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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 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae

Bottlenecks in the efficient conversion of xylose into cost-effective biofuels have limited the widespread use of plant lignocellulose as a renewable feedstock. The yeast Saccharomyces cerevisiae ferments glucose into ethanol with such high metabolic flux that it ferments high concentrations of glucose aerobically, a trait called the Crabtree/Warburg Effect. In contrast to glucose, most engineered S. cerevisiae strains do not ferment xylose at economically viable rates and yields, and they require respiration to achieve sufficient xylose metabolic flux and energy return for growth aerobically. Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose. Through genome sequence comparisons and directed engineering, we determined that duplications of genes encoding engineered xylose metabolism enzymes, as well as TKL1, a gene encoding a transketolase in the pentose phosphate pathway, were the causative genetic changes for the evolved phenotype. Reengineered duplications of these enzymes, in combination with deletion mutations in HOG1, ISU1, GRE3, and IRA2, increased the rates of aerobic and anaerobic xylose fermentation. Importantly, we found that these genetic modifications function in another genetic background and increase the rate and yield of xylose-to-ethanol conversion in industrially relevant switchgrass hydrolysate, indicating that these specific genetic modifications may enable the sustainable production of industrial biofuels from yeast. We propose a model for how key regulatory mutations prime yeast for aerobic xylose fermentation by lowering the threshold for overflow metabolism, allowing mutations to increase xylose flux and to redirect it into fermentation products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Uncertainty quantification in machine learning for engineering design and health prognostics: A tutorial

On top of machine learning (ML) models, uncertainty quantification (UQ) functions as an essential layer of safety assurance that could lead to more principled decision making by enabling sound risk assessment and management. The safety and reliability improvement of ML models empowered by UQ has the potential to significantly facilitate the broad adoption of ML solutions in high-stakes decision settings, such as healthcare, manufacturing, and aviation, to name a few. In this tutorial, we aim to provide a holistic lens on emerging UQ methods for ML models with a particular focus on neural networks and the applications of these UQ methods in tackling engineering design as well as prognostics and health management problems. Towards this goal, we start with a comprehensive classification of uncertainty types, sources, and causes pertaining to UQ of ML models. Next, we provide a tutorial-style description of several state-of-the-art UQ methods: Gaussian process regression, Bayesian neural network, neural network ensemble, and deterministic UQ methods focusing on spectral-normalized neural Gaussian process. Established upon the mathematical formulations, we subsequently examine the soundness of these UQ methods quantitatively and qualitatively (by a toy regression example) to examine their strengths and shortcomings from different dimensions. Then, we review quantitative metrics commonly used to assess the quality of predictive uncertainty in classification and regression problems. Afterward, we discuss the increasingly important role of UQ of ML models in solving challenging problems in engineering design and health prognostics. In conclusion, two case studies with source codes available on GitHub are used to demonstrate these UQ methods and compare their performance in the life prediction of lithium-ion batteries at the early stage (case study 1) and the remaining useful life prediction of turbofan engines (case study 2).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Extracting Natural Biosurfactants from Humus Deposits for Subsurface Engineering Applications

Environmentally benign, economical, and effective surfactants and additives are needed in engineering subsurface energy recovery processes. Biosurfactants have some advantages over chemically synthesized surfactants, but the high costs of microbial-biosynthesis limit their applications in subsurface engineering. In this work, we propose to use naturally occurring biosurfactants contained within Earth's readily available and inexpensive humus deposits for subsurface engineering applications. We collected humus samples of different types from four different regions, and developed a simple method for extracting natural biosurfactant (NBS) using only four common chemicals. The average NBS extraction yields are 16 ± 3% of the raw humus. No significant differences in elemental composition and functional group chemistry were found among the NBS extracted from humus of different origins, suggesting that any humus deposit can be used for NBS extraction. Measurements of interfacial tensions between air-water and supercritical (sc) CO 2 -water interfaces indicate that the NBS is a highly effective surfactant. NBS has good foaming ability. Preliminary tests with only 0.5 mass % NBS in the aqueous phase (no other additives) yielded scCO 2 -in-water foams of 83% foam quality. The apparent viscosity of 13 cP measured at a shear rate of 2320 s -1 indicates that much higher viscosities are achievable at lower shear rates. Finally, these results suggest that NBS merits further research and development for potential applications in subsurface energy production.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

Recovery of Rare Earth Elements from Low-Grade Feedstock Leachates Using Engineered Bacteria

The use of biomass for sorption of rare earth elements (REEs) for bioremediation and biomining applications has been the subject of many recent investigations. However, REE adsorption by bioengineered systems has been scarcely documented, and rarely tested with complex natural feedstocks. In this study, we engineered E. coli cells for enhanced cell surface-mediated extraction of REEs. Using Lpp-OmpA as an anchor, up to 16 copies of a Lanthanide binding tag (LBT) per OmpA protein were displayed on the E. coli cell surface, resulting in a 2-fold increase in Tb adsorption capacity compared to control cells. To test the efficacy of engineered E. coli cells to extract REEs from complex source materials, biosorption was performed with leachates from two mine tailings and two rare earth deposits. Although control E. coli cells exhibited preferential adsorption of REEs over most metals, functionalization of the cell surface with LBT yielded several notable advantages. First, the efficiency of REE adsorption from all tested leachates was enhanced with distribution coefficients for individual REEs increased by 2-10 fold. Second, although, Cu, Al, Ga and Pb were found to be the best competitors for REE binding to the E. coli cell surface, LBT-display enhanced the cell surface affinity for REEs over all non-REEs except Cu. Third, LBT-display systematically enhanced the affinity of the cell surface for REEs as a function of decreasing atomic radii, providing a means to separate high value HREEs such as Dy and Tb from more common LREEs such as La. Altogether, our results demonstrate that REE biosorption of high efficiency and selectivity can be achieved by engineering the native bacterial surface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Stable and Catalytically Active Shape-Engineered Cerium Oxide Nanorods by Controlled Doping of Aluminum Cations

Shape-engineered nanocrystals (SENs) promise a better selectivity and a higher activity in catalytic reactions than the corresponding non-shape-engineered ones because of their larger specific surface areas and desirable crystal facets. However, often, it is challenging to apply SENs in practical catalytic applications at high reaction temperatures, where SENs deforms into more stable, less active nanoparticles. In this paper, we show that atomic layer deposition (ALD) of Al 2 O 3 at 200 °C can controllably dope Al cations into the shape-engineered CeO 2 nanorods (NRs) to not only increase their shape transition temperature from 400 °C to beyond 700 °C but also greatly increase their specific reversible oxygen storage capacity (srOSC). Furthermore, the substituted Al3+ ions impede the surface diffusion of Ce ions and therefore improve the thermal stability of CeO 2 NRs. These Al3+ dopants form -Al–O–Ce–O– clusters, which are new Ce species and can be reversibly reduced and oxidized at 500–700 °C. This low-temperature chemical doping method decouples the synthesis process of SENs from the doping process and maintains the shape of the SENs during the activation of dopants. This concept could be adopted to enable the applications of other SENs in challenging high-temperature environments.

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

An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus

Rhodococcus opacus is a non-model bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in non-model organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T 7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool’s utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. In conclusion, our CRISPRi tool will be useful to facilitate functional studies of this non-model organism and engineer this promising microbial chassis for lignin valorization.

09 BIOMASS FUELS↗
DOE OSTI2023

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

With advances in machine learning (ML)-assisted protein engineering, models based on data, biophysics, and natural evolution are being used to propose informed libraries of protein variants to explore. Synthesizing these libraries for experimental screens is a major bottleneck, as the cost of obtaining large numbers of exact gene sequences is often prohibitive. Degenerate codon (DC) libraries are a cost-effective alternative for generating combinatorial mutagenesis libraries where mutations are targeted to a handful of amino acid sites. However, existing computational methods to optimize DC libraries to include desired protein variants are not well suited to design libraries for ML-assisted protein engineering. To address these drawbacks, we present DEgenerate Codon Optimization for Informed Libraries (DeCOIL), a generalized method which directly optimizes DC libraries to be useful for protein engineering: to sample protein variants that are likely to have both high fitness and high diversity in the sequence search space. Using computational simulations and wet-lab experiments, we demonstrate that DeCOIL is effective across two specific case studies, with potential to be applied to many other use cases. DeCOIL offers several advantages over existing methods, as it is direct, easy-to-use, generalizable, and scalable. With accompanying software, DeCOIL can be readily implemented to generate desired informed libraries.

59 BASIC BIOLOGICAL SCIENCES↗
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↗
DOE OSTI2022

Scalable and automated CRISPR-based strain engineering using droplet microfluidics

Abstract We present a droplet-based microfluidic system that enables CRISPR-based gene editing and high-throughput screening on a chip. The microfluidic device contains a 10 × 10 element array, and each element contains sets of electrodes for two electric field-actuated operations: electrowetting for merging droplets to mix reagents and electroporation for transformation. This device can perform up to 100 genetic modification reactions in parallel, providing a scalable platform for generating the large number of engineered strains required for the combinatorial optimization of genetic pathways and predictable bioengineering. We demonstrate the system’s capabilities through the CRISPR-based engineering of two test cases: (1) disruption of the function of the enzyme galactokinase ( galK ) in E. coli and (2) targeted engineering of the glutamine synthetase gene ( glnA ) and the blue-pigment synthetase gene ( bpsA ) to improve indigoidine production in E. coli .

42 ENGINEERING↗
DOE OSTI2018

Improving formaldehyde consumption drives methanol assimilation in engineered E. coli

Abstract Due to volatile sugar prices, the food vs fuel debate, and recent increases in the supply of natural gas, methanol has emerged as a promising feedstock for the bio-based economy. However, attempts to engineer Escherichia coli to metabolize methanol have achieved limited success. Here, we provide a rigorous systematic analysis of several potential pathway bottlenecks. We show that regeneration of ribulose 5-phosphate in E. coli is insufficient to sustain methanol assimilation, and overcome this by activating the sedoheptulose bisphosphatase variant of the ribulose monophosphate pathway. By leveraging the kinetic isotope effect associated with deuterated methanol as a chemical probe, we further demonstrate that under these conditions overall pathway flux is kinetically limited by methanol dehydrogenase. Finally, we identify NADH as a potent kinetic inhibitor of this enzyme. These results provide direction for future engineering strategies to improve methanol utilization, and underscore the value of chemical biology methodologies in metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Grain engineering for efficient near-infrared perovskite light-emitting diodes

Metal halide perovskites show promise for next-generation light-emitting diodes, particularly in the near-infrared range, where they outperform organic and quantum-dot counterparts. However, they still fall short of costly III-V semiconductor devices, which achieve external quantum efficiencies above 30% with high brightness. Among several factors, controlling grain growth and nanoscale morphology is crucial for further enhancing device performance. This study presents a grain engineering methodology that combines solvent engineering and heterostructure construction to improve light outcoupling efficiency and defect passivation. Solvent engineering enables precise control over grain size and distribution, increasing light outcoupling to ~40%. Constructing 2D/3D heterostructures with a conjugated cation reduces defect densities and accelerates radiative recombination. The resulting near-infrared perovskite light-emitting diodes achieve a peak external quantum efficiency of 31.4% and demonstrate a maximum brightness of 929 W sr -1 m -2 . These findings indicate that perovskite light-emitting diodes have potential as cost-effective, high-performance near-infrared light sources for practical applications.

42 ENGINEERING↗
DOE OSTI2022

Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network’s various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. Furthermore, these elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Finite Element Analysis and Die Design of Non-specific Engineering Structure of Aluminum Alloy during Extrusion

Aluminum extension applies to industrial structure, light load, framework rolls and conveyer system platform. Many factors must be controlled in processing the non-specific engineering structure (hollow shape) of the aluminum alloy during extrusion, to obtain the required plastic strain and desired tolerance values. The major factors include the forming angle of the die and temperature of billet and various materials. This paper employs rigid-plastic finite element (FE) DEFORM 3D software to investigate the plastic deformation behavior of an aluminum alloy (A6061, A5052, A3003) workpiece during extrusion for the engineering structure of the aluminum alloy. This work analyzes effective strain, effective stress, damage and die radius load distribution of the billet under various conditions. The analytical results confirm the suitability of the current finite element software for the non-specific engineering structure of aluminum alloy extrusion.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Preliminary engineering design of sodium-cooled CANDLE core

The CANDLE burning process is characterized by the autonomous shifting of burning region with constant reactivity and constant spacial power distribution. Evaluations of such critical burning process by using widely used neutron diffusion and burning codes under some realistic engineering constraints are valuable to confirm the technical feasibility of the CANDLE concept and to put the idea into concrete core design. In the first part of this paper, it is discussed that whether the sustainable and stable CANDLE burning process can be reproduced even by using conventional core analysis tools such as SLAROM and CITATION-FBR. As a result, it is certainly possible to demonstrate it if the proper core configuration and initial fuel composition required as CANDLE core are applied to the analysis. In the latter part, an example of a concrete image of sodium cooled, metal fuel, 2000MWt rating CANDLE core has been presented by assuming an emerging inevitable technology of recladding. The core satisfies engineering design criteria including cladding temperature, pressure drop, linear heat rate, and cumulative damage fraction (CDF) of cladding, fast neutron fluence and sodium void reactivity which are defined in the Japanese FBR design project. It can be concluded that it is feasible to design CANDLE core by using conventional codes while satisfying some realistic engineering design constraints assuming that recladding at certain time interval is technically feasible.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2015

Engineering Escherichia coli coculture systems for the production of biochemical products

Significance Production of industrial compounds by using engineered microorganisms is a robust method to reduce our reliance on nonrenewable petroleum resources and increase the utility of renewable resources, such as lignocellulose. Because there are major limitations for engineering a single microbial cell to achieve high-yield production, we developed microbial coculture systems consisting of two different microbial cell types to use sugar mixtures that can be derived from lignocellulose efficiently. We demonstrate that this approach is successful for achieving high-level production of two important value-added molecules, cis , cis -muconic acid and 4-hydroxybenzoic acid. This accomplishment establishes a previously unidentified technology for advancing future research in metabolic engineering and synthetic biology.

4-hydroxybenzoic acid↗
DOE OSTI2022

CRISPR-based engineering of phages for in situ bacterial base editing

Investigation of microbial gene function is essential to the elucidation of ecological roles and complex genetic interactions that take place in microbial communities. While microbiome studies have increased in prevalence, the lack of viable in situ editing strategies impedes experimental progress, rendering genetic knowledge and manipulation of microbial communities largely inaccessible. Here, we demonstrate the utility of phage-delivered CRISPR-Cas payloads to perform targeted genetic manipulation within a community context, deploying a fabricated ecosystem (EcoFAB) as an analog for the soil microbiome. First, we detail the engineering of two classical phages for community editing using recombination to replace nonessential genes through Cas9-based selection. We show efficient engineering of T7, then demonstrate the expression of antibiotic resistance and fluorescent genes from an engineered λ prophage within an Escherichia coli host. Next, we modify λ to express an APOBEC-1-based cytosine base editor (CBE), which we leverage to perform C-to-T point mutations guided by a modified Cas9 containing only a single active nucleolytic domain (nCas9). We strategically introduce these base substitutions to create premature stop codons in-frame, inactivating both chromosomal ( lacZ ) and plasmid-encoded genes (mCherry and ampicillin resistance) without perturbation of the surrounding genomic regions. Furthermore, using a multigenera synthetic soil community, we employ phage-assisted base editing to induce host-specific phenotypic alterations in a community context both in vitro and within the EcoFAB, observing editing efficiencies from 10 to 28% across the bacterial population. The concurrent use of a synthetic microbial community, soil matrix, and EcoFAB device provides a controlled and reproducible model to more closely approximate in situ editing of the soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metabolic engineering strategies for sesquiterpene production in microorganism

Sesquiterpenes are a large variety of terpene natural products, widely existing in plants, fungi, marine organisms, insects, and microbes. Value-added sesquiterpenes are extensively used in industries such as: food, drugs, fragrances, and fuels. With an increase in market demands and the price of sesquiterpenes, the biosynthesis of sesquiterpenes by microbial fermentation methods from renewable feedstocks is acquiring increasing attention. Synthetic biology provides robust tools of sesquiterpene production in microorganisms. This review presents a summary of metabolic engineering strategies on the hosts and pathway engineering for sesquiterpene production. Advances in synthetic biology provide new strategies on the creation of desired hosts for sesquiterpene production. Especially, metabolic engineering strategies for the production of sesquiterpenes such as: amorphadiene, farnesene, bisabolene, and caryophyllene are emphasized in: Escherichia coli , Saccharomyces cerevisiae , and other microorganisms. Herein, challenges and future perspectives of the bioprocess for translating sesquiterpene production into practical industrial work are also discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural maturation of myofilaments in engineered 3D cardiac microtissues characterized using small angle x-ray scattering

Abstract Understanding the structural and functional development of human-induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) is essential to engineering cardiac tissue that enables pharmaceutical testing, modeling diseases, and designing therapies. Here we use a method not commonly applied to biological materials, small angle x-ray scattering, to characterize the structural development of hiPSC-CMs within three-dimensional engineered tissues during their preliminary stages of maturation. An x-ray scattering experimental method enables the reliable characterization of the cardiomyocyte myofilament spacing with maturation time. The myofilament lattice spacing monotonically decreases as the tissue matures from its initial post-seeding state over the span of 10 days. Visualization of the spacing at a grid of positions in the tissue provides an approach to characterizing the maturation and organization of cardiomyocyte myofilaments and has the potential to help elucidate mechanisms of pathophysiology, and disease progression, thereby stimulating new biological hypotheses in stem cell engineering.

36 MATERIALS SCIENCE↗