Search NASA⌕ Search

Engineering topics

Chen, Yan

Publications and source records attributed to Chen, Yan.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2

ABSTRACT Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds ( p- coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p -coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+ p -coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+ p -coumarate) condition compared to when repression was absent ( p -coumarate or glucose only). IMPORTANCE A newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Neutronic engine

An internal combustion engine for neutron diffraction analysis is provided. The engine includes an elongated piston chamber formed from an aluminum alloy to ensure maximum neutron visibility into the combustion chamber. An elongated piston assembly reciprocates within the elongated piston chamber, the piston assembly including an upper piston joined to a lower piston. The upper piston and the lower piston are hollow, thereby reducing the reciprocating mass and increasing neutron access to the combustion chamber. The upper piston is lubricated with a neutron-transparent fluorocarbon lubricant such as perfluoropolyether (PFPE), while the lower piston and the crankcase are lubricated with hydrocarbon lubricant. The engine enables 3D and time-resolved measurements of strain, stress, and temperature, as well as phase transformation, texture, and microstructure.

Wissink, Martin L.↗
DOE OSTI2023

A Review of the Evaluation of Building Energy Code Compliance in the United States

Building energy codes are essential tools for achieving energy efficiency in buildings. However, the full energy savings potential of these codes can only be realized if buildings are constructed in compliance with them. Therefore, evaluating building energy code compliance is crucial in bridging the gap between the energy efficiency requirements set by energy codes and the actualized energy savings achieved. An energy code compliance evaluation serves as a mechanism to assess construction practices, evaluate the effectiveness of code enforcement, identify gaps in compliance, and guide strategies for improvement through training and education. Conducting code compliance evaluation activities involves field studies that require careful design and significant resources. Historically, more emphasis has been placed on developing and adopting building energy codes, while efforts to evaluate compliance have been relatively limited and lacking consistent approaches. The passage of the 2009 American Recovery and Reinvestment Act (ARRA), which mandated that states create plans for achieving 90% compliance within eight years, stimulated the need for an energy code compliance evaluation. As a result, federal, state, and local governments, and utilities have invested in the development of methodologies and tools for code compliance evaluation studies. This paper reviews the code compliance evaluation studies conducted in the United States over the past three decades. It describes and compares the methodologies and metrics used to assess building energy code compliance, summarizes the general elements and steps involved in the evaluation process, and discusses common issues in these studies. Over time, code compliance evaluation methodologies have evolved from isolated development within individual states, regions, and utilities, to widely accepted protocols applicable across different states and local jurisdictions. There has been a transition in compliance metrics, shifting from historical compliance rates to energy-consumption-oriented approaches.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Adopting occupancy-based HVAC controls in commercial building energy codes: Analysis of cost-effectiveness and decarbonization potential

Recent research has shown the energy-saving potential of occupancy-based HVAC controls (OBCs) in commercial buildings. However, building energy codes have not fully adopted this technology. This study aims to evaluate the cost-effectiveness and decarbonization benefits of OBCs and provide guidance for integrating occupancy sensors into building energy code development. To this end, a parametric simulation using EnergyPlus and a nationwide cost-effectiveness analysis are carried out considering three building types and 40 representative cities in the U.S. Here, the findings reveal that the current cost-effectiveness performance of OBCs is limited due to the high cost of occupancy sensors. However, incorporating the societal cost of carbon factor in future energy and environmental policy could greatly enhance the actual cost-effectiveness performance. Besides, a reduction in the cost of occupancy sensors to approximately 60% of the current price level could also greatly shorten the discounted payback period of OBCs. Additionally, OBCs demonstrate significant potential in building decarbonization, with potential CO 2 emissions savings of more than 5.56 million metric tons across the three building types and 40 selected cities. Finally, policy implications are provided to guide the incorporation of occupancy-based HVAC controls in future energy codes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Deformation mechanisms in an additively manufactured dual-phase eutectic high-entropy alloy

Nanostructured metals and alloys often exhibit high strengths but at the expense of reduced ductility. Through harnessing the far-from-equilibrium processing conditions of laser powder-bed fusion (L-PBF) additive manufacturing, we develop a dual-phase nanolamellar structure comprised of FCC/L1 2 and BCC/B2 phases in a Ni 40 Co 20 Fe 10 Cr 10 Al 18 W 2 eutectic high-entropy alloy (EHEA), which exhibits a combination of ultrahigh yield strength (>1.4 GPa) and large tensile ductility (~17%). The deformation mechanisms of the additively manufactured EHEA are studied via in-situ synchrotron X-ray diffraction and high-resolution transmission electron microscopy. The high yield strength mainly results from effective blockage of dislocation motion by the high density of lamellar interfaces. The refined nanolamellar structures and low stacking fault energy (SFE) promote stacking fault (SF)-mediated deformation in FCC/L1 2 nanolamellae. The accumulation of abundant dislocations and SFs at lamellar interfaces can effectively elevate local stresses to promote dislocation multiplication and martensitic transformation in BCC/B2 nanolamellae. The cooperative deformation of the dual phases, assisted by the semi-coherent lamellar interfaces, gives rise to the large ductility of the as-printed EHEA. In addition, here we also demonstrate that post-printing heat treatment allows us to tune the non-equilibrium microstructures and deformation mechanisms. After annealing, the significantly reduced SFE and thicknesses of the FCC nanolamellae facilitate the formation of massive SFs. The dissolution of nano-precipitates in the BCC/B2 nanolamellae reduces spatial confinement and further promotes martensitic transformation to enhance work hardening. Our work provides fundamental insights into the rich variety of deformation mechanisms underlying the exceptional mechanical properties of the additively manufactured dual-phase nanolamellar EHEAs.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes ( e . g ., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5–2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Expression of blue pigment synthetase a from Streptomyces lavenduale reveals insights on the effects of refactoring biosynthetic megasynthases for heterologous expression in Escherichia coli .

High GC bacteria from the genus Streptomyces harbor expansive secondary metabolism. The expression of biosynthetic proteins and the characterization and identification of biological "parts" for synthetic biology purposes from such pathways are of interest. However, the high GC content of proteins from actinomycetes in addition to the large size and multi-domain architecture of many biosynthetic proteins (such as non-ribosomal peptide synthetases; NRPSs, and polyketide synthases; PKSs often called "megasynthases") often presents issues with full-length translation and folding. Here we evaluate a non-ribosomal peptide synthetase (NRPS) from Streptomyces lavenduale, a multidomain "megasynthase" gene that comes from a high GC (72.5%) genome. While a preliminary step in revealing differences, to our knowledge this presents the first head-to-head comparison of codon-optimized sequences versus a native sequence of proteins of streptomycete origin heterologously expressed in E. coli. We found that any disruption in co-translational folding from codon mismatch that reduces the titer of indigoidine is explainable via the formation of more inclusion bodies as opposed to compromising folding or posttranslational modification in the soluble fraction. In conclusion, this result supports that one could apply any refactoring strategies that improve soluble expression in E. coli without concern that the protein that reaches the soluble fraction is differentially folded.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Neutron diffraction probing hydrogen in monoclinic H 2 VOPO 4

Light hydrogen atoms are resolvable with neutrons; however, the massive incoherent background inhibits the diffraction quality. To improve the signal, isotope treatment by deuteration becomes a prerequisite for a successful crystallographic understanding of hydrogen-containing materials by neutron diffraction. Thanks to the low-background and high-resolution time-of-flight neutron diffractometer, this work demonstrates a direct and successful measurement of high-quality neutron diffraction patterns of H 2 VOPO 4 powders, a precursor of a high-capacity alkali-ion battery cathode. The Rietveld refinement identifies the hydrogen coordinates, occupancy, and thermal parameters in the H 2 VOPO 4 lattice. Finally, the result highlights the unique capability of neutron diffraction for the structure characterization of hydrogen-containing materials, potentially without requiring costly and possibly artifact-inducing deuteration for neutron diffraction.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Superior zero thermal expansion dual-phase alloy via boron-migration mediated solid-state reaction

Rapid progress in modern technologies demands zero thermal expansion (ZTE) materials with multi-property profiles to withstand harsh service conditions. Thus far, the majority of documented ZTE materials have shortcomings in different aspects that limit their practical utilization. Here, we report on a superior isotropic ZTE alloy with collective properties regarding wide operating temperature windows, high strength-stiffness, and cyclic thermal stability. A boron-migration-mediated solid-state reaction (BMSR) constructs a salient “plum pudding” structure in a dual-phase Er-Fe-B alloy, where the precursor ErFe 10 phase reacts with the migrated boron and transforms into the target Er 2 Fe 14 B (pudding) and α-Fe phases (plum). The formation of such microstructure helps to eliminate apparent crystallographic texture, tailor and form isotropic ZTE, and simultaneously enhance the strength and toughness of the alloy. These findings suggest a promising design paradigm for comprehensive performance ZTE alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ultra-strong tungsten refractory high-entropy alloy via stepwise controllable coherent nanoprecipitations

High-performance refractory alloys with ultrahigh strength and ductility are in demand for a wide range of critical applications, such as plasma-facing components. However, it remains challenging to increase the strength of these alloys without seriously compromising their tensile ductility. Here, we put forward a strategy to “defeat” this trade-off in tungsten refractory high-entropy alloys by stepwise controllable coherent nanoprecipitations (SCCPs). The coherent interfaces of SCCPs facilitate the dislocation transmission and relieve the stress concentrations that can lead to premature crack initiation. As a consequence, our alloy displays an ultrahigh strength of 2.15 GPa with a tensile ductility of 15% at ambient temperature, with a high yield strength of 1.05 GPa at 800 °C. The SCCPs design concept may afford a means to develop a wide range of ultrahigh-strength metallic materials by providing a pathway for alloy design.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Complete integration of carbene-transfer chemistry into biosynthesis

Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here, in this paper, we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule—styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Chemical heterogeneity modulated zero thermal expansion alloy over super-wide temperature range

Chemical heterogeneity is usually avoided in solution chemistry, but it may still occur with sometimes dramatic effects on target materials and their properties. Here, we propose chemical heterogeneity as a counterintuitive strategy to design high-performance zero thermal expansion (ZTE) alloys. We apply this approach in a Hf-Ti-Fe alloy with excess Fe in the Hf/Ti sublattice and produce Hf/Ti concentration alternations at the micro level. Such chemical heterogeneity regulates local magnetic interactions in alloy and triggers a dispersed magnetic phase transition that modulates the thermal expansions at the micro level and hence results in a remarkable ZTE behavior over a super-wide temperature window from 10 to 480 K. This mechanism is supported by comprehensive studies on morphological microstructures, crystal and magnetic structures, and theoretical calculations. The strategy of local chemical heterogeneity opens up an avenue to design ZTE and the related functional materials directly via microstructure engineering.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Mixed heavy metal stress induces global iron starvation response

Abstract Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Revealing oxidative pentose metabolism in new Pseudomonas putida isolates

Abstract The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well‐characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth‐promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism ( xylDXA ) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism ( araDXA ). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.

59 BASIC BIOLOGICAL SCIENCES↗