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At least 631 records · Page 35

Towards a Standard Process Management Infrastructure for Workflows Using Python

Orchestrating the execution of ensembles of processes lies at the core of scientific workflow engines on large scale parallel platforms. This is usually handled using platform-specific command line tools, with limited process management control and potential strain on system resources. The PMIx standard provides a uniform interface to system resources. The low level C implementation of PMIx has hampered its use in workflow engines, leading to the development of Python binding that has yet to gain traction. In this paper, we present our work to harden the PMIx Python client, demonstrating its usability using a prototype Python driver to orchestrate the execution of an ensemble of processes. We present experimental results using the prototype on the Summit supercomputer at Oak Ridge National Laboratory. This work lays the foundation for wider adoption of PMIx for workflow engines, and encourages wider support of more PMIx functionality in vendor provided system software stacks.

Elwasif, Wael↗

The bright frontiers of microbial metabolic optogenetics

In recent years, light-responsive systems from the field of optogenetics have been applied to several areas of metabolic engineering with remarkable success. By taking advantage of light's high tunability, reversibility, and orthogonality to host endogenous processes, optogenetic systems have enabled unprecedented dynamical controls of microbial fermentations for chemical production, metabolic flux analysis, and population compositions in co-cultures. In this article, we share our opinions on the current state of this new field of metabolic optogenetics. Furthermore, we make the case that it will continue to impact metabolic engineering in increasingly new directions, with the potential to challenge existing paradigms for metabolic pathway and strain optimization as well as bioreactor operation.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanical properties and strain localization of WA-DED printed P91 steel

This paper discusses a P91 steel block that was additively manufactured by wire arc direct energy deposition (WA-DED) followed by two types of post-process heat treatment (PPHT). Vickers microhardness and digital image correlation tensile tests were performed along the building direction. The global mechanical properties (i.e., microhardness and tensile properties) and the local mechanical responses (i.e., hardness fluctuation and strain localization) were systematically investigated. Results showed that (1) all P91 specimens showed higher strengths than American Society of Mechanical Engineers standard requirements for wrought P91 steel, (2) the as-printed P91 exhibited much higher average hardness and fluctuations than that after PPHT, (3) PPHT reduced P91 strengths but improved the ductility significantly, and (4) strain localization presented in the as-printed specimen during uniform deformation in tensile tests. The hardness fluctuation and strain localization along the building direction of the AP P91 were caused by different thermal histories received during WA-DED. The study indicated that PPHT, ideally tempering-only heat treatment, is necessary for the WA-DED printed P91 steel.

Mechanical properties↗

Rear Heterojunction GaAs Solar Cells With Strain-Balanced GaInAs/GaAsP Quantum Wells

We have fabricated GaAs rear-heterojunction solar cells with strain-balanced GaInAs/GaAsP multiple quantum wells to increase the range of absorption. The overall device architecture includes a thick n-type GaAs emitter layer, followed by undoped multiple quantum wells (QWs) and then a heterojunction with a higher bandgap GaInP p-type base. The QWs shift the band edge to from ~870 nm to 930 nm and results in >2 mA/cm 2 collection below the GaAs bandgap. Due to the heterojunction, the cell demonstrated a high open-circuit voltage of Voc=1.03V and an efficiency of 26.4% at 1000 W/m 2.

14 SOLAR ENERGY↗

A Database of Stress-Strain Properties Auto-generated from the Scientific Literature using ChemDataExtractor

Abstract There has been an ongoing need for information-rich databases in the mechanical-engineering domain to aid in data-driven materials science. To address the lack of suitable property databases, this study employs the latest version of the chemistry-aware natural-language-processing (NLP) toolkit, ChemDataExtractor, to automatically curate a comprehensive materials database of key stress-strain properties. The database contains information about materials and their cognate properties: ultimate tensile strength, yield strength, fracture strength, Young’s modulus, and ductility values. 720,308 data records were extracted from the scientific literature and organized into machine-readable databases formats. The extracted data have an overall precision, recall and F-score of 82.03%, 92.13% and 86.79%, respectively. The resulting database has been made publicly available, aiming to facilitate data-driven research and accelerate advancements within the mechanical-engineering domain.

