Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Strain engineering”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Defining the Minimal Set of Microbial Genes Required for Valorization of Lignin Biomass (Final Report)

Project Goals: Lignin is the second most abundant biopolymer on earth and represents a critically underutilized biomass resource for hydrocarbon feedstocks. Despite substantial effort, there is still no efficient process to convert lignin to useable carbon-based platform chemicals and materials. The goal of this project is identify a minimal set of microbial enzymes necessary for lignin breakdown and sufficient for the synthesis of valuable chemical intermediates from lignin isolated as a byproduct of lignocellulosic ethanol production. These genes will be then used to engineer functional whole cell biocatalysts for tunable lignin metabolism. To date, although a number of enzymes have been associated with lignin degradation, most have been tested in isolation (as individual enzymes) and on drastically different substrates -- often dyes that are not related to lignin. In contrast, lignin utilization in nature likely occurs by microbial consortia with multiple enzymes acting synergistically. We propose to examine two separate stages of lignin breakdown carried out by the microbes that do it best: (1) early breakdown of native polymeric lignin into soluble fragments by a set of sequenced wood-rotting fungal species, and (2) downstream metabolism of these soluble lignin fragments to useful chemical intermediates by a panel of sequenced soil saprophytes. Our approach involves testing sets of genes that will be assayed combinatorially in the context of a heterologous expression host. The resulting engineered strains will be systematically assayed using soluble lignin fragments, synthetic defined polymeric lignin, and finally lignin directly sourced from lignocellulosic processing streams. In addition to resulting in a functional whole cell biocatalyst for lignin utilization, we anticipate that this approach will allow us to address key unanswered questions about lignin metabolism in nature, including: (1) Why does the Trametes versicolor genome contain 25 different class II peroxidases? (2) What is the role of laccases in lignin metabolism? Why do some aggressive lignin degraders have many laccases (e.g. >7 in T. versicolor) while others have none (e.g. P. chrysosporium)? (3) How is peroxide provided in a controlled manner to drive peroxidase activity without causing the enzyme inhibition that is so often observed in vitro? (4) What strategies do microbial lignin degraders use to avoid the problem of repolymerization during active lignin degradation? and (5) Can microbial lignin metabolism be diverted for high level production of defined aromatics? A final critical question is whether combining key minimal sets of enzymes from a wide range of organisms will result in engineered strains capable of highly efficient, streamlined pathways for lignin utilization that can be tuned for a specific carbon output. This effort will leverage DOE investments in microbial genome sequencing, and secure a critical channel for lignin biomass utilization that will also help to render lignocellulosic a viable feedstock for the production of renewable liquid biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Biosystem design of Corynebacterium glutamicum for bioproduction

Corynebacterium glutamicum, a natural glutamate-producing bacterium adopted for industrial production of amino acids, has been extensively explored recently for high-level biosynthesis of amino acid derivatives, bulk chemicals such as organic acids and short-chain alcohols, aromatics, and natural products, including polyphenols and terpenoids. Here, we review the recent advances with a focus on biosystem design principles, metabolic characterization and modeling, omics analysis, utilization of nonmodel feedstock, emerging CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) tools for Corynebacterium strain engineering, biosensors, and novel strains of C. glutamicum. Further, future research directions for developing C. glutamicum cell factories are also discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Numerical prediction of the decline of the shale gas production rate with considering the geomechanical effects based on the two-part Hooke’s model

The production rate of a typical shale gas well generally has steep decline trend at the initial stage but small declines at later times. Some empirical relationships have been proposed to describe the declining production rates and thus forecast the final cumulative production of a shale gas well. However, these empirical relationships can hardly elucidate the mechanisms that cause the special shale gas production trend. In this paper, a novel two-part Hooke’s model (TPHM) for the permeability and effective stress relationship is developed and incorporated into the hydro-mechanical COMSOL solver to determine the production rate of shale gas wells against time. The TPHM conceptualizes shale rock into soft part and hard part, which comply with the natural-strain-based and engineering-strain-based Hooke’s laws, respectively, and contribute differently to the decreasing permeability with increasing effective stresses. The simulation results are analyzed and compared with those for which the permeability change effect is not considered. Finally, the analysis indicates that the decrease in stress-induced permeability plays a non-negligible part in the decline of the production rate.

