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At least 127 records · Page 7

Exploring Sustainability in Scientific Software through Code Quality & Test Coverage Metrics

Context: Scientific open-source software (SciOSS) plays a foundational role in research and engineering, yet its long-term sustainability has often been overlooked and remains a significant concern. Objective: This study investigates the long-term sustainability of SciOSS through code and test quality metrics. Method: We analyze CASS Software Portfolio projects, classifying them by sustainability and comparing their code structure, test coverage, and links between code quality and testing across the dataset. Results: Sustainable projects show higher, more consistent test coverage and clearer code-test correlations, while unsustainable ones show weaker patterns. Overall, test coverage is low in scientific software, and high complexity and coupling reduce testability. Conclusion: In this study, we present a practical, data-driven approach for assessing sustainability in scientific software, offering a foundation for evaluating long-term software health and supporting future efforts in quality assurance and sustainability monitoring.

Md mushfiqur rahman, Sheikh [University of Tenness↗

Shadow of the Future: Developing Trust and Software within the Exascale Computing Project

Collaboration and team science are emerging areas of interest in software production. Historically, multi-institutional research collaborations are difficult to initiate and maintain, negatively impacting communication, negotiation, and dialogue between industry, government, and academic researchers. The Exascale Computing Project (ECP), a massive, multi-team, high-stakes initiative, facilitated broader research collaboration under a shared funding structure and extended timeline to support scientific discovery. Here, we conducted interviews with ECP teams, representing a variety of domain specialties, research institutions, and programming backgrounds. Using thematic analysis, we assessed how ECP’s structure created an environment of increased trust among projects and how software shared between teams facilitated sustained collaboration. We found that the expectation of future collaboration, i.e., the shadow of the future, greatly enhanced trust among teams and the quality of scientific software produced. Based on our findings within ECP projects, we connect to the existing literature on trust in software engineering and share recommendations for sustainable multi-institutional collaboration and shared best software practices.

Exascale computing project↗

RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ (R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. Furthermore, this result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides, providing a streamlined method for addressing genetic engineering challenges in the yeast.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data for "RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides"

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ ( R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides , providing a streamlined method for addressing genetic engineering challenges in the yeast.

gene editing↗

Lepidopteran mevalonate pathway optimization in Escherichia coli efficiently produces isoprenol analogs for next-generation biofuels

Terpenes constitute the largest class of natural products with over 55,000 compounds with versatile applications including drugs and biofuels. Introducing structural modifications to terpenes through metabolic engineering is an efficient and sustainable way to improve their properties. Here, in this study, we report the optimization of the lepidopteran mevalonate (LMVA) pathway towards the efficient production of isopentenyl pyrophosphate (IPP) analogs as terpene precursors. First, we linked the LMVA pathway to NudB, a promiscuous phosphatase, resulting in the production of the six-carbon analog of 3-methyl-3-buten-1-ol (isoprenol), 3-ethyl-3-buten-1-ol (C6-isoprenol). Using C6-isoprenol as the final product, we then engineered the LMVA pathway by redirecting its upstream portion from a thiolase-dependent pathway to a beta-oxidation pathway. The beta-oxidation LMVA pathway transforms valeric acid, a platform chemical that can be produced from biomass, into C6-isoprenol at a titer of 110.3 mg/L, improved from 5.5 mg/L by the thiolase LMVA pathway, which used propionic acid as a feedstock. Knockout of the E. coli endogenous thiolase genes further improved the C6-isoprenol titer to 390 mg/L, implying efficient production of homo isopentenyl pyrophosphate (HIPP). The beta-oxidation LMVA-NudB pathway also converts butanoic acid and hexanoic acid into isoprenol and isoprenol’s seven-carbon analog, 3-propyl-3-buten-1-ol (C7-isoprenol), respectively, suggesting the beta-oxidation LMVA pathway produces IPP and C7-IPP from the corresponding fatty acids. Fuel property tests revealed the longer chain isoprenol analogs have lower water solubilities, similar or higher energy densities, and comparable research octane number (RON) boosting effects to isopentenols. This work not only optimizes the LMVA pathway, setting the basis for homoterpene biosynthesis to expand terpene chemical space, but provides an efficient pathway to produce isoprenol analogs as next-generation biofuels from sustainable feedstocks.

59 BASIC BIOLOGICAL SCIENCES↗

Recent advancements in the genetic engineering of microalgae

The development of more sustainable food, feed, and bio-products is critical to mitigating the environmental stresses facing our world today. Algae, which includes seaweeds, eukaryotic microalgae, and cyanobacteria, are a promising platform to achieving this, as they have low energy and space requirements, are safe for human and animal consumption, and can be manipulated to produce a diversity of valuable bioproducts. This review focuses on microalgae, both eukaryotic and cyanobacteria. In the past, addressing the major challenges of bringing microalgal production systems to an economically viable scale only had a relatively small genetic toolset to work with, in comparison to other microbial systems such as bacteria and yeast. Expanding the molecular tools available for genetic engineering of microalgae will lead to higher product yields, and accelerate the development of new microalgal bioproducts for commercial applications, thereby supporting the shift towards more environmentally friendly products. In this review, we highlight significant advances from recent years on the design of microalgal expression vectors, discovery of genetic regulatory elements (promoters and transcription factors), optimization of transformation methods, and development of new strain improvement techniques, all aimed at advancing microalgae to become a more efficient biomanufacturing platform. We then discuss how these tools have been applied to improving recombinant protein production, and to enhance metabolic pathway engineering.

09 BIOMASS FUELS↗

Reaction engineering: a lost (and found) art for a decarbonized future [Slides]

The heart (or, perhaps more appropriately, the stomach) of any chemical manufacturing process is the reactor, where chemical and physical transformations occur under precisely controlled conditions. For traditional industrial processes, the design, optimization and operation of chemical reactors are extremely well developed, drawing upon the principles of chemistry, physics, calculus and economics. However, new-age process concepts proposing to use "exotic" reactors and/or sustainable inputs (e.g., renewable carbon resources, electrons, photons, plasma) face a dearth of well documented reaction engineering principles & design practices that eclipses their rapid adoption. This presentation features two vignettes of (the return of) reaction engineering in sustainable process science, first in the valorization of lignin from biomass, and second in understanding multimodal catalyst deactivation in industrial-scale reactors within the Catofin process for propane dehydrogenation. Overall, this seminar seeks to educate student researchers on practical means of advancing laboratory reactor technologies towards commercial practice.

09 BIOMASS FUELS↗

Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum

The industrial amino acid production workhorse, Corynebacterium glutamicum naturally produces low levels of 2,3,5,6-tetramethylpyrazine (TMP), a valuable flavor, fragrance, and commodity chemical. Here, we demonstrate TMP production (~0.8 g L –1 ) in C. glutamicum type strain ATCC13032 via overexpression of acetolactate synthase and/or α-acetolactate decarboxylase from Lactococcus lactis in CGXII minimal medium supplemented with 40 g L –1 glucose. This engineered strain also demonstrated growth and TMP production when the minimal medium was supplemented with up to 40% (v v –1 ) hydrolysates derived from ionic liquid-pretreated sorghum biomass. Further, a key objective was to take the fully engineered strain developed in this study and interrogate medium parameters that influence the production of TMP, a critical post-strain engineering optimization. Design of experiments in a high-throughput plate format identified glucose, urea, and their ratio as significant components affecting TMP production. These two components were further optimized using response surface methodology. In the optimized CGXII medium, the engineered strain could produce up to 3.56 g L –1 TMP (4-fold enhancement in titers and 2-fold enhancement in yield, mol mol –1 ) from 80 g L –1 glucose and 11.9 g L –1 urea in shake flask batch cultivation.

59 BASIC BIOLOGICAL SCIENCES↗

Engineered disorder in CO 2 photocatalysis

Light harvesting, separation of charge carriers, and surface reactions are three fundamental steps that are essential for an efficient photocatalyst. Here we show that these steps in the TiO 2 can be boosted simultaneously by disorder engineering. A solid-state reduction reaction between sodium and TiO 2 forms a core-shell c-TiO 2 @a-TiO 2-x (OH) y heterostructure, comprised of HO-Ti-[O]-Ti surface frustrated Lewis pairs (SFLPs) embedded in an amorphous shell surrounding a crystalline core, which enables a new genre of chemical reactivity. Specifically, these SFLPs heterolytically dissociate dihydrogen at room temperature to form charge-balancing protonated hydroxyl groups and hydrides at unsaturated titanium surface sites, which display high reactivity towards CO 2 reduction. This crystalline-amorphous heterostructure also boosts light absorption, charge carrier separation and transfer to SFLPs, while prolonged carrier lifetimes and photothermal heat generation further enhance reactivity. The collective results of this study motivate a general approach for catalytically generating sustainable chemicals and fuels through engineered disorder in heterogeneous CO 2 photocatalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DME-to-Propane Mixture Effects on a Light Duty Compression Ignition Engine

Fuels that can be produced in a sustainable manner are of high interest because they can provide an essential step toward net zero emissions vehicles. This study examines the combustion of two such fuels, Dimethyl Ether (DME) and propane, in a compression ignition, 4-cylinder, 2.2L engine running with mixtures of DME-to-Propane ranging of 100%-0%, 85%-15%, 75%-25%, and 65%-35% by weight. Testing was conducted at 2000rpm - 100Nm, an important representative point in the FTP certification cycle. For each fuel mixture, conditions tested include sweeps of boost, EGR and injection pressure. Here, tests are mainly conducted at a constant combustion timing with CA10 of -1 deg with respect to TDC, with an engine controller combustion feedback system based on in-cylinder sampling of pressure. Trends of NOx, HC, and CO are similar for the range of DME-to-propane, from 100%-0% to 75%-25%. Boost and injection pressures had the most notable impact on the heat release traces. Higher boost, from stoichiometric to lean resulted in approximately a 3-5% increase on cycle efficiency. Fuel injection pressures resulted in about 1% gain per 200bar. Results also illustrated that EGR is effective in reducing NOx but causes notable degradation of cycle efficiency. The emissions for DME-propane mixtures with 65%-35% had a different trend, with CO and HC exceeding the runs with lower propane content by 2 to 3-fold. As propane content increases, the pressure rise rates become higher, and with 65%-35% mixtures, rates easily exceed 12bar/deg. The increased rise rates correlate with early injection timings but the rates can be reduced, with higher boost and lower injection pressures. The result of the approach, however, leads to lower thermal efficiencies, decreasing efficiency by over 5% between neat DME and the highest propane ratios.

Combustion and combustion processes↗

Editorial: Future perspectives on separation technologies

Sustainable separation process development is crucial in promoting economic and environmental sustainability. Separation processes can be energy-intensive, and early-stage or emerging separation technologies can also be costly. For instance, separations in biomass-based fuels and chemicals production can account for up to 50% of the production cost, while industrial separations can consume up to 15% of the total energy used in the United States. Separations are essential to many industrial processes and play a crucial role in helping industry achieve several United Nations sustainable development goals (SDG), such as clean energy, responsible production, and climate change mitigation. Therefore, it is imperative to have a comprehensive discussion within the scientific community to identify innovative approaches for sustainable separation processes. This editorial highlights the key insights and research findings presented in this research topic titled "Future Perspectives on Separation Technologies."

42 ENGINEERING↗

Attempting to Develop the World’s Most Cost-Effective Metal 3D Printing Technology Through Industrial Adoption of a High-Temperature Electro-Magnetic Nozzle for 3D Printing and Computer Numerical Control Integration

This project aimed to make a practical system capable of sustained metal deposition in air engineered with industrial integration and controls. The Al-Ce wire feedstock was tailored with appropriate deposition and solidification properties for direct reactive interface printing (DRIP), and the goal was to integrate onto a Hybrid Manufacturing Technologies system for producing test parts without a controlled environment.

36 MATERIALS SCIENCE↗

Attempting to Develop the World’s Most Cost-Effective Metal 3D Printing Technology Through Industrial Adoption of a High-Temperature Electro-Magnetic Nozzle for 3D Printing and Computer Numerical Control Integration

This project aimed to make a practical system capable of sustained metal deposition in air engineered with industrial integration and controls. The Al-Ce wire feedstock was tailored with appropriate deposition and solidification properties for direct reactive interface printing (DRIP), and the goal was to integrate onto a Hybrid Manufacturing Technologies system for producing test parts without a controlled environment.

36 MATERIALS SCIENCE↗

Density functional modeling of the binding energies between aluminosilicate oligomers and different metal cations

Interactions between negatively charged aluminosilicate species and positively charged metal cations are critical to many important engineering processes and applications, including sustainable cements and aluminosilicate glasses. In an effort to probe these interactions, here we have calculated the pair-wise interaction energies (i.e., binding energies) between aluminosilicate dimer/trimer and 17 different metal cations M n+ (M n+ = Li + , Na + , K + , Cu + , Cu 2+ , Co 2+ , Zn 2+ , Ni 2+ , Mg 2+ , Ca 2+ , Ti 2+ , Fe 2+ , Fe 3+ , Co 3+ , Cr 3+ , Ti 4+ and Cr 6+ ) using a density functional theory (DFT) approach. Analysis of the DFT-optimized structural representations for the clusters (dimer/trimer + M n+ ) shows that their structural attributes (e.g., interatomic distances) are generally consistent with literature observations on aluminosilicate glasses. The DFT-derived binding energies are seen to vary considerably depending on the type of cations (i.e., charge and ionic radii) and aluminosilicate species (i.e., dimer or trimer). A survey of the literature reveals that the difference in the calculated binding energies between different M n+ can be used to explain many literature observations associated with the impact of metal cations on materials properties (e.g., glass corrosion, mineral dissolution, and ionic transport). Analysis of all the DFT-derived binding energies reveals that the correlation between these energy values and the ionic potential and field strength of the metal cations are well captured by 2nd order polynomial functions ( R 2 values of 0.99–1.00 are achieved for regressions). Given that the ionic potential and field strength of a given metal cation can be readily estimated using well-tabulated ionic radii available in the literature, these simple polynomial functions would enable rapid estimation of the binding energies of a much wider range of cations with the aluminosilicate dimer/trimer, providing guidance on the design and optimization of sustainable cements and aluminosilicate glasses and their associated applications. Finally, the limitations associated with using these simple model systems to model complex interactions are also discussed.

Gong, Kai↗

Safety-Related Instrumentation and Control Upgrade Pilot Project: NUREG- 0711 Process Development, Planning and Analysis Activities, and Lessons Learned

Constellation Energy and the United States Department of Energy (DOE) have established a public/private partnership to implement a pilot digital upgrade to replace legacy analog, safety-related reactor protection and emergency safety feature actuation systems (RPS/ESFAS) with modern digital systems. This effort is occurring at Constellation’s Limerick Generating Station. This project is being performed in accordance with industry processes that have been adapted to better support digital upgrades. These processes include IP-ENG-001, Standard Design Process, NISP-EN-04, Standard Digital Engineering Process and Electric Power Research Institute Report 3002011816, Digital Engineering Guide. The Light Water Reactor Sustainability (LWRS) Program at the Idaho National Laboratory (INL) has been supporting this effort. Latest INL HFE efforts in support of this project have focused on definition and implementation of the Human Factors Engineering (HFE) Program in support of Constellation design and related licensing efforts. This paper presents the development execution of the HFE Program through completion of the Planning and Analysis Phase as defined by NUREG-0711 as well as HFE lessons learned.

99 GENERAL AND MISCELLANEOUS↗

Using Ionic Liquid Additive to Enhance Lubricating Performance for Low-Viscosity Engine Oil

Energy efficient lubricants are essential for sustainable transportation, and the trend is to develop and implement lower viscosity lubricants with more effective additives. Ionic liquids (ILs) have been reported as candidate additives with superior friction and wear reducing capabilities. Unlike most literature relying on bench-scale testing of simple oil–IL blends, this study produced low-viscosity (SAE 0W-12) fully formulated engine oils using a phosphonium-organophosphate IL as an antiwear additive and evaluated them in both bench-scale tribological testing and full-scale fired engine dynamometer testing. The experimental formulation containing a combination of ZDDP and IL outperformed the formulations using either ZDDP or IL alone, as well as a commercial SAE 0W-20 engine oil in terms of mitigating boundary friction, wear, and contact fatigue-induced micropitting. Furthermore, racing engine dynamometer tests demonstrated 3–4 °C lower oil temperature, 4–5 ft-lbs higher horsepower output, and up to 9.9% better fuel economy for the IL-containing SAE 0W-12 experimental oil compared with selected commercial SAE 5W-30 and 0W-20 engine oils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Advances in engineering algae for biofuel production

While algae demonstrate potential as a sustainable fuel source, low productivities limit the economic realization of algal biofuels. High-throughput strain engineering, omics-informed genome-scale modeling, and microbiome engineering are key technologies for enabling algal biofuels. High-throughput strain engineering efforts generate improved traits, including high biomass productivity and lipid content, in diverse algal species. Genome-scale models, constructed with the aid of omics data, provide insight into metabolic limitations and guide rational algal strain engineering efforts. As outdoor cultivation systems introduce exogenous organisms, microbiome engineering seeks to eliminate harmful organisms and introduce beneficial species. In conclusion, optimizing algal biomass production and lipid content using these technologies may overcome the productivity barrier for the commercialization of algal biofuels.

09 BIOMASS FUELS↗