Kumar, Pankaj↗

Modeling deformation and failure in AlSi-polyester abradable sealcoating material using microstructure-based finite element simulation

A plasma-sprayed aluminum-silicon (AlSi)/polyester coating is applied in modern gas turbine engines as an abradable sealcoating to maintain tight clearances between the rotating blades and the static casing. While running the engine, the rotating blades “rub” with the abradable coating, which results in extreme strain rate (up to 10 6 ) dynamics and a high-temperature environment. Due to the difficulty of collecting direct measurements, predictive computational models are important for analyzing the deformation and failure of the abradable material, to help meet the design target of avoiding damage to the blade tip and maintaining high fuel efficiency. In this research, a microstructure-based finite element (FE) computational model was developed to capture the complex mechanical behavior of the AlSi/polyester microstructure. The model is based on a virtual representative-volume-element (RVE) of a metal-polymer microstructure, reconstructed from x-ray computed tomography. It models the plastic deformation of, and damage to, each AlSi and polyester constituents, as well as the failure at their interface. The model was calibrated and validated with uniaxial tension and compression experiments, conducted at two temperatures (298 K and 533 K) at an applied strain rate of 10 3 - 10 4 s -1 . The material exhibited strongly asymmetric tension-compression behavior and a sensitivity to temperature, which was well captured by the model. The model was further applied to investigate changes in mechanical behavior due to variations in constituents’ volume fractions, which provides guidance to the microstructural design of AlSi/polyester abradable materials. The model is expected to facilitate the development of improved abradable materials by bypassing the conventional trial-and-error approach and extensive testing requirements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metabolic Modification of Sphingobium lignivorans SYK-6 for Lignin Valorization Through the Discovery of an Unusual Transcriptional Repressor of Lignin-Derived Dimer Catabolism

Sphingobium lignivorans SYK-6 catabolizes guaiacylglycerol-..beta..-guaiacyl ether (GGE, a ..beta..-O-4-type dimer) and 1,2-diguaiacylpropane-1,3-diol (DGPD, a ..beta..-1-type dimer) derived from lignin. Recently, SLG_35860 containing TetR- and MarR-type transcriptional regulator motifs was suggested to be involved in the regulation of GGE and DGPD catabolism. Here we investigated the role of SLG_35860 in the transcriptional regulation of GGE and DGPD catabolism genes. SLG_35860 designated ligS repressed 11 genes involved in GGE and DGPD catabolism. LigS binds directly to specific sequences in the promoter region of each gene. The MarR domain was shown to be involved in these bindings; however, GGE, DGPD, and their metabolites did not function as effectors of LigS. We discovered unidentified compound(s) in the black liquor of oxygen-soda anthraquinone pulping of Japanese cedar that SYK-6 cannot metabolize and that acted as effector(s). Therefore, LigS constantly represses the transcription of the GGE and DGPD catabolism genes to low levels. Based on these findings, we examined the productivity of a polymer building block, 2-pyrone-4,6-dicarboxylic acid (PDC), from GGE, DGPD, and a GGE metabolite using an engineered ligS mutant. The rates of PDC production from each compound by this strain were 1.5-6.0 times higher than those of a PDC-producing strain carrying ligS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation

Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation using carbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. Here, we review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental Investigation of Concrete Fatigue in Axial Compression

The use of concrete in fatigue critical structures, such as wind turbine towers, has necessitated the replacement of simplistic (and therefore insufficient) fatigue design recommendations with more accurate and advanced fatigue models that can consider a greater complexity of stress states and materials. As the first part of a multistage test series, an experimental investigation was conducted to determine the fatigue life of concrete subjected to axial compressive fatigue loading, focusing on the relatively high-cycle fatigue domain. Here, a wide range of values for maximum stress levels and stress ratios were considered. The experimental results were compared against existing predictive models, and the most applicable model was identified. Concrete strain and stiffness behavior during fatigue loading were also investigated and reported. Based on the observed behavior, a hypothesis for identifying the impending occurrence of fatigue failure, based on the monotonic stress-strain curve, is examined.