58 GEOSCIENCES↗
DOE OSTI2026

Elucidation of odd-chain dicarboxylate metabolism in Acinetobacter baylyi and application to polyethylene upcycling

Polyethylene (PE) is a versatile polymer, but its end-of-life management is challenging due to its recalcitrant structure. We present a promising approach combining chemical degradation and bio-upcycling to convert postconsumer PE waste into a value-added bioproduct. Specifically, PE was degraded into acetic acid and C 4 –C 7 dicarboxylic acids by nitric acid. We then elucidated the catabolic pathways for glutarate (C 5 ) and pimelate (C 7 ) in the nonmodel bacterium Acinetobacter baylyi ADP1 through RNA sequencing, phenotyping, and enzymatic assays. Whole-genome sequencing of evolved isolates also identified a crucial IclR family transcriptional regulator, DcaS, which acts as a repressor of dicarboxylate metabolism. The reverse-engineered strain exhibited enhanced substrate utilization compared to the wild-type strain. Using rational metabolic engineering, the PE deconstruction products were bioconverted into the valuable chemical lycopene, highlighting the potential of this microbial chassis to produce value-added bioproducts from postconsumer PE waste, thus promoting a circular economy for plastics.

metabolic engineering↗
DOE OSTI2016

13 C Metabolic Flux Analysis of acetate conversion to lipids by Yarrowia lipolytica

We report volatile fatty acids (VFAs) are an inexpensive and renewable carbon source that can be generated from gas fermentation and anaerobic digestion of fermentable wastes. The oleaginous yeast Yarrowia lipolytica is a promising biocatalyst that can utilize VFAs and convert them into triacylglycerides (TAGs). However, currently there is limited knowledge on the metabolism of Y. lipolytica when cultured on VFAs. To develop a better understanding, we used acetate as the sole carbon source to culture two strains, a control strain and a previously engineered strain for lipid overaccumulation. For both strains, metabolism during the growth phase and lipid production phase were investigated by metabolic flux analysis using two parallel sodium acetate tracers. The resolved flux distributions demonstrate that the glyoxylate shunt pathway is constantly active and the flux through gluconeogenesis varies depending on strain and phase. In particular, by regulating the activities of malate transport and pyruvate kinase, the cells divert only a portion of the glyoxylate shunt flux required to satisfy the needs for anaplerotic reactions and NADPH production through gluconeogenesis and the oxidative pentose phosphate pathway (PPP). Excess flux flows back to the tricarboxylic acid (TCA) cycle for energy production. As with the case of glucose as the substrate, the primary source for lipogenic NADPH is derived from the oxidative PPP.

13C metabolic flux analysis↗
DOE OSTI2016

Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae

Enhancing xylose utilization has been a major focus in Saccharomyces cerevisiae strain-engineering efforts. The incentive for these studies arises from the need to use all sugars in the typical carbon mixtures that comprise standard renewable plant-biomass-based carbon sources. While major advances have been made in developing utilization pathways, the efficient import of five carbon sugars into the cell remains an important bottleneck in this endeavor. Here we use an engineered S. cerevisiae BY4742 strain, containing an established heterologous xylose utilization pathway, and imposed a laboratory evolution regime with xylose as the sole carbon source. We obtained several evolved strains with improved growth phenotypes and evaluated the best candidate using genome resequencing. We observed remarkably few single nucleotide polymorphisms in the evolved strain, among which we confirmed a single amino acid change in the hexose transporter HXT7 coding sequence to be responsible for the evolved phenotype. Lastly, the mutant HXT7(F79S) shows improved xylose uptake rates (Vmax = 186.4 ± 20.1 nmol•min -1 •mg -1 ) that allows the S. cerevisiae strain to show significant growth with xylose as the sole carbon source, as well as partial co-utilization of glucose and xylose in a mixed sugar cultivation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Tunable metal-insulator transition in Nd{sub 1−x}Y{sub x}NiO{sub 3} (x = 0.3, 0.4) perovskites thin film at near room temperature

Metal-insulator transition (MIT) occurs due to the charge disproportionation and lattice distortions in rare-earth nickelates. Existing studies revealed that the MIT behavior of rare-earth nickelates is fairly sensitive to external stress/pressure, suggesting a viable route for MIT strain engineering. Unlike applying extrinsic strain, the MIT can also be modulated by through rare-earth cation mixing, which can be viewed as intrinsic quantum stress. We choose Nd{sub 1−X}Y{sub X}NiO{sub 3} (x = 0.3, 0.4) perovskites thin films as a prototype system to exhibit the tunable sharp MIT at near room temperature. By adjusting Y concentration, the transition temperature of the thin films can be changed within the range of 340–360 K. X-ray diffraction, X-ray absorption fine structure (XAFS), and in situ infrared spectroscopy are employed to probe the structural and optical property variation affected by composition and temperature. The infrared transmission intensity decreases with temperature across the MIT, indicating a pronounced thermochromic effect. Meanwhile, the XAFS result exhibits that the crystal atomistic structure changes accompanying with the Y atoms incorporation and MIT phase transition. The heavily doped Y atoms result in the pre-edge peak descent and Ni-O bond elongation, suggesting an enhanced charge disproportionation effect and the weakening of hybridization between Ni-3d and O-2p orbits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Engineering local strain for single-atom nuclear acoustic resonance in silicon

Mechanical strain plays a key role in the physics and operation of nanoscale semiconductor systems, including quantum dots and single-dopant devices. In this report we describe the design of a nanoelectronic device, where a single nuclear spin is coherently controlled via nuclear acoustic resonance (NAR) through the local application of dynamical strain. The strain drives spin transitions by modulating the nuclear quadrupole interaction. We adopt an AlN piezoelectric actuator compatible with standard silicon metal–oxide–semiconductor processing and optimize the device layout to maximize the NAR drive. We predict NAR Rabi frequencies of order 200 Hz for a single 123Sb nucleus in a wide region of the device. Spin transitions driven directly by electric fields are suppressed in the center of the device, allowing the observation of pure NAR. Using electric field gradient-elastic tensors calculated by the density-functional theory, we extend our predictions to other high-spin group-V donors in silicon and to the isoelectronic 73Ge atom.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Higher thermoelectric performance of Zintl phases (Eu 0.5 Yb 0.5 ) 1−x Ca x Mg 2 Bi 2 by band engineering and strain fluctuation

Significance The search for high-efficiency thermoelectric materials encompasses many classes of semiconductors. Zintl phases are attractive thermoelectric materials for thermoelectric applications. Here, we report the high thermoelectric performance of the rarely studied bismuth (Bi)-based Zintl phases (Eu 0.5 Yb 0.5 ) 1−x Ca x Mg 2 Bi 2 with the record figure-of-merit ZT as high as 1.3 at 873 K. This ZT value is, to our knowledge, the highest ever reported in CaAl 2 Si 2 -based structures, especially compared with the best antimony (Sb)-based YbZn 0.4 Cd 1.6 Sb 2 compound. Because Sb-based Zintl compounds have been studied for many decades, this Bi-based Zintl phase with high thermoelectric properties could be a good thermoelectric material candidate in the future.

Shuai, Jing↗
DOE OSTI2025

Mechanically and electrically tunable Rashba-Edelstein effect in ferroelectric semiconductors, CsGe⁢𝑋 3 (𝑋 = I, Br, Cl)

The ability of materials to convert charge current into spin current is fundamental to many spintronics applications. One means of realizing this conversion is via Rashba-Edelstein effect (REE). Using density functional theory simulations, we predict that REE can be induced in the recently discovered family of semiconducting ferroelectrics, CsGe⁢𝑋 3 (𝑋 = I, Br, Cl). The effect is quantified through Rashba-Edelstein coefficients, 𝜒 𝑥⁢𝑦 =−𝜒 𝑦⁢𝑥 , which are nonzero in valence and conduction bands. The largest values, obtained for CsGeI 3 , are 3.45 × 10 10 $\frac{ℏ}{Λ cm}$ and 0.97 × 10 10 $\frac{ℏ}{Λ cm}$ in the conduction and valence bands, respectively. The values are comparable to, and sometimes exceed, those of other inorganic materials, although the maximal values occur away from the band edges. The coefficients' sign couples to the direction of spontaneous polarization, offering opportunities for nonvolatile spin current manipulation via external electric field. Furthermore, these coefficients are highly tunable through strain engineering owing to strain-induced variations in spin textures and energy isosurfaces. Specifically, 𝜒 in the valence band of CsGeI 3 is enhanced to 3.61 × 10 10 $\frac{ℏ}{Λ cm}$ under 5% biaxial strain. Given this potential, we synthesized CsGeI 3 to validate our simulation structure and found excellent agreement between experiment and simulation, thereby allowing extrapolation of our findings to practically significant temperatures. Furthermore, our study identifies promising materials for nonvolatile, multifunctional spintronic applications.

Electronic structure↗
DOE OSTI2016

Enhanced production of 2,3‐butanediol in pyruvate decarboxylase‐deficient Saccharomyces cerevisiae through optimizing ratio of glucose/galactose

Abstract Galactose and glucose are two of the most abundant monomeric sugars in hydrolysates of marine biomasses. While Saccharomyces cerevisiae can ferment galactose, its uptake is tightly controlled in the presence of glucose by catabolite repression. It is desirable to construct engineered strains capable of simultaneous utilization of glucose and galactose for producing biofuels and chemicals from marine biomass. The MTH1 gene coding for transcription factor in glucose signaling was mutated in a pyruvate decarboxylase (Pdc)‐deficient S. cerevisiae expressing heterologous 2,3‐butanediol (2,3‐BD) biosynthetic genes. The engineered S. cerevisiae strain consumed glucose and galactose simultaneously and produced 2,3‐BD as a major product. Total sugar consumption rates increased with a low ratio of glucose/galactose, though, occurrence of the glucose depletion in a fed‐batch fermentation decreased 2,3‐BD production substantially. Through optimizing the profiles of sugar concentrations in a fed‐batch cultivation with the engineered strain, 99.1 ± 1.7 g/L 2,3‐BD was produced in 143 hours with a yield of 0.353 ± 0.022 g 2,3‐BD/g sugars. This result suggests that simultaneous and efficient utilization of glucose and galactose by the engineered yeast might be applicable to the economical production of not only 2,3‐BD, but also other biofuels and chemicals from marine biomass.

Choi, Eun‐Ji↗
DOE OSTI2016

Engineering the Transformation Strain in LiMn y Fe 1– y PO 4 Olivines for Ultrahigh Rate Battery Cathodes

Alkali ion intercalation compounds used as battery electrodes often exhibit first-order phase transitions during electro-chemical cycling, accompanied by significant transformation strains. Despite 30 years of research into the behavior of such compounds, the relationship between transformation strain and electrode performance, especially the rate at which working ions (e.g., Li) can be intercalated and deintercalated, is still absent. In this work, we use the LiMn y Fe 1-y PO 4 system for a systematic study, and measure using operando synchrotron radiation powder X-ray diffraction (SR-PXD) the dynamic strain behavior as a function of the Mn content (y) in powders of similar to 50 nm average diameter. The dynamically produced strain deviates significantly from what is expected from the equilibrium phase diagrams and demonstrates metastability but nonetheless spans a wide range from 0 to 8 vol % with y. For the first time, we show that the discharge capacity at high C-rates (20-50C rate) varies in inverse proportion to the transformation strain, implying that engineering electrode materials for reduced strain can be used to maximize the power capability of batteries.

cathode↗
DOE OSTI2021

Introduction of NADH-dependent nitrate assimilation in Synechococcus sp. PCC 7002 improves photosynthetic production of 2-methyl-1-butanol and isobutanol

Cyanobacteria hold promise for renewable chemical production due to their photosynthetic nature, but engineered strains frequently display poor production characteristics. These difficulties likely arise in part due to the distinctive photoautotrophic metabolism of cyanobacteria. Here, in this work, we apply a genome-scale metabolic model of the cyanobacteria Synechococus sp. PCC 7002 to identify strain designs accounting for this unique metabolism that are predicted to improve the production of various biofuel alcohols (e.g. 2-methyl-1-butanol, isobutanol, and 1-butanol) synthesized via an engineered biosynthesis pathway. Using the model, we identify that the introduction of a large, non-native NADH-demand into PCC 7002's metabolic network is predicted to enhance production of these alcohols by promoting NADH-generating reactions upstream of the production pathways. To test this, we construct strains of PCC 7002 that utilize a heterologous, NADH-dependent nitrite reductase in place of the native, ferredoxin-dependent enzyme to create an NADH-demand in the cells when grown on nitrate-containing media. We find that photosynthetic production of both isobutanol and 2-methyl-1-butanol is significantly improved in the engineered strain background relative to that in a wild-type background. We additionally identify that the use of high-nutrient media leads to a substantial prolongment of the production curve in our alcohol production strains. The metabolic engineering strategy identified and tested in this work presents a novel approach to engineer cyanobacterial production strains that takes advantage of a unique aspect of their metabolism and serves as a basis on which to further develop strains with improved production of these alcohols and related products.

2-methyl-1-butanol↗