Based on density functional theory calculations, the underlying mechanism is hypothesized to be the ease of creating oxygen vacancies in the vicinity of electronegative dopants due to the capture of the associated electrons by dopant midgap states and the weakening of Al-O bonds. These oxygen vacancies and vacancy clusters also bind significantly to the dopant, thereby serving as preferential sites and building blocks in the formation of conducting paths. Throughout this work, we validate this theory experimentally by implanting different dopants over a range of electronegativities in devices made of multiple alternating layers of Al 2 ⁢O 3 and WN and find superior repeatability and yield with highly electronegative metals, Au, Pt, and Pd. These devices also exhibit a gradual SET transition, enabling multibit switching that is desirable for analog computing.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Understanding Microstructure Variability in Vapor-Deposited Energetic Materials by Using Phase-Field Methods

Critical components, such as detonators, in Sandia's stockpile contain heterogeneous materials whose performance and reliability depend on accurate, predictive models of coupled, complex phenomena to predict their synthesis, processing, and operation. Ongoing research in energetic materials has shown that microstructural properties, such as density, pore-size, morphology, and specific surface area are correlated to their initiation threshold and detonation behavior. However, experiments to study these specific characteristics of energetic materials are challenging and time consuming. Therefore, in this work, we turn to mesoscale modeling methods that may be capable of reproducing some observed phenomena to refine and predict outcomes beforehand. Even so, we have no physics-based modeling capability to predict how the microstructure of an energetic material will evolve over near- and long-term time scales. Thus, the goal of this work is to (i) identify any knowledge gaps in how the underlying microstructure forms and evolves during the synthesis process, and (ii) develop and test a mesoscale phase-field model for vapor deposition to capture critical mechanisms of microstructure formation, evolution, and variability in vapor-deposited energetic materials, such as processing conditions, material properties, and substrate interactions. Based on this work, the phase-field method is shown to be a valuable tool for developing the necessary models containing coupled, complex phenomena to investigate and understand the synthesis and processing of energetic materials.

36 MATERIALS SCIENCE↗
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 OSTI2026

Electrostatic Gating of Ionic Conductance through Heterogeneous van der Waals Nanopores

Nanofluidic ionic transistors typically require gate voltages above 1 V and operate only at submillimolar ionic strengths, limiting their biocompatible applications. We demonstrate ionic transistors consisting of single sub-10 nm nanopores drilled in van der Waals (vdW) heterostructures with internal gate electrodes made of few-layer graphene. These devices deliver up to 10-fold current modulation at gate voltages as low as 0.3 V in 10 mM KCl, and ∼2-fold modulation at near-physiological 100 mM KCl. Baseline conductance with no gate shows surface-charge-dominated transport below 100 mM KCl, consistent with negatively charged hBN walls and ∼5 nm opening of the pores. The surface charge and the electrochemical asymmetry introduced by the three-electrode configuration govern the device’s behavior: negative gate voltage (V G ) enriches ionic concentrations and enhances current, whereas positive V G induces a local depletion zone that suppresses transport. The current modulation by V G is dependent on the polarity of the transmembrane potential and leads to ion current rectification. Molecular dynamics simulations of a nanopore in a hBN–graphene–hBN stack reveal confinement and surface charge-dependent suppression of the relative permittivity of interfacial water. Continuum modeling with radially varying interfacial water permittivity reproduces the asymmetric I–V characteristics and explains how the embedded gate sculpts local potential and ion concentrations. By enabling sub-0.5 V control of ionic transport at up to 100 mM salt concentrations, these devices address a key need in nanofluidics to create low-power ionic circuits and biosensing.

Materials science↗
DOE OSTI2024

Raman enhancement induced by exciton hybridization in molecules and 2D materials

Abstract Surface-enhanced Raman spectroscopy (SERS) is a powerful technique for trace-level fingerprinting. Recently, layered two-dimensional (2D) materials have gained significant interest as SERS substrates for providing stable, uniform, and reproducible Raman enhancement with the potential for trace-level detection. Yet, the development of effective 2D SERS substrates is still hindered by the lack of fundamental understanding of the coupling mechanism between target molecules and substrates. Here, we report a systematic excitation-dependent Raman spectroscopy investigation on the coupling between 2D materials such as SnS 2 , MoS 2 , WSe 2 , and graphene and small organic molecules like rhodamine 6G (Rh 6G). Strong coupling between SnS 2 and Rh 6G is found due to their degenerate excitons through Raman excitation profiles (REP), leading to the enhancement of Rh 6G vibrational modes that are observable down to 10 −13 M. Our study shows that exciton coupling in the substrate-adsorbate complex plays a vital role in the Raman enhancement effect, opening a new route for designing SERS substrates for high sensitivity.

Materials Science↗
DOE OSTI2025

Edge-localized mode mitigation enabled by active control of pedestal density gradient with new EAST tokamak divertor

Mitigation of large edge-localized modes (ELMs) has been achieved by actively reducing the pedestal density gradient with the EAST new right-angled lower divertor through changing the strike point position from the vertical target to the horizontal target. A series of dedicated experiments in the 2021–2024 EAST campaigns demonstrate that this ELM control solution is highly reproducible in a broad parameter space of edge safety factor q 95 = 4.7–7.1, heating power P total = 2.3–5 MW, and pedestal collisionality $ν_{e,ped}^{*}$ = 1–6, under both favorable and unfavorable magnetic configurations. Higher plasma density could facilitate the achievement of this ELM control solution. Statistical results indicate that the ELM mitigation effect can be observed at relatively larger Greenwald density fraction of f GW > 0.47. In addition, this ELM mitigation effect can be achieved with both lithium-coated and boronized metal walls. The pedestal density gradient is systematically lower in the horizontal target case than that of the vertical target case when the ELM mitigation effect can be observed. SOLPS-ITER simulation results indicate that the pedestal fueling from divertor recycling is significantly lower in the horizontal target case. This could contribute to the formation of a flattened pedestal density profile with small ELMs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Wavelet-based local mesh refinement for rainfall–runoff simulations

A wavelet-based local mesh refinement (wLMR) strategy is designed to generate multiresolution and unstructured triangular meshes from real digital elevation model (DEM) data for efficient hydrological simulations at the catchment scale. The wLMR strategy is studied considering slope- and curvature-based refinement criteria to analyze DEM inputs: the slope-based criterion uses bed elevation data as input to the wLMR strategy, whereas the curvature-based criterion feeds the bed slope data into it. The performance of the wLMR meshes generated by these two criteria is compared for hydrological simulations; first, using three analytical tests with the systematic variation in topography types and then by reproducing laboratory- and real-scale case studies. The bed elevation on the wLMR meshes and their simulation results are compared relative to those achieved on the finest uniform mesh. Repeated analytical tests show that the slope- and curvature-based criteria are equally effective with the wLMR strategy, and that it is easier to decide which criterion to take in relation to the (regular) shape of the topography. For the realistic case studies: (i) slope analysis provides a better metric to assess the correlation of a wLMR mesh to the fine uniform mesh and (ii) both criteria predict outlet hydrographs with a close predictive accuracy to that on the uniform mesh, but the curvature-based criterion is found to slightly better capture the channeling patterns of real DEM data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design

Solving environmental and social challenges such as climate change requires a shift from our current non-renewable manufacturing model to a sustainable bioeconomy. To lower carbon emissions in the production of fuels and chemicals, plant biomass feedstocks can replace petroleum using microorganisms as biocatalysts. The anaerobic thermophile Clostridium thermocellum is a promising bacterium for bioconversion due to its capability to efficiently degrade lignocellulosic biomass. However, the complex metabolism of C. thermocellum is not fully understood, hindering metabolic engineering to achieve high titers, rates, and yields of targeted molecules. In this study, we developed an updated genome-scale metabolic model of C. thermocellum that accounts for recent metabolic findings, has improved prediction accuracy, and is standard-conformant to ensure easy reproducibility. We illustrated two applications of the developed model. We first formulated a multi-omics integration protocol and used it to understand redox metabolism and potential bottlenecks in biofuel (e.g., ethanol) production in C. thermocellum. Second, we used the metabolic model to design modular cells for efficient production of alcohols and esters with broad applications as flavors, fragrances, solvents, and fuels. The proposed designs not only feature intuitive push-and-pull metabolic engineering strategies, but also present novel manipulations around important central metabolic branch-points. We anticipate the developed genome-scale metabolic model will provide a useful tool for system analysis of C. thermocellum metabolism to fundamentally understand its physiology and guide metabolic engineering strategies to rapidly generate modular production strains for effective biosynthesis of biofuels and biochemicals from lignocellulosic biomass.

59 BASIC BIOLOGICAL SCIENCES↗