17 WIND ENERGY↗

Optimization of matrix viscosity improves polypropylene fiber dispersion and properties of engineered cementitious composites

Engineered cementitious composites (ECC) is a durable cementitious material with high tensile ductility and strain-hardening characteristics. Although considered as a cost-effective fiber for ECC, polypropylene (PP) fiber is reportedly difficult to disperse in mortar matrix due to its high aspect ratio and hydrophobicity. In this study, the matrix viscosity of a low-carbon ECC based on limestone calcined clay cement was tailored as a variable to improve PP fiber dispersion under a pre-determined mixing protocol. The effect of matrix viscosity on the composite fresh and hardened properties was investigated experimentally. Results suggested an optimal range of matrix viscosity (10.3–11.5 Pa . s) favors the composite tensile strength and strain capacity at 28 days. At the optimal state with a 0.1 % viscosity modifying admixture (VMA)-to-binder mass ratio, PP-ECC achieved 7.0 % tensile strain capacity and 3.5 MPa ultimate tensile strength. When matrix viscosity falls outside the desired range, both ultimate tensile strength and strain capacity were diminished. By tailoring the VMA dosage, the matrix viscosity can be adjusted for desired fiber dispersion, workability, and mechanical properties. Finally, the findings of this study provide a technical reference for the practical design and application of PP-ECC.

36 MATERIALS SCIENCE↗

Prediction of residual stresses in additively manufactured parts using lumped capacitance and classical lamination theory

Several industries are interested in Laser Powder Bed Fusion (L-PBF) Additively Manufactured (AM) metal parts because their designs can be made arbitrarily complex while retaining bulk-type material properties. However, the residual stresses (RS) and distortions caused by the heat gradients inherent to L-PBF processes are detrimental to the structural integrity of the parts and must be taken into consideration during the part design cycle. Predicting the state of stresses in as-built 3D printed parts is a difficult problem that is typically approached with the use of transient thermomechanical Finite Element Models (FEMs). However, the nonlinearities associated with AM processes are difficult to capture in these FEMs without increasing the computational cost of the simulation, limiting their ability to be incorporated into practical design cycles. This work presents a novel analytical framework that combines lumped capacitance nonlinear heat transfer with time dependent classical lamination theory to efficiently and accurately predict RS in as-built L-PBF parts without the need of FEMs. The simulation was compared to Neutron Diffraction (ND) residual strain measurements taken at Oak Ridge National Laboratories (ORNL) as well as Synchrotron X-ray Diffraction (XRD) strain data published by the National Institute of Standards and Technology (NIST). The simulation predictions and the experimental data showed excellent agreement for the in-plane strain directions, and general agreement for the out of plane strain component, highlighting an area where further development can be implemented.

42 ENGINEERING↗

Chapter 4: What We Can Learn from Measuring Metabolic Fluxes in Cyanobacteria

Cyanobacteria with the capability of oxygen-evolving photosynthesis play a vital role in the global carbon, oxygen, and nitrogen cycles. From a biochemical perspective, all phenotypic traits and functions of cyanobacteria are derived from the potential of their metabolism and mirrored in metabolic fluxes through an integrated metabolic network. Metabolic flux, the rate of turnover of molecules through a metabolic pathway, is therefore of great importance for an in-depth understanding of the role of cyanobacteria in the biosphere. Recent interest in cyanobacteria metabolic fluxes is also motivated by the prospect to utilize their light-driven CO2 fixation for sustainable production of valuable chemicals and biofuels. Valorization of cyanobacterial metabolism will require engineering of the native metabolic network - a challenge that can benefit from a quantitative understanding of metabolic reactions taking place intracellularly. In this chapter, we will discuss some intriguing questions relevant to metabolic fluxes in cyanobacteria: How are metabolic fluxes predicted or measured? What do we know about the fluxome inside various cyanobacteria thus far? How are they different between strains as well as in different conditions? And how can we use fluxomics information to guide metabolic engineering and synthetic biology? This chapter will highlight updated knowledge on cyanobacterial metabolism. Specifically, we will focus on providing readers a quantitative vision to understand how this photosynthetic model works.

BASIC BIOLOGICAL SCIENCES,INORGANIC, ORGANIC, PHYS↗

Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape

Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin–antitoxin modules, polymorphic exotoxin–immunity systems, restriction endonuclease–methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Here, the results of our study reveal that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems.

59 BASIC BIOLOGICAL SCIENCES↗

High-level co-production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol: Metabolic engineering and process optimization

3-Hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) are value-added chemicals with versatile applications in the chemical, pharmaceutical, and food industries. Nevertheless, sustainable production of 3-HP and 1,3-PDO is often limited by the lack of efficient strains and suitable fermentation configurations. We report attempts have been made to improve the co-production of both metabolites through metabolic engineering of Escherichia coli and process optimization. First, the 3-HP and 1,3-PDO co-biosynthetic pathways were recruited and optimized in E. coli, followed by coupling the pathways to the transhydrogenase-mediated cofactor regeneration systems that increased cofactor availability and product synthesis. Next, pathway rebalancing and block of by-product formation significantly improved 3-HP and 1,3-PDO net titer. Subsequently, glycerol flux toward 3-HP and 1,3-PDO synthesis was maximized by removing metabolic repression and fine-tuning the glycerol oxidation pathway. Lastly, the combined fermentation process optimization and two-stage pH-controlled fed-batch fermentation co-produced 140.50 g/L 3-HP and 1,3-PDO, with 0.85 mol/mol net yield.

1,3-propanediol↗

Cantor-derived medium-entropy alloys: bridging the gap between traditional metallic and high-entropy alloys

The year 2004 marked the beginning of a new era in the design of metallic materials, as the concept of multiple principal component alloys, commonly known as High-Entropy Alloys (HEAs), was proposed by Cantor and Yeh. The unexpected single-phase microstructure, instead of the expected brittle intermetallic compounds, was attributed to the large entropy of mixing and immediately caught the attention of the scientific community. Today, HEAs are considered important advanced materials and a broad range of alloys using nominally the same design principle have been investigated. Despite that, the CrMnFeCoNi (Cantor) alloy stands out as the most successful HEA due to its outstanding mechanical properties and microstructure. In this scenario, variants of the Cantor alloy, named medium-entropy alloys (MEAs), are gaining significant interest as they display a better industrial potential than both HEAs and traditional alloys. These variants of the Cantor alloy with only three or four main elements result in 15 possible combinations. The microstructure of these alloys is discussed in terms of advanced characterization as well as thermodynamic parameters and computational simulation. Their phase stability is addressed over a wide range of temperatures and strain rates. The mechanical properties, especially the fracture toughness, of the CrFeCoNi and CrCoNi alloys have been reported to be even superior to those of the Cantor alloy and most modern engineering alloys. This is associated with the formation of a continuous sequence of strengthening mechanisms, including hierarchical twin networks, which serve to prolong the strain hardening. The present article reviews and critically assesses, for the first time, recent advances in these Cantor-derived MEAs.

36 MATERIALS SCIENCE↗

Degradable Biocomposite Thermoplastic Polyurethanes

In this project, the team developed tough and degradable biocomposite thermoplastic polyurethanes (TPUs) by incorporating bacterial spores into TPUs as a biofunctional living filler. The team screened various bacteria and selected the Bacillus subtilis ATCC 6633 strain as the final candidate, primarily due to its genomic availability, sporulation ability and TPU assimilation activity. The heat-shock tolerance of ATCC 6633 spores was further improved through evolutionary engineering via Adaptive Laboratory Evolution (ALE), demonstrating a 17.7-fold enhanced germination efficiency post heat-shock treatment compared to the wild-type strain (WT). The team fabricated biocomposite TPUs by incorporating lyophilized powder of heat-shock tolerized (HST) spores during the hot melt extrusion (HME) of TPU at 135 °C. The baseline TPU used in this project is a commercially available soft-grade TPU (BCF45) manufactured by BASF. Colony forming unit (CFU) assays quantified that WT and HST spores in the TPU matrix retained approximately 20% and 100% survivability, respectively, after HME. Tensile testing demonstrated that the spores behaved as a polymer-reinforcing filler, positively affecting the overall tensile properties of the biocomposite TPU. For example, biocomposite TPU with WT and HST spores (BC TPU WT and BC TPU HST , respectively) exhibited up to 25% and 37% improved toughness, respectively, compared to TPU without spores. BC TPU HST showed remarkably improved disintegration in autoclaved compost (92% mass loss in 5 months), which simulated a microbially poor environment for TPU degradation. When compared to TPU without spores (44% mass loss in 5 months) the acceleration of degradation is marked. Respirometry confirmed that 72% of BC TPU HST was biomineralized into CO2 within 6 months, indicating that spores in the biocomposite TPU were germinated by utilizing nutrients in the autoclaved compost, facilitating TPU degradation at the end of the material's life. The team demonstrated the scale-up of biocomposite TPU fabrication using continuous extrusion and injection molding techniques. Processing conditions optimized in a lab-scale microcompounder were successfully transferred to a continuous extruder with a 30-fold increased throughput. Biocomposite TPUs prepared using these industry-relevant processes showed comparable toughness improvements to samples prepared in the lab-scale extruder. Excitingly, following compounding in the pilot-extruder the composite material could be injection molded, while retaining high spore viability and similar toughness improvements. The team also found that spores in biocomposite TPU served as antioxidants, preventing toughness decay during the recycled extrusion of BC TPU HST . Long-term storage tests over one year showed that the addition of spores had no negative effect on the longevity of the TPU. Furthermore, the team demonstrated the fabrication of spore-bearing biocomposite polymers with other polyesters such as PBAT, PLA, and PCL. We obtained promising preliminary data that showed overall toughness improvements for all polymers with spore addition. Finally, life cycle assessment (LCA) and techno-economic analysis (TEA) were carried out, which indicated minimal additional cost of fabrication. Overall, a tough and degradable biocomposite thermoplastic was successfully developed through this project, with all tasks completed successfully, achieving >100% of the objectives.

36 MATERIALS SCIENCE↗

Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture

To meet the ever-increasing need for high-throughput screening in metabolic engineering, information-rich, fast screening methods are needed. Mass spectrometry (MS) provides an efficient and general approach for metabolite screening and offers the capability of characterizing a broad range of analytes in a label-free manner, but often requires a range of sample clean-up and extraction steps. Liquid extraction surface analysis (LESA) coupled MS is an image-guided MS surface analysis approach that directly samples and introduces metabolites from a surface to MS. Here, we combined the advantages of LESA–MS and an acoustic liquid handler with stable isotope-labeled internal standards. This approach provides absolute quantitation of target chemicals from liquid culture-dried droplets and enables high-throughput quantitative screening for microbial metabolites. In this paper, LESA–MS was successfully applied to quantify several different metabolites (itaconic acid, triacetic acid lactone, and palmitic acid) from different yeast strains in different mediums, demonstrating its versatility, accuracy, and efficiency across a range of microbial engineering applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Abstract Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

59 BASIC BIOLOGICAL SCIENCES